4H1T

X-RAY Structure of the Complex VchUPh with Phosphate ion at 1.92A Resolution.

• PDB DOI: https://doi.org/10.2210/pdb4H1T/pdb

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


• Deposited: 2012-09-11 Released: 2013-09-11 
• Deposition Author(s): Prokofev, I.I., Lashkov, A.A., Gabdoulkhakov, A.G., Sotnichenko, S.E., Betzel, C., Mikhailov, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 0.217 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 

Starting Model: experimental

Literature

X-RAY Structure of the Complex VchUPh with Phosphate ion at 1.92A Resolution.

Prokofev, I.I., Lashkov, A.A., Gabdoulkhakov, A.G., Sotnichenko, S.E., Betzel, C., Mikhailov, A.M.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 169.78 kDa 
• Atom Count: 13,160 
• Modelled Residue Count: 1,504 
• Deposited Residue Count: 1,518 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine phosphorylase	A, B, C, D, E, F	253	Vibrio cholerae	Mutation(s): 0  Gene Names: udp EC: 2.4.2.3
UniProt
Find proteins for Q9K4U1 (Vibrio cholerae) Explore Q9K4U1  Go to UniProtKB:  Q9K4U1

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	AA [auth A], AC [auth E], BA [auth A], BC [auth E], CA [auth A], CC [auth E], DA [auth A], EA [auth A], EB [auth C], FA [auth A], FB [auth C], GB [auth C], HB [auth C], IB [auth C], JB [auth C], OC [auth F], PC [auth F], QA [auth B], QB [auth D], QC [auth F], RA [auth B], RB [auth D], RC [auth F], SA [auth B], SC [auth F], TC [auth F], UC [auth F], Z [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	FC [auth F], IA [auth B], JA [auth B], KB [auth D], TB [auth E], UB [auth E], WA [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
PO4	DC [auth F], GA [auth B], HA [auth B], TA [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	AB [auth C], BB [auth C], CB [auth C], GC [auth F], H [auth A], HC [auth F], I [auth A], IC [auth F], J [auth A], JC [auth F], K [auth A], KA [auth B], KC [auth F], L [auth A], LA [auth B], LB [auth D], LC [auth F], M [auth A], MA [auth B], MB [auth D], MC [auth F], N [auth A], NB [auth D], O [auth A], OA [auth B], OB [auth D], P [auth A], PA [auth B], Q [auth A], S [auth A], T [auth A], U [auth A], V [auth A], VB [auth E], W [auth A], WB [auth E], X [auth A], XA [auth C], XB [auth E], YA [auth C], YB [auth E], ZA [auth C], ZB [auth E]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
EOH	DB [auth C], NA [auth B], NC [auth F], PB [auth D], R [auth A], Y [auth A]	ETHANOL C2 H6 O LFQSCWFLJHTTHZ-UHFFFAOYSA-N
K	UA [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	EC [auth F], VA [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	G [auth A], SB [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 0.217 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.691	α = 69.62
b = 71.08	β = 72.56
c = 87.937	γ = 85.74

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-11 
Deposition Author(s): Prokofev, I.I., Lashkov, A.A., Gabdoulkhakov, A.G., Sotnichenko, S.E., Betzel, C., Mikhailov, A.M.

Revision History  

• Version 1.0: 2013-09-11
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description