5DIB | pdb_00005dib

2.25 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) Y450L point mutant from Staphylococcus aureus in complex with NAD+ and BME-modified Cys289

PDB DOI: https://doi.org/10.2210/pdb5DIB/pdb

Classification: OXIDOREDUCTASE
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2015-08-31 Released: 2015-10-14
Deposition Author(s): Halavaty, A.S., Minasov, G., Chen, C., Joo, J.C., Yakunin, A.F., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.255 (Depositor), 0.250 (DCC)
R-Value Work:
0.216 (Depositor), 0.220 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

2.25 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) Y450L point mutant from Staphylococcus aureus in complex with NAD+ and BME-modified Cys289

Halavaty, A.S., Minasov, G., Chen, C., Joo, J.C., Yakunin, A.F., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 231.77 kDa
Atom Count: 16,596
Modeled Residue Count: 1,988
Deposited Residue Count: 2,068
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Betaine aldehyde dehydrogenase	A, B, C, D	517	Staphylococcus aureus	Mutation(s): 1 Gene Names: gbsA, CH51_13935, ERS157365_02065, ERS157366_01277, ERS157367_01590, ERS157368_01276, ERS157369_01327, ERS157370_01780, ERS157371_01447, ERS157372_01660... gbsA, CH51_13935, ERS157365_02065, ERS157366_01277, ERS157367_01590, ERS157368_01276, ERS157369_01327, ERS157370_01780, ERS157371_01447, ERS157372_01660, ERS157373_01815, ERS157374_00943, ERS157376_02019, ERS157379_02102, ERS157380_01277, ERS157381_01481, ERS157382_01327, ERS157383_01276, ERS157384_01683, ERS157385_01328, ERS157386_01590, ERS157387_01983, ERS157388_01278, ERS157389_01857, ERS157390_01571, ERS157391_01874, ERS157393_01280, ERS157394_01487, ERS157395_01059, ERS157409_01038, ERS195389_01428, ERS195391_02004, ERS445052_00785 EC: 1.2.1.8
UniProt
Find proteins for Q9L4P8 (Staphylococcus aureus) Explore Q9L4P8 Go to UniProtKB: Q9L4P8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9L4P8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain M [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth D] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth D]	E [auth A], J [auth B], L [auth C], M [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth D]
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	G [auth A], H [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B]	F [auth A], I [auth A], K [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth A] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain I [auth A] Focus chain K [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME Query on CME	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₃ S₂		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.255 (Depositor), 0.250 (DCC)
R-Value Work: 0.216 (Depositor), 0.220 (DCC)
R-Value Observed: 0.218 (Depositor)

Diffraction Data: https://doi.org/10.18430/m35dib

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 224.866	α = 90
b = 102.633	β = 104.83
c = 118.243	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-10-14

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2015-10-14
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary