3K28 | pdb_00003k28

Crystal Structure of a glutamate-1-semialdehyde aminotransferase from Bacillus anthracis with bound Pyridoxal 5'Phosphate

PDB DOI: https://doi.org/10.2210/pdb3K28/pdb

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

Deposited: 2009-09-29 Released: 2010-01-19
Deposition Author(s): Sharma, S.S., Brunzelle, J.S., Wawrzak, Z., Skarina, T., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.185 (Depositor), 0.186 (DCC)
R-Value Work:
0.147 (Depositor), 0.149 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of a glutamate-1-semialdehyde aminotransferase from Bacillus anthracis with bound Pyridoxal 5'Phosphate

Sharma, S.S., Brunzelle, J.S., Wawrzak, Z., Skarina, T., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 188.58 kDa
Atom Count: 14,509
Modeled Residue Count: 1,687
Deposited Residue Count: 1,716
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate-1-semialdehyde 2,1-aminomutase 2	A, B, C, D	429	Bacillus anthracis str. 'Ames Ancestor	Mutation(s): 0 Gene Names: BAS4358, BA_4693, GBAA_4693, hemL-2, hemL2 EC: 5.4.3.8
UniProt
Find proteins for Q81LD0 (Bacillus anthracis) Explore Q81LD0 Go to UniProtKB: Q81LD0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q81LD0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download:Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain N [auth C] SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain R [auth D] MOL2 format, chain N [auth C] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain R [auth D] mmCIF format, chain N [auth C] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B], N [auth C], R [auth D]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain R [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain R [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain T [auth D] SDF format, chain S [auth D] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain U [auth D] MOL2 format, chain T [auth D] MOL2 format, chain S [auth D] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain U [auth D] mmCIF format, chain T [auth D] mmCIF format, chain S [auth D] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] J [auth B] K [auth B] L [auth B] F [auth A], G [auth A], J [auth B], K [auth B], L [auth B], O [auth C], P [auth C], S [auth D], T [auth D], U [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain Q [auth C] SDF format, chain M [auth B] SDF format, chain H [auth A] MOL2 format, chain V [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain M [auth B] MOL2 format, chain H [auth A] mmCIF format, chain V [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain M [auth B] mmCIF format, chain H [auth A]	H [auth A], M [auth B], Q [auth C], V [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain V [auth D] Interactions & Density Focus chain H [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain V [auth D]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.185 (Depositor), 0.186 (DCC)
R-Value Work: 0.147 (Depositor), 0.149 (DCC)

Diffraction Data:

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.809	α = 90
b = 113.688	β = 118.65
c = 113.955	γ = 90

Software Package:

Software Name	Purpose
BLU-MAX	data collection
CRANK	phasing
ARP/wARP	model building
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-01-19

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2010-01-19
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2025-03-26
Changes: Data collection, Database references, Derived calculations, Structure summary