4E77 | pdb_00004e77

2.0A Crystal Structure of a Glutamate-1-Semialdehyde Aminotransferase from Yersinia pestis CO92

• PDB DOI: https://doi.org/10.2210/pdb4E77/pdb

• Classification: ISOMERASE
• Organism(s): Yersinia pestis Pestoides F
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-03-16 Released: 2012-04-04 
• Deposition Author(s): Brunzelle, J.S., Wawrzak, W., Onopriyenko, O., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.197 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Literature

2.0A Crystal Structure of a Glutamate-1-Semialdehyde Aminotransferase from Yersinia pestis CO92

Brunzelle, J.S., Wawrzak, W., Onopriyenko, O., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 46.99 kDa 
• Atom Count: 3,429 
• Modelled Residue Count: 406 
• Deposited Residue Count: 429 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate-1-semialdehyde 2,1-aminomutase	A	429	Yersinia pestis Pestoides F	Mutation(s): 0  Gene Names: hemL, YPDSF_2968 EC: 5.4.3.8
UniProt
Find proteins for Q8ZBL9 (Yersinia pestis) Explore Q8ZBL9  Go to UniProtKB:  Q8ZBL9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NO3	C [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.197 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34e77

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.54	α = 90
b = 60.54	β = 90
c = 182.48	γ = 120

Software Package:

Software Name	Purpose
BLU-MAX	data collection
PHENIX	model building
BUSTER	refinement
XDS	data reduction
xia2	data reduction
SCALA	data scaling
xia2	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-04 
Deposition Author(s): Brunzelle, J.S., Wawrzak, W., Onopriyenko, O., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2012-04-04
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary