3UWQ | pdb_00003uwq

1.80 Angstrom resolution crystal structure of orotidine 5'-phosphate decarboxylase from Vibrio cholerae O1 biovar eltor str. N16961 in complex with uridine-5'-monophosphate (UMP)

• PDB DOI: https://doi.org/10.2210/pdb3UWQ/pdb

• Classification: LYASE
• Organism(s): Vibrio cholerae
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-12-02 Released: 2011-12-14 
• Deposition Author(s): Halavaty, A.S., Minasov, G., Winsor, J., Shuvalova, L., Kuhn, M., Filippova, E.V., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.178 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.150 (Depositor) 
• R-Value Observed: 
  0.152 (Depositor) 

Starting Model: experimental

Literature

1.80 Angstrom resolution crystal structure of orotidine 5'-phosphate decarboxylase from Vibrio cholerae O1 biovar eltor str. N16961 in complex with uridine-5'-monophosphate (UMP)

Halavaty, A.S., Minasov, G., Winsor, J., Shuvalova, L., Kuhn, M., Filippova, E.V., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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: 57.51 kDa 
• Atom Count: 4,254 
• Modeled Residue Count: 446 
• Deposited Residue Count: 510 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orotidine 5'-phosphate decarboxylase	A, B	255	Vibrio cholerae	Mutation(s): 0  Gene Names: pyrF, VC_1911 EC: 4.1.1.23
UniProt
Find proteins for Q9KQT7 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KQT7  Go to UniProtKB:  Q9KQT7

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XPE	D [auth A]	3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL C20 H42 O11 DTPCFIHYWYONMD-UHFFFAOYSA-N
U5P	C [auth A], I [auth B]	URIDINE-5'-MONOPHOSPHATE C9 H13 N2 O9 P DJJCXFVJDGTHFX-XVFCMESISA-N
PGE	G [auth A], L [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
TRS	H [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG	E [auth A], F [auth A], J [auth B], K [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.178 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.150 (Depositor) 
• R-Value Observed: 0.152 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33uwq

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.14	α = 90
b = 96.944	β = 90
c = 104.082	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-14 
Deposition Author(s): Halavaty, A.S., Minasov, G., Winsor, J., Shuvalova, L., Kuhn, M., Filippova, E.V., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2011-12-14
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description