2PN1 | pdb_00002pn1

Crystal structure of carbamoylphosphate synthase large subunit (split gene in MJ) (ZP_00538348.1) from Exiguobacterium sp. 255-15 at 2.00 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2PN1/pdb

• Classification: LIGASE
• Organism(s): Exiguobacterium artemiae 255-15
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-04-23 Released: 2007-05-08 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Literature

Crystal structure of carbamoylphosphate synthase large subunit (split gene in MJ) (ZP_00538348.1) from Exiguobacterium sp. 255-15 at 2.00 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,PQS (software)

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content 

• Total Structure Weight: 37.36 kDa 
• Atom Count: 2,583 
• Modeled Residue Count: 308 
• Deposited Residue Count: 331 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbamoylphosphate synthase large subunit	A	331	Exiguobacterium artemiae 255-15	Mutation(s): 7  Gene Names: ZP_00538348.1, ExigDRAFT_2250
UniProt
Find proteins for B1YM69 (Exiguobacterium sibiricum (strain DSM 17290 / CCUG 55495 / CIP 109462 / JCM 13490 / 255-15)) Explore B1YM69  Go to UniProtKB:  B1YM69

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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:  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32PN1

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.6	α = 90
b = 61.21	β = 124.02
c = 76.88	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-08 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-05-08
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2017-10-25
  Changes: Author supporting evidence
• Version 1.5: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.6: 2024-10-30
  Changes: Data collection, Structure summary