4HKM | pdb_00004hkm

Crystal Structure of an Anthranilate Phosphoribosyltransferase (target ID NYSGRC-016600) from Xanthomonas campestris

• PDB DOI: https://doi.org/10.2210/pdb4HKM/pdb

• Classification: TRANSFERASE
• Organism(s): Xanthomonas campestris pv. campestris str. ATCC 33913
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-10-15 Released: 2012-10-31 
• Deposition Author(s): Ghosh, A., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.227 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Literature

Crystal Structure of an Anthranilate Phosphoribosyltransferase (target ID NYSGRC-016600) from Xanthomonas campestris

Ghosh, A., Ahmed, A., Banu, R., Bhoshle, R., Bonanno, J., Chamala, S., Chowdhury, S., Fiser, A., Glenn, A.S., Hillerich, B., Khafizov, K., Lafleur, J., Love, J.D., Seidel, R., Stead, M., Toro, R., 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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 75.59 kDa 
• Atom Count: 5,155 
• Modeled Residue Count: 649 
• Deposited Residue Count: 692 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anthranilate phosphoribosyltransferase	A, B	346	Xanthomonas campestris pv. campestris str. ATCC 33913	Mutation(s): 0  Gene Names: trpD, XCC0469 EC: 2.4.2.18
UniProt
Find proteins for Q8PD71 (Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25)) Explore Q8PD71  Go to UniProtKB:  Q8PD71

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CXS	F [auth B]	3-CYCLOHEXYL-1-PROPYLSULFONIC ACID C9 H19 N O3 S PJWWRFATQTVXHA-UHFFFAOYSA-N
PO4	C [auth A], D [auth A], G [auth B], H [auth B], I [auth B], J [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	E [auth A], K [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	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:  0.227 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.25	α = 90
b = 161.13	β = 90
c = 56.3	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-3000	data reduction
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-31 
Deposition Author(s): Ghosh, A., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2012-10-31
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary