1VKM | pdb_00001vkm

Crystal structure of an indigoidine synthase a (idga)-like protein (tm1464) from thermotoga maritima msb8 at 1.90 A resolution

PDB DOI: https://doi.org/10.2210/pdb1VKM/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Thermotoga maritima MSB8
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2004-06-09 Released: 2004-06-29
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.200 (Depositor), 0.210 (DCC)
R-Value Work:
0.154 (Depositor), 0.170 (DCC)
R-Value Observed:
0.156 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of an indigoidine synthase A (IndA)-like protein (TM1464) from Thermotoga maritima at 1.90 A resolution reveals a new fold.

Levin, I., Miller, M.D., Schwarzenbacher, R., McMullan, D., Abdubek, P., Ambing, E., Biorac, T., Cambell, J., Canaves, J.M., Chiu, H.J., Deacon, A.M., DiDonato, M., Elsliger, M.A., Godzik, A., Grittini, C., Grzechnik, S.K., Hale, J., Hampton, E., Han, G.W., Haugen, J., Hornsby, M., Jaroszewski, L., Karlak, C., Klock, H.E., Koesema, E., Kreusch, A., Kuhn, P., Lesley, S.A., Morse, A., Moy, K., Nigoghossian, E., Ouyang, J., Page, R., Quijano, K., Reyes, R., Robb, A., Sims, E., Spraggon, G., Stevens, R.C., van den Bedem, H., Velasquez, J., Vincent, J., Wang, X., West, B., Wolf, G., Xu, Q., Zagnitko, O., Hodgson, K.O., Wooley, J., Wilson, I.A.

(2005) Proteins 59: 864-868

PubMed: 15822122 Search on PubMed
DOI: https://doi.org/10.1002/prot.20420
Primary Citation of Related Structures:
1VKM

Organizational Affiliation

Joint Center for Structural Genomics, La Jolla, California 92037, USA.

Macromolecule Content

Total Structure Weight: 203.87 kDa
Atom Count: 14,927
Modeled Residue Count: 1,752
Deposited Residue Count: 1,782
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
conserved hypothetical protein TM1464	A, B, C, D, E A, B, C, D, E, F	297	Thermotoga maritima MSB8	Mutation(s): 10 Gene Names: TM1464 EC: 4.2.1.70
UniProt
Find proteins for Q9X1H5 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X1H5 Go to UniProtKB: Q9X1H5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9X1H5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain GA [auth E] SDF format, chain HA [auth E] SDF format, chain IA [auth E] SDF format, chain K [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain V [auth C] SDF format, chain W [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain GA [auth E] MOL2 format, chain HA [auth E] MOL2 format, chain IA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain GA [auth E] mmCIF format, chain HA [auth E] mmCIF format, chain IA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C]	AA [auth D] BA [auth D] GA [auth E] HA [auth E] IA [auth E] AA [auth D], BA [auth D], GA [auth E], HA [auth E], IA [auth E], K [auth A], O [auth B], P [auth B], Q [auth B], V [auth C], W [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain V [auth C] Focus chain W [auth C]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain DA [auth E] SDF format, chain EA [auth E] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain JA [auth F] SDF format, chain KA [auth F] SDF format, chain L [auth B] SDF format, chain LA [auth F] SDF format, chain M [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain X [auth D] SDF format, chain Y [auth D] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain EA [auth E] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain JA [auth F] MOL2 format, chain KA [auth F] MOL2 format, chain L [auth B] MOL2 format, chain LA [auth F] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] mmCIF format, chain CA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain EA [auth E] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain JA [auth F] mmCIF format, chain KA [auth F] mmCIF format, chain L [auth B] mmCIF format, chain LA [auth F] mmCIF format, chain M [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D]	CA [auth E] DA [auth E] EA [auth E] G [auth A] H [auth A] CA [auth E], DA [auth E], EA [auth E], G [auth A], H [auth A], I [auth A], JA [auth F], KA [auth F], L [auth B], LA [auth F], M [auth B], R [auth C], S [auth C], T [auth C], X [auth D], Y [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain JA [auth F] Focus chain KA [auth F] Focus chain L [auth B] Focus chain LA [auth F] Focus chain M [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain JA [auth F] Focus chain KA [auth F] Focus chain L [auth B] Focus chain LA [auth F] Focus chain M [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain X [auth D] Focus chain Y [auth D]
UNL Query on UNL Download Ideal Coordinates CCD File	FA [auth E] J [auth A] MA [auth F] N [auth B] U [auth C] FA [auth E], J [auth A], MA [auth F], N [auth B], U [auth C], Z [auth D]	Unknown ligand WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain FA [auth E] Focus chain J [auth A] Focus chain MA [auth F] Focus chain N [auth B] Focus chain U [auth C] Focus chain Z [auth D] Interactions & Density Focus chain FA [auth E] Focus chain J [auth A] Focus chain MA [auth F] Focus chain N [auth B] Focus chain U [auth C] Focus chain Z [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.200 (Depositor), 0.210 (DCC)
R-Value Work: 0.154 (Depositor), 0.170 (DCC)
R-Value Observed: 0.156 (Depositor)

Diffraction Data: https://doi.org/10.18430/M31VKM

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.958	α = 90
b = 130.799	β = 90
c = 138.75	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing
SHARP	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2004-06-29

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2004-06-29
Type: Initial release
Version 1.1: 2008-04-26
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.3: 2023-01-25
Changes: Advisory, Database references, Derived calculations
Version 1.4: 2024-11-06
Changes: Data collection, Refinement description, Structure summary