4ZWL | pdb_00004zwl

2.60 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) H448F/Y450L double mutant from Staphylococcus aureus in complex with NAD+ and BME-free Cys289

PDB DOI: https://doi.org/10.2210/pdb4ZWL/pdb

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

Deposited: 2015-05-19 Released: 2015-05-27
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: 2.60 Å
R-Value Free:
0.232 (Depositor), 0.230 (DCC)
R-Value Work:
0.158 (Depositor), 0.160 (DCC)
R-Value Observed:
0.162 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

2.60 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) H448F/Y450L double mutant from Staphylococcus aureus in complex with NAD+ and BME-free Cys289

Halavaty, A.S., Minasov, G., Chen, C., Joo, J.C., Yakunin, A.F., Anderson, W.F.

To be published.

Macromolecule Content

Total Structure Weight: 463.35 kDa
Atom Count: 32,907
Modeled Residue Count: 3,979
Deposited Residue Count: 4,136
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, E A, B, C, D, E, F, G, H	517	Staphylococcus aureus subsp. aureus COL	Mutation(s): 2 Gene Names: betB, SACOL2628 EC: 1.2.1.8
UniProt
Find proteins for A0A0M3KL40 (Staphylococcus aureus (strain COL)) Explore A0A0M3KL40 Go to UniProtKB: A0A0M3KL40
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0M3KL40
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain EA [auth H] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain T [auth E] SDF format, chain W [auth F] MOL2 format, chain AA [auth G] MOL2 format, chain EA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain T [auth E] MOL2 format, chain W [auth F] mmCIF format, chain AA [auth G] mmCIF format, chain EA [auth H] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D] mmCIF format, chain T [auth E] mmCIF format, chain W [auth F]	AA [auth G] EA [auth H] I [auth A] L [auth B] O [auth C] AA [auth G], EA [auth H], I [auth A], L [auth B], O [auth C], R [auth D], T [auth E], W [auth F]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain AA [auth G] Focus chain EA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain W [auth F] Interactions & Density Focus chain AA [auth G] Focus chain EA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain W [auth F]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth G] SDF format, chain CA [auth G] SDF format, chain DA [auth G] SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain S [auth D] SDF format, chain U [auth E] SDF format, chain V [auth E] SDF format, chain X [auth F] SDF format, chain Y [auth F] SDF format, chain Z [auth F] SDF format, chain J [auth A] MOL2 format, chain BA [auth G] MOL2 format, chain CA [auth G] MOL2 format, chain DA [auth G] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth D] MOL2 format, chain U [auth E] MOL2 format, chain V [auth E] MOL2 format, chain X [auth F] MOL2 format, chain Y [auth F] MOL2 format, chain Z [auth F] MOL2 format, chain J [auth A] mmCIF format, chain BA [auth G] mmCIF format, chain CA [auth G] mmCIF format, chain DA [auth G] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain S [auth D] mmCIF format, chain U [auth E] mmCIF format, chain V [auth E] mmCIF format, chain X [auth F] mmCIF format, chain Y [auth F] mmCIF format, chain Z [auth F] mmCIF format, chain J [auth A]	BA [auth G] CA [auth G] DA [auth G] J [auth A] K [auth A] BA [auth G], CA [auth G], DA [auth G], J [auth A], K [auth A], M [auth B], N [auth B], P [auth C], Q [auth C], S [auth D], U [auth E], V [auth E], X [auth F], Y [auth F], Z [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth G] Focus chain CA [auth G] Focus chain DA [auth G] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain V [auth E] Focus chain X [auth F] Focus chain Y [auth F] Focus chain Z [auth F] Interactions & Density Focus chain BA [auth G] Focus chain CA [auth G] Focus chain DA [auth G] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain V [auth E] Focus chain X [auth F] Focus chain Y [auth F] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.232 (Depositor), 0.230 (DCC)
R-Value Work: 0.158 (Depositor), 0.160 (DCC)
R-Value Observed: 0.162 (Depositor)

Diffraction Data: https://doi.org/10.18430/m34zwl

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.14	α = 90
b = 170.974	β = 102.77
c = 137.576	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-05-27

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2015-05-27
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy