3I3O | pdb_00003i3o

2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone

PDB DOI: https://doi.org/10.2210/pdb3I3O/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bacillus anthracis str. 'Ames Ancestor
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-06-30 Released: 2009-08-04
Deposition Author(s): Halavaty, A.S., Minasov, G., Skarina, T., Onopriyenko, O., Peterson, S., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free:
0.205 (Depositor), 0.220 (DCC)
R-Value Work:
0.161 (Depositor), 0.180 (DCC)
R-Value Observed:
0.163 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone

Halavaty, A.S., Minasov, G., Skarina, T., Onopriyenko, O., Peterson, S., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 259.89 kDa
Atom Count: 18,804
Modeled Residue Count: 2,193
Deposited Residue Count: 2,328
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short chain dehydrogenase	A, B, C, D, E A, B, C, D, E, F, G, H	291	Bacillus anthracis str. 'Ames Ancestor	Mutation(s): 0 Gene Names: BAS0712, BA_0748, GBAA0748, GBAA_0748
UniProt
Find proteins for A0A6L8PL20 (Bacillus anthracis) Explore A0A6L8PL20 Go to UniProtKB: A0A6L8PL20
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A6L8PL20
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAE Query on NAE Download Ideal Coordinates CCD File SDF format, chain X [auth E] SDF format, chain U [auth D] SDF format, chain Q [auth C] SDF format, chain M [auth B] SDF format, chain J [auth A] SDF format, chain EA [auth H] SDF format, chain AA [auth F] MOL2 format, chain X [auth E] MOL2 format, chain U [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain M [auth B] MOL2 format, chain J [auth A] MOL2 format, chain EA [auth H] MOL2 format, chain AA [auth F] mmCIF format, chain X [auth E] mmCIF format, chain U [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain M [auth B] mmCIF format, chain J [auth A] mmCIF format, chain EA [auth H] mmCIF format, chain AA [auth F]	AA [auth F] EA [auth H] J [auth A] M [auth B] Q [auth C] AA [auth F], EA [auth H], J [auth A], M [auth B], Q [auth C], U [auth D], X [auth E]	NICOTINAMIDE ADENINE DINUCLEOTIDE ACETONE ADDUCT C₂₄ H₃₁ N₇ O₁₅ P₂ SGHBFOOIAAJJMI-YDKVLQLQSA-N		Interactions Focus chain AA [auth F] Focus chain EA [auth H] Focus chain J [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain X [auth E] Interactions & Density Focus chain AA [auth F] Focus chain EA [auth H] Focus chain J [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain X [auth E]
CAC Query on CAC Download Ideal Coordinates CCD File SDF format, chain Y [auth E] SDF format, chain V [auth D] SDF format, chain R [auth C] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain K [auth A] SDF format, chain FA [auth H] SDF format, chain CA [auth G] SDF format, chain BA [auth F] MOL2 format, chain Y [auth E] MOL2 format, chain V [auth D] MOL2 format, chain R [auth C] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain K [auth A] MOL2 format, chain FA [auth H] MOL2 format, chain CA [auth G] MOL2 format, chain BA [auth F] mmCIF format, chain Y [auth E] mmCIF format, chain V [auth D] mmCIF format, chain R [auth C] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain K [auth A] mmCIF format, chain FA [auth H] mmCIF format, chain CA [auth G] mmCIF format, chain BA [auth F]	BA [auth F] CA [auth G] FA [auth H] K [auth A] N [auth B] BA [auth F], CA [auth G], FA [auth H], K [auth A], N [auth B], O [auth B], R [auth C], V [auth D], Y [auth E]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain BA [auth F] Focus chain CA [auth G] Focus chain FA [auth H] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain V [auth D] Focus chain Y [auth E] Interactions & Density Focus chain BA [auth F] Focus chain CA [auth G] Focus chain FA [auth H] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain V [auth D] Focus chain Y [auth E]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain T [auth D] MOL2 format, chain T [auth D] mmCIF format, chain T [auth D]	T [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain T [auth D] Interactions & Density Focus chain T [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain Z [auth F] SDF format, chain W [auth E] SDF format, chain S [auth D] SDF format, chain P [auth C] SDF format, chain L [auth B] SDF format, chain I [auth A] SDF format, chain DA [auth H] MOL2 format, chain Z [auth F] MOL2 format, chain W [auth E] MOL2 format, chain S [auth D] MOL2 format, chain P [auth C] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain DA [auth H] mmCIF format, chain Z [auth F] mmCIF format, chain W [auth E] mmCIF format, chain S [auth D] mmCIF format, chain P [auth C] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain DA [auth H]	DA [auth H] I [auth A] L [auth B] P [auth C] S [auth D] DA [auth H], I [auth A], L [auth B], P [auth C], S [auth D], W [auth E], Z [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain DA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain W [auth E] Focus chain Z [auth F] Interactions & Density Focus chain DA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain W [auth E] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free: 0.205 (Depositor), 0.220 (DCC)
R-Value Work: 0.161 (Depositor), 0.180 (DCC)
R-Value Observed: 0.163 (Depositor)

Diffraction Data: https://doi.org/10.18430/m33i3o

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.757	α = 90
b = 168.156	β = 90
c = 107.194	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
BALBES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-08-04

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2009-08-04
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description