3KIZ | pdb_00003kiz

Crystal structure of Putative phosphoribosylformylglycinamidine cyclo-ligase (YP_676759.1) from CYTOPHAGA HUTCHINSONII ATCC 33406 at 1.50 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3KIZ/pdb

• Classification: LIGASE
• Organism(s): Cytophaga hutchinsonii ATCC 33406
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-11-02 Released: 2009-11-17 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.187 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.159 (Depositor) 
• R-Value Observed: 
  0.160 (Depositor) 

Literature

Crystal structure of Putative phosphoribosylformylglycinamidine cyclo-ligase (YP_676759.1) from CYTOPHAGA HUTCHINSONII ATCC 33406 at 1.50 A resolution

Joint Center for Structural Genomics (JCSG)

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 Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 88.01 kDa 
• Atom Count: 6,801 
• Modeled Residue Count: 738 
• Deposited Residue Count: 788 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoribosylformylglycinamidine cyclo-ligase	A, B	394	Cytophaga hutchinsonii ATCC 33406	Mutation(s): 0  Gene Names: purM, CHU_0126 EC: 6.3.3.1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	F [auth A], G [auth A], H [auth A], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	C [auth A], D [auth A], E [auth A], I [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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: 1.50 Å
• R-Value Free:  0.187 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.159 (Depositor) 
• R-Value Observed: 0.160 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33KIZ

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.93	α = 90
b = 95.182	β = 90
c = 106.277	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-17 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-11-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-10-30
  Changes: Data collection, Structure summary