3PNS | pdb_00003pns

Crystal Structure of Uridine Phosphorylase Complexed with Uracil from Vibrio cholerae O1 biovar El Tor

PDB DOI: https://doi.org/10.2210/pdb3PNS/pdb

Classification: TRANSFERASE
Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-11-19 Released: 2010-12-15
Deposition Author(s): Maltseva, N., Kim, Y., Hasseman, J., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.226 (Depositor), 0.217 (DCC)
R-Value Work:
0.174 (Depositor), 0.168 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure of Uridine Phosphorylase Complexed with Uracil from Vibrio cholerae O1 biovar El Tor

Maltseva, N., Kim, Y., Hasseman, J., Anderson, W.F., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 346.36 kDa
Atom Count: 25,215
Modeled Residue Count: 2,968
Deposited Residue Count: 3,132
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine phosphorylase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	261	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0 Gene Names: VC_1034 EC: 2.4.2.3
UniProt
Find proteins for Q9KT71 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KT71 Go to UniProtKB: Q9KT71
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KT71
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
URA Query on URA Download:Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain BB [auth K] SDF format, chain EB [auth L] SDF format, chain HA [auth F] SDF format, chain MA [auth G] SDF format, chain OA [auth H] SDF format, chain SA [auth I] SDF format, chain V [auth C] SDF format, chain Y [auth D] SDF format, chain YA [auth J] SDF format, chain Q [auth B] MOL2 format, chain BA [auth E] MOL2 format, chain BB [auth K] MOL2 format, chain EB [auth L] MOL2 format, chain HA [auth F] MOL2 format, chain MA [auth G] MOL2 format, chain OA [auth H] MOL2 format, chain SA [auth I] MOL2 format, chain V [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain YA [auth J] MOL2 format, chain Q [auth B] mmCIF format, chain BA [auth E] mmCIF format, chain BB [auth K] mmCIF format, chain EB [auth L] mmCIF format, chain HA [auth F] mmCIF format, chain MA [auth G] mmCIF format, chain OA [auth H] mmCIF format, chain SA [auth I] mmCIF format, chain V [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain YA [auth J] mmCIF format, chain Q [auth B]	BA [auth E] BB [auth K] EB [auth L] HA [auth F] MA [auth G] BA [auth E], BB [auth K], EB [auth L], HA [auth F], MA [auth G], OA [auth H], Q [auth B], SA [auth I], V [auth C], Y [auth D], YA [auth J]	URACIL C₄ H₄ N₂ O₂ ISAKRJDGNUQOIC-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain BB [auth K] Focus chain EB [auth L] Focus chain HA [auth F] Focus chain MA [auth G] Focus chain OA [auth H] Focus chain Q [auth B] Focus chain SA [auth I] Focus chain V [auth C] Focus chain Y [auth D] Focus chain YA [auth J] Interactions & Density Focus chain BA [auth E] Focus chain BB [auth K] Focus chain EB [auth L] Focus chain HA [auth F] Focus chain MA [auth G] Focus chain OA [auth H] Focus chain Q [auth B] Focus chain SA [auth I] Focus chain V [auth C] Focus chain Y [auth D] Focus chain YA [auth J]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain JA [auth G] SDF format, chain TA [auth I] SDF format, chain W [auth C] MOL2 format, chain JA [auth G] MOL2 format, chain TA [auth I] MOL2 format, chain W [auth C] mmCIF format, chain JA [auth G] mmCIF format, chain TA [auth I] mmCIF format, chain W [auth C]	JA [auth G], TA [auth I], W [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain JA [auth G] Focus chain TA [auth I] Focus chain W [auth C] Interactions & Density Focus chain JA [auth G] Focus chain TA [auth I] Focus chain W [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain AB [auth K] SDF format, chain CB [auth K] SDF format, chain DA [auth E] SDF format, chain DB [auth L] SDF format, chain EA [auth E] SDF format, chain FA [auth F] SDF format, chain GA [auth F] SDF format, chain KA [auth G] SDF format, chain LA [auth G] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth G] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain PA [auth H] SDF format, chain R [auth C] SDF format, chain RA [auth I] SDF format, chain U [auth C] SDF format, chain UA [auth I] SDF format, chain X [auth D] SDF format, chain XA [auth J] SDF format, chain Z [auth D] SDF format, chain ZA [auth J] SDF format, chain S [auth C] MOL2 format, chain AB [auth K] MOL2 format, chain CB [auth K] MOL2 format, chain DA [auth E] MOL2 format, chain DB [auth L] MOL2 format, chain EA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain GA [auth F] MOL2 format, chain KA [auth G] MOL2 format, chain LA [auth G] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth G] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth H] MOL2 format, chain R [auth C] MOL2 format, chain RA [auth I] MOL2 format, chain U [auth C] MOL2 format, chain UA [auth I] MOL2 format, chain X [auth D] MOL2 format, chain XA [auth J] MOL2 format, chain Z [auth D] MOL2 format, chain ZA [auth J] MOL2 format, chain S [auth C] mmCIF format, chain AB [auth K] mmCIF format, chain CB [auth K] mmCIF format, chain DA [auth E] mmCIF format, chain DB [auth L] mmCIF format, chain EA [auth E] mmCIF format, chain FA [auth F] mmCIF format, chain GA [auth F] mmCIF format, chain KA [auth G] mmCIF format, chain LA [auth G] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth G] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth H] mmCIF format, chain R [auth C] mmCIF format, chain RA [auth I] mmCIF format, chain U [auth C] mmCIF format, chain UA [auth I] mmCIF format, chain X [auth D] mmCIF format, chain XA [auth J] mmCIF format, chain Z [auth D] mmCIF format, chain ZA [auth J] mmCIF format, chain S [auth C]	AB [auth K] CB [auth K] DA [auth E] DB [auth L] EA [auth E] AB [auth K], CB [auth K], DA [auth E], DB [auth L], EA [auth E], FA [auth F], GA [auth F], KA [auth G], LA [auth G], M [auth A], N [auth A], NA [auth G], O [auth B], P [auth B], PA [auth H], R [auth C], RA [auth I], S [auth C], U [auth C], UA [auth I], X [auth D], XA [auth J], Z [auth D], ZA [auth J]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AB [auth K] Focus chain CB [auth K] Focus chain DA [auth E] Focus chain DB [auth L] Focus chain EA [auth E] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain KA [auth G] Focus chain LA [auth G] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth G] Focus chain O [auth B] Focus chain P [auth B] Focus chain PA [auth H] Focus chain R [auth C] Focus chain RA [auth I] Focus chain S [auth C] Focus chain U [auth C] Focus chain UA [auth I] Focus chain X [auth D] Focus chain XA [auth J] Focus chain Z [auth D] Focus chain ZA [auth J] Interactions & Density Focus chain AB [auth K] Focus chain CB [auth K] Focus chain DA [auth E] Focus chain DB [auth L] Focus chain EA [auth E] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain KA [auth G] Focus chain LA [auth G] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth G] Focus chain O [auth B] Focus chain P [auth B] Focus chain PA [auth H] Focus chain R [auth C] Focus chain RA [auth I] Focus chain S [auth C] Focus chain U [auth C] Focus chain UA [auth I] Focus chain X [auth D] Focus chain XA [auth J] Focus chain Z [auth D] Focus chain ZA [auth J]
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain IA [auth F] MOL2 format, chain IA [auth F] mmCIF format, chain IA [auth F]	IA [auth F]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain IA [auth F] Interactions & Density Focus chain IA [auth F]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain QA [auth H] MOL2 format, chain CA [auth E] MOL2 format, chain QA [auth H] mmCIF format, chain CA [auth E] mmCIF format, chain QA [auth H]	CA [auth E], QA [auth H]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain CA [auth E] Focus chain QA [auth H] Interactions & Density Focus chain CA [auth E] Focus chain QA [auth H]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain T [auth C] SDF format, chain VA [auth I] SDF format, chain WA [auth I] MOL2 format, chain AA [auth E] MOL2 format, chain T [auth C] MOL2 format, chain VA [auth I] MOL2 format, chain WA [auth I] mmCIF format, chain AA [auth E] mmCIF format, chain T [auth C] mmCIF format, chain VA [auth I] mmCIF format, chain WA [auth I]	AA [auth E], T [auth C], VA [auth I], WA [auth I]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth E] Focus chain T [auth C] Focus chain VA [auth I] Focus chain WA [auth I] Interactions & Density Focus chain AA [auth E] Focus chain T [auth C] Focus chain VA [auth I] Focus chain WA [auth I]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	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: 0.226 (Depositor), 0.217 (DCC)
R-Value Work: 0.174 (Depositor), 0.168 (DCC)
R-Value Observed: 0.177 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.276	α = 90
b = 174.455	β = 90
c = 180.021	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
MOLREP	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-12-15

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2010-12-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2023-12-06
Changes: Data collection
Version 1.4: 2024-11-27
Changes: Structure summary