8EP7 | pdb_00008ep7

Crystal Structure of the Ketol-acid Reductoisomerase from Bacillus anthracis in complex with NADP

PDB DOI: https://doi.org/10.2210/pdb8EP7/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bacillus anthracis str. 'Ames Ancestor
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-10-05 Released: 2022-10-19
Deposition Author(s): Kim, Y., Maltseva, N., Osipiuk, J., Gu, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID), Center for Structural Biology of Infectious Diseases (CSBID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.262 (Depositor), 0.262 (DCC)
R-Value Work:
0.217 (Depositor), 0.217 (DCC)
R-Value Observed:
0.219 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal Structure of the Ketol-acid Reductoisomerase from Bacillus anthracis in the complex with NADP.

Kim, Y., Maltseva, N., Osipiuk, J., Gu, M., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 114.82 kDa
Atom Count: 7,881
Modeled Residue Count: 969
Deposited Residue Count: 1,005
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ketol-acid reductoisomerase (NADP(+)) 2	A, B, C	335	Bacillus anthracis str. 'Ames Ancestor	Mutation(s): 0 Gene Names: ilvC2, ilvC-2, BA_1852, GBAA_1852, BAS1716 EC: 1.1.1.86
UniProt
Find proteins for Q81S27 (Bacillus anthracis) Explore Q81S27 Go to UniProtKB: Q81S27
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q81S27
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP (Subject of Investigation/LOI) Query on NAP Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain G [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain G [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain G [auth C]	D [auth A], E [auth B], G [auth C]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain G [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain G [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth C] MOL2 format, chain H [auth C] mmCIF format, chain H [auth C]	H [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth C] Interactions & Density Focus chain H [auth C]
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.262 (Depositor), 0.262 (DCC)
R-Value Work: 0.217 (Depositor), 0.217 (DCC)
R-Value Observed: 0.219 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.575	α = 90
b = 131.86	β = 90
c = 132.614	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-10-19

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Center for Structural Biology of Infectious Diseases (CSBID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2022-10-19
Type: Initial release
Version 1.1: 2023-02-01
Changes: Other, Structure summary
Version 1.2: 2023-10-25
Changes: Data collection, Refinement description
Version 1.3: 2023-11-15
Changes: Data collection
Version 1.4: 2024-10-16
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.