3IJR | pdb_00003ijr

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

PDB DOI: https://doi.org/10.2210/pdb3IJR/pdb

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

Deposited: 2009-08-04 Released: 2009-09-08
Deposition Author(s): Halavaty, A.S., Minasov, G., Skarina, T., Onopriyenko, O., Gordon, E., Kwon, K., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.193 (Depositor), 0.246 (DCC)
R-Value Work:
0.157 (Depositor), 0.220 (DCC)
R-Value Observed:
0.159 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

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

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

To be published.

Macromolecule Content

Total Structure Weight: 262.14 kDa
Atom Count: 19,037
Modeled Residue Count: 2,266
Deposited Residue Count: 2,328
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidoreductase, short chain dehydrogenase/reductase family	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A6L8PL20
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 BA [auth F] SDF format, chain FA [auth G] SDF format, chain I [auth A] SDF format, chain JA [auth H] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain V [auth D] SDF format, chain Y [auth E] MOL2 format, chain BA [auth F] MOL2 format, chain FA [auth G] MOL2 format, chain I [auth A] MOL2 format, chain JA [auth H] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain V [auth D] MOL2 format, chain Y [auth E] mmCIF format, chain BA [auth F] mmCIF format, chain FA [auth G] mmCIF format, chain I [auth A] mmCIF format, chain JA [auth H] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C] mmCIF format, chain V [auth D] mmCIF format, chain Y [auth E]	BA [auth F] FA [auth G] I [auth A] JA [auth H] M [auth B] BA [auth F], FA [auth G], I [auth A], JA [auth H], M [auth B], P [auth C], V [auth D], Y [auth E]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain BA [auth F] Focus chain FA [auth G] Focus chain I [auth A] Focus chain JA [auth H] Focus chain M [auth B] Focus chain P [auth C] Focus chain V [auth D] Focus chain Y [auth E] Interactions & Density Focus chain BA [auth F] Focus chain FA [auth G] Focus chain I [auth A] Focus chain JA [auth H] Focus chain M [auth B] Focus chain P [auth C] Focus chain V [auth D] Focus chain Y [auth E]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain DA [auth F] SDF format, chain EA [auth F] SDF format, chain HA [auth G] SDF format, chain IA [auth G] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth H] SDF format, chain O [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain X [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain EA [auth F] MOL2 format, chain HA [auth G] MOL2 format, chain IA [auth G] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth H] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain X [auth D] mmCIF format, chain AA [auth E] mmCIF format, chain DA [auth F] mmCIF format, chain EA [auth F] mmCIF format, chain HA [auth G] mmCIF format, chain IA [auth G] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth H] mmCIF format, chain O [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain X [auth D]	AA [auth E] DA [auth F] EA [auth F] HA [auth G] IA [auth G] AA [auth E], DA [auth F], EA [auth F], HA [auth G], IA [auth G], K [auth A], L [auth A], LA [auth H], O [auth B], R [auth C], S [auth C], T [auth C], U [auth C], X [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth E] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain HA [auth G] Focus chain IA [auth G] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth H] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain X [auth D] Interactions & Density Focus chain AA [auth E] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain HA [auth G] Focus chain IA [auth G] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth H] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain X [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain GA [auth G] SDF format, chain J [auth A] SDF format, chain KA [auth H] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain W [auth D] SDF format, chain Z [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain GA [auth G] MOL2 format, chain J [auth A] MOL2 format, chain KA [auth H] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain W [auth D] MOL2 format, chain Z [auth E] mmCIF format, chain CA [auth F] mmCIF format, chain GA [auth G] mmCIF format, chain J [auth A] mmCIF format, chain KA [auth H] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain W [auth D] mmCIF format, chain Z [auth E]	CA [auth F] GA [auth G] J [auth A] KA [auth H] N [auth B] CA [auth F], GA [auth G], J [auth A], KA [auth H], N [auth B], Q [auth C], W [auth D], Z [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth F] Focus chain GA [auth G] Focus chain J [auth A] Focus chain KA [auth H] Focus chain N [auth B] Focus chain Q [auth C] Focus chain W [auth D] Focus chain Z [auth E] Interactions & Density Focus chain CA [auth F] Focus chain GA [auth G] Focus chain J [auth A] Focus chain KA [auth H] Focus chain N [auth B] Focus chain Q [auth C] Focus chain W [auth D] Focus chain Z [auth E]

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, G, H	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.193 (Depositor), 0.246 (DCC)
R-Value Work: 0.157 (Depositor), 0.220 (DCC)
R-Value Observed: 0.159 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.749	α = 90
b = 123.203	β = 90
c = 169.767	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-09-08

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2009-09-08
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, 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
Version 1.4: 2023-11-22
Changes: Data collection
Version 1.5: 2024-10-30
Changes: Structure summary