3I4S | pdb_00003i4s

CRYSTAL STRUCTURE OF HISTIDINE TRIAD PROTEIN blr8122 FROM Bradyrhizobium japonicum

• PDB DOI: https://doi.org/10.2210/pdb3I4S/pdb

• Classification: HYDROLASE
• Organism(s): Bradyrhizobium japonicum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-07-02 Released: 2009-07-14 
• Deposition Author(s): Patskovsky, Y., Ramagopal, U., Toro, R., Freeman, J., Do, J., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.218 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Literature

CRYSTAL STRUCTURE OF HISTIDINE TRIAD PROTEIN FROM Bradyrhizobium japonicum

Patskovsky, Y., Ramagopal, U., Toro, R., Freeman, J., Do, J., Sauder, J.M., Burley, S.K., Almo, S.C.

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: 34.02 kDa 
• Atom Count: 2,451 
• Modeled Residue Count: 268 
• Deposited Residue Count: 298 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HISTIDINE TRIAD PROTEIN	A, B	149	Bradyrhizobium japonicum	Mutation(s): 0  Gene Names: blr8122
UniProt
Find proteins for Q89BM6 (Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110)) Explore Q89BM6  Go to UniProtKB:  Q89BM6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.218 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.02	α = 90
b = 104.02	β = 90
c = 53.563	γ = 90

Software Package:

Software Name	Purpose
SHELXD	phasing
REFMAC	refinement
DENZO	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-14 
Deposition Author(s): Patskovsky, Y., Ramagopal, U., Toro, R., Freeman, J., Do, J., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-07-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references