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- PDB-3pns: Crystal Structure of Uridine Phosphorylase Complexed with Uracil ... -

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Basic information

Entry
Database: PDB / ID: 3pns
TitleCrystal Structure of Uridine Phosphorylase Complexed with Uracil from Vibrio cholerae O1 biovar El Tor
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta-alpha sandwich / phosphorylase / cytosol
Function / homology
Function and homology information


nucleotide catabolic process / uridine phosphorylase / uridine phosphorylase activity / UMP salvage / nucleoside catabolic process / cytosol
Similarity search - Function
Uridine phosphorylase / Nucleoside phosphorylase, conserved site / Purine and other phosphorylases family 1 signature. / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / FORMIC ACID / URACIL / Uridine phosphorylase
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 Å
AuthorsMaltseva, N. / Kim, Y. / Hasseman, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Uridine Phosphorylase Complexed with Uracil from Vibrio cholerae O1 biovar El Tor
Authors: Maltseva, N. / Kim, Y. / Hasseman, J. / Anderson, W.F. / Joachimiak, A.
History
DepositionNov 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uridine phosphorylase
B: Uridine phosphorylase
C: Uridine phosphorylase
D: Uridine phosphorylase
E: Uridine phosphorylase
F: Uridine phosphorylase
G: Uridine phosphorylase
H: Uridine phosphorylase
I: Uridine phosphorylase
J: Uridine phosphorylase
K: Uridine phosphorylase
L: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)346,35857
Polymers342,33312
Non-polymers4,02545
Water36,1922009
1
A: Uridine phosphorylase
B: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5367
Polymers57,0552
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-23 kcal/mol
Surface area18140 Å2
MethodPISA
2
C: Uridine phosphorylase
D: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,87211
Polymers57,0552
Non-polymers8169
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-34 kcal/mol
Surface area18170 Å2
MethodPISA
3
E: Uridine phosphorylase
F: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,79011
Polymers57,0552
Non-polymers7349
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-37 kcal/mol
Surface area18150 Å2
MethodPISA
4
G: Uridine phosphorylase
H: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,79010
Polymers57,0552
Non-polymers7358
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-24 kcal/mol
Surface area18170 Å2
MethodPISA
5
I: Uridine phosphorylase
J: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,81511
Polymers57,0552
Non-polymers7609
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-39 kcal/mol
Surface area17410 Å2
MethodPISA
6
K: Uridine phosphorylase
L: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5567
Polymers57,0552
Non-polymers5005
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-20 kcal/mol
Surface area18090 Å2
MethodPISA
7
G: Uridine phosphorylase
H: Uridine phosphorylase
hetero molecules

A: Uridine phosphorylase
B: Uridine phosphorylase
hetero molecules

K: Uridine phosphorylase
L: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,88224
Polymers171,1666
Non-polymers1,71618
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y+1/2,-z+1/21
crystal symmetry operation4_566x+1/2,-y+3/2,-z+11
Buried area25980 Å2
ΔGint-133 kcal/mol
Surface area44740 Å2
MethodPISA
8
C: Uridine phosphorylase
D: Uridine phosphorylase
E: Uridine phosphorylase
F: Uridine phosphorylase
I: Uridine phosphorylase
J: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,47633
Polymers171,1666
Non-polymers2,31027
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27840 Å2
ΔGint-185 kcal/mol
Surface area43700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.276, 174.455, 180.021
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Uridine phosphorylase


Mass: 28527.713 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria)
Strain: N16961 / Gene: VC_1034 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q9KT71

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Non-polymers , 7 types, 2054 molecules

#2: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-URA / URACIL


Mass: 112.087 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C4H4N2O2
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#7: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2009 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.07 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES pH7.5, 10% PEG 4000, 20% Isopropanol, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 9, 2010 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 208594 / Num. obs: 208594 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rsym value: 0.093 / Net I/σ(I): 6.6
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.38 / Rsym value: 0.472 / % possible all: 85

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 3o6v

3o6v


Resolution: 2.002→49.636 Å / SU ML: 0.27 / Isotropic thermal model: mixed / σ(F): 1.34 / Phase error: 24.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2255 10074 5.02 %
Rwork0.1744 --
obs0.177 200821 92.04 %
all-200821 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.58 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.7431 Å2-0 Å2-0 Å2
2---0.5371 Å2-0 Å2
3----0.206 Å2
Refinement stepCycle: LAST / Resolution: 2.002→49.636 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22176 0 261 2009 24446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01123621
X-RAY DIFFRACTIONf_angle_d1.27732104
X-RAY DIFFRACTIONf_dihedral_angle_d13.7428591
X-RAY DIFFRACTIONf_chiral_restr0.0833736
X-RAY DIFFRACTIONf_plane_restr0.0054212
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0021-2.07370.30928680.242816383X-RAY DIFFRACTION80
2.0737-2.15670.27059460.207417530X-RAY DIFFRACTION85
2.1567-2.25490.25289520.189717764X-RAY DIFFRACTION87
2.2549-2.37380.25889460.191618253X-RAY DIFFRACTION89
2.3738-2.52250.25179770.179518900X-RAY DIFFRACTION92
2.5225-2.71720.256510360.184219700X-RAY DIFFRACTION95
2.7172-2.99060.237410660.171720451X-RAY DIFFRACTION99
2.9906-3.42330.205910530.160620702X-RAY DIFFRACTION99
3.4233-4.31260.189811530.147820550X-RAY DIFFRACTION99
4.3126-49.65160.203310770.175420514X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.38980.2306-0.1060.18880.06220.3260.0173-0.1435-0.03750.0199-0.0477-0.0216-0.04230.04940.02550.0567-0.0088-0.00770.12880.00410.04829.19892.163849.5196
20.16420.07750.15360.06760.17280.47220.0233-0.00170.02810.0389-0.02460.02180.0584-0.04170.00330.0408-0.01810.00160.0610.0160.038830.186366.428353.2041
30.71760.3407-0.2330.3952-0.33210.53820.1282-0.1812-0.06880.2237-0.1776-0.0455-0.25350.14110.04830.1442-0.0702-0.05140.09380.02160.005480.443591.7957116.3732
40.30830.16030.25180.08780.18790.49620.017-0.07110.04310.0462-0.05240.06520.0869-0.07970.03560.0791-0.02260.00840.07840.00660.08981.886866.5953120.0802
50.3801-0.1433-0.08860.0882-0.09870.4468-0.00950.0115-0.1041-0.1107-0.04450.09080.1735-0.0050.03920.14010.0185-0.03150.0378-0.03160.124480.378456.728872.7716
60.08970.24690.08190.70960.310.37930.04190.02430.00370.10380.0138-0.01810.10950.0432-0.05640.05890.0083-0.03140.04790.00420.102787.937648.767895.5433
70.3834-0.0393-0.04880.04840.13630.4016-0.03790.0126-0.05740.0710.025-0.03630.15320.02640.01310.07040.01820.00290.00740.01780.046575.6725143.828183.7277
80.2256-0.07680.03260.0718-0.10820.43870.0198-0.0021-0.0549-0.02280.0610.00240.1618-0.0187-0.05850.0554-0.0201-0.0146-0.02940.00830.031567.4099135.66861.3355
90.35850.0209-0.05970.1578-0.07220.40790.02770.00350.0176-0.0167-0.03480.0062-0.1699-0.0310.01990.05510.0432-0.0453-0.01710.02820.016572.7057101.949887.8372
100.2031-0.15480.06960.30270.26610.5567-0.02190.0250.0287-0.1839-0.0792-0.0245-0.2538-0.04630.08650.19890.0338-0.05070.0680.00750.077978.792786.750668.4701
110.2015-0.0058-0.02950.22450.00770.4453-0.0306-0.0232-0.0108-0.02510.0059-0.0050.14250.06650.02320.08250.01310.02130.0528-0.0090.049330.989372.4456111.184
120.3197-0.23740.00940.3503-0.09330.4271-0.04240.0813-0.0471-0.0862-0.0140.05350.0675-0.02140.04970.053-0.01110.01380.0552-0.02520.035625.228387.257591.6259
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F
7X-RAY DIFFRACTION7chain G
8X-RAY DIFFRACTION8chain H
9X-RAY DIFFRACTION9chain I
10X-RAY DIFFRACTION10chain J
11X-RAY DIFFRACTION11chain K
12X-RAY DIFFRACTION12chain L

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