8YUG | pdb_00008yug

X-ray Crystal structure of glycoside hydrolase family 18 chitinase from Serratia marcescens hexahistigine-tagged SmChiB apo enzyme

PDB DOI: https://doi.org/10.2210/pdb8YUG/pdb

Classification: HYDROLASE
Organism(s): Serratia marcescens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-03-27 Released: 2025-04-02
Deposition Author(s): Ebi, S., Sunagawa, N., Yamaguchi, S., Igarashi, K.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.71 Å
R-Value Free:
0.173 (Depositor), 0.172 (DCC)
R-Value Work:
0.152 (Depositor), 0.151 (DCC)
R-Value Observed:
0.152 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

X-ray Crystal structure of glycoside hydrolase family 18 chitinase from Serratia marcescens hexahistigine-tagged SmChiB apo enzyme

Ebi, S., Igarashi, K.

To be published.

Macromolecule Content

Total Structure Weight: 61.46 kDa
Atom Count: 5,344
Modelled Residue Count: 497
Deposited Residue Count: 511
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitinase B	A	511	Serratia marcescens	Mutation(s): 0 Gene Names: chiB EC: 3.2.1.14
UniProt
Find proteins for P11797 (Serratia marcescens) Explore P11797 Go to UniProtKB: P11797
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11797
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain N [auth A] SDF format, chain R [auth A] SDF format, chain W [auth A] MOL2 format, chain J [auth A] MOL2 format, chain N [auth A] MOL2 format, chain R [auth A] MOL2 format, chain W [auth A] mmCIF format, chain J [auth A] mmCIF format, chain N [auth A] mmCIF format, chain R [auth A] mmCIF format, chain W [auth A]	J [auth A], N [auth A], R [auth A], W [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain J [auth A] Focus chain N [auth A] Focus chain R [auth A] Focus chain W [auth A] Interactions & Density Focus chain J [auth A] Focus chain N [auth A] Focus chain R [auth A] Focus chain W [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain AB [auth A] SDF format, chain B [auth A] SDF format, chain BA [auth A] SDF format, chain BB [auth A] SDF format, chain C [auth A] SDF format, chain CA [auth A] SDF format, chain CB [auth A] SDF format, chain D [auth A] SDF format, chain DA [auth A] SDF format, chain EA [auth A] SDF format, chain F [auth A] SDF format, chain FA [auth A] SDF format, chain G [auth A] SDF format, chain GA [auth A] SDF format, chain H [auth A] SDF format, chain HA [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain VA [auth A] SDF format, chain WA [auth A] SDF format, chain X [auth A] SDF format, chain XA [auth A] SDF format, chain Y [auth A] SDF format, chain YA [auth A] SDF format, chain Z [auth A] SDF format, chain ZA [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth A] MOL2 format, chain B [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain BB [auth A] MOL2 format, chain C [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth A] MOL2 format, chain D [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth A] MOL2 format, chain WA [auth A] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain AB [auth A] mmCIF format, chain B [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain BB [auth A] mmCIF format, chain C [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain CB [auth A] mmCIF format, chain D [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth A] mmCIF format, chain WA [auth A] mmCIF format, chain X [auth A] mmCIF format, chain XA [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain YA [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain ZA [auth A]	AA [auth A] AB [auth A] B [auth A] BA [auth A] BB [auth A] AA [auth A], AB [auth A], B [auth A], BA [auth A], BB [auth A], C [auth A], CA [auth A], CB [auth A], D [auth A], DA [auth A], EA [auth A], F [auth A], FA [auth A], G [auth A], GA [auth A], H [auth A], HA [auth A], K [auth A], L [auth A], M [auth A], O [auth A], P [auth A], Q [auth A], S [auth A], T [auth A], U [auth A], V [auth A], VA [auth A], WA [auth A], X [auth A], XA [auth A], Y [auth A], YA [auth A], Z [auth A], ZA [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth A] Focus chain B [auth A] Focus chain BA [auth A] Focus chain BB [auth A] Focus chain C [auth A] Focus chain CA [auth A] Focus chain CB [auth A] Focus chain D [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain F [auth A] Focus chain FA [auth A] Focus chain G [auth A] Focus chain GA [auth A] Focus chain H [auth A] Focus chain HA [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain VA [auth A] Focus chain WA [auth A] Focus chain X [auth A] Focus chain XA [auth A] Focus chain Y [auth A] Focus chain YA [auth A] Focus chain Z [auth A] Focus chain ZA [auth A] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth A] Focus chain B [auth A] Focus chain BA [auth A] Focus chain BB [auth A] Focus chain C [auth A] Focus chain CA [auth A] Focus chain CB [auth A] Focus chain D [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain F [auth A] Focus chain FA [auth A] Focus chain G [auth A] Focus chain GA [auth A] Focus chain H [auth A] Focus chain HA [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain VA [auth A] Focus chain WA [auth A] Focus chain X [auth A] Focus chain XA [auth A] Focus chain Y [auth A] Focus chain YA [auth A] Focus chain Z [auth A] Focus chain ZA [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain DB [auth A] SDF format, chain E [auth A] SDF format, chain I [auth A] SDF format, chain IA [auth A] SDF format, chain JA [auth A] SDF format, chain KA [auth A] SDF format, chain LA [auth A] SDF format, chain MA [auth A] SDF format, chain NA [auth A] SDF format, chain OA [auth A] SDF format, chain PA [auth A] SDF format, chain QA [auth A] SDF format, chain RA [auth A] SDF format, chain SA [auth A] SDF format, chain TA [auth A] SDF format, chain UA [auth A] MOL2 format, chain DB [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain OA [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain QA [auth A] MOL2 format, chain RA [auth A] MOL2 format, chain SA [auth A] MOL2 format, chain TA [auth A] MOL2 format, chain UA [auth A] mmCIF format, chain DB [auth A] mmCIF format, chain E [auth A] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain KA [auth A] mmCIF format, chain LA [auth A] mmCIF format, chain MA [auth A] mmCIF format, chain NA [auth A] mmCIF format, chain OA [auth A] mmCIF format, chain PA [auth A] mmCIF format, chain QA [auth A] mmCIF format, chain RA [auth A] mmCIF format, chain SA [auth A] mmCIF format, chain TA [auth A] mmCIF format, chain UA [auth A]	DB [auth A] E [auth A] I [auth A] IA [auth A] JA [auth A] DB [auth A], E [auth A], I [auth A], IA [auth A], JA [auth A], KA [auth A], LA [auth A], MA [auth A], NA [auth A], OA [auth A], PA [auth A], QA [auth A], RA [auth A], SA [auth A], TA [auth A], UA [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain DB [auth A] Focus chain E [auth A] Focus chain I [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth A] Focus chain RA [auth A] Focus chain SA [auth A] Focus chain TA [auth A] Focus chain UA [auth A] Interactions & Density Focus chain DB [auth A] Focus chain E [auth A] Focus chain I [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth A] Focus chain RA [auth A] Focus chain SA [auth A] Focus chain TA [auth A] Focus chain UA [auth A]