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- PDB-5cyg: Crystal Structure of isoform 2 of uridine phosphorylase from Schi... -

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Basic information

Entry
Database: PDB / ID: 5cyg
TitleCrystal Structure of isoform 2 of uridine phosphorylase from Schistosoma mansoni APO form
ComponentsPutative uridine phosphorylase
KeywordsTRANSFERASE
Function / homology
Function and homology information


nucleotide catabolic process / nucleoside metabolic process / identical protein binding / cytosol
Similarity search - Function
Uridine phosphorylase, eukaryotic / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Inactive uridine phosphorylase B
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.017 Å
AuthorsRomanello, L. / Torini, J.R. / DeMarco, R. / Pereira, H.M.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2012/14223-9 Brazil
CitationJournal: Biochimie / Year: 2016
Title: Analysis of two Schistosoma mansoni uridine phosphorylases isoforms suggests the emergence of a protein with a non-canonical function.
Authors: da Silva Neto, A.M. / Torini de Souza, J.R. / Romanello, L. / Cassago, A. / Serrao, V.H. / DeMarco, R. / Brandao-Neto, J. / Garratt, R.C. / Pereira, H.D.
History
DepositionJul 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uridine phosphorylase
B: Putative uridine phosphorylase


Theoretical massNumber of molelcules
Total (without water)65,5842
Polymers65,5842
Non-polymers00
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-28 kcal/mol
Surface area22240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.697, 76.277, 118.965
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative uridine phosphorylase


Mass: 32791.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: Smp_082420 / Production host: Escherichia coli (E. coli) / References: UniProt: G4VGH9, uridine phosphorylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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 Å3/Da / Density % sol: 38.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 25% PEG2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.017→20 Å / Num. all: 32883 / Num. obs: 32883 / % possible obs: 93 % / Observed criterion σ(I): -3 / Redundancy: 3.49 % / Biso Wilson estimate: 25.87 Å2 / Rmerge F obs: 0.122 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.092 / Χ2: 0.916 / Net I/σ(I): 10.07 / Num. measured all: 114824
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.017-2.140.4060.3042.6512360558645460.36981.4
2.14-2.280.280.2394.2916122524948090.28191.6
2.28-2.460.2440.25.5616292491846030.23493.6
2.46-2.690.1790.157.615733451343000.17595.3
2.69-3.010.1370.11410.2314925415940280.13396.9
3.01-3.460.0790.0814.7913222366435530.09497
3.46-4.20.0510.0619.3511276315230590.0797
4.2-5.810.0390.05221.599168250924460.06197.5
5.81-200.0330.04622.295726162215390.05494.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
d*TREKdata scaling
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CYF

5cyf


Resolution: 2.017→19.828 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 24.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2439 1645 5 %Random selection
Rwork0.1958 ---
obs0.1982 32882 93.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.017→19.828 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4352 0 0 241 4593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034470
X-RAY DIFFRACTIONf_angle_d0.7086045
X-RAY DIFFRACTIONf_dihedral_angle_d12.0441613
X-RAY DIFFRACTIONf_chiral_restr0.024708
X-RAY DIFFRACTIONf_plane_restr0.002771
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0166-2.07580.27531080.23362046X-RAY DIFFRACTION74
2.0758-2.14280.28161290.2192458X-RAY DIFFRACTION90
2.1428-2.21920.24151330.21492515X-RAY DIFFRACTION91
2.2192-2.3080.30131340.22132547X-RAY DIFFRACTION92
2.308-2.41280.27271350.23542567X-RAY DIFFRACTION94
2.4128-2.53980.30761390.2282638X-RAY DIFFRACTION95
2.5398-2.69860.29221390.22752651X-RAY DIFFRACTION96
2.6986-2.90630.29291430.23232709X-RAY DIFFRACTION97
2.9063-3.19770.25811420.22032704X-RAY DIFFRACTION96
3.1977-3.65790.22361440.18372735X-RAY DIFFRACTION97
3.6579-4.59910.1981450.15932759X-RAY DIFFRACTION97
4.5991-19.82840.21491540.16382908X-RAY DIFFRACTION98
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)
11.66180.03210.02811.4859-0.77451.379-0.0906-0.0826-0.03360.10010.09320.05810.0695-0.1503-0.00760.1840.0292-0.0150.1347-0.02810.118216.7780.06467.7808
23.291-0.65891.81991.9779-1.12884.1979-0.1294-0.25860.52330.2501-0.1403-0.2973-0.2176-0.09910.16360.2792-0.046-0.03370.154-0.04790.228224.292313.54914.9433
31.73930.07170.40241.60760.85552.16640.11580.2646-0.1163-0.00920.0469-0.5367-0.04650.3279-0.05740.1633-0.0271-0.03740.2172-0.00350.306938.87766.403-5.0184
41.90030.5964-0.74481.5299-1.09892.0359-0.1785-0.1182-0.12920.1728-0.0734-0.23210.10730.12660.19570.18240.0044-0.05920.1452-0.02710.195630.8352.11398.3009
55.06332.0969-2.83174.0567-2.59585.909-0.04370.0690.1319-0.20910.1764-0.37520.21470.9073-0.08890.2225-0.00340.0470.4497-0.04230.41141.0857-6.3065-15.7196
62.80260.02410.25751.4085-0.18272.68760.1637-0.0717-0.7020.1898-0.02190.20660.47440.0658-0.0870.36590.04470.0330.1664-0.0030.369426.6581-19.3415-15.5751
71.926-0.5973-0.18910.9001-0.03791.48810.02710.1488-0.19730.0003-0.0820.04450.09-0.04710.03750.18530.00420.00980.15-0.01240.171520.2203-5.4169-19.6228
85.05640.54442.66582.24281.31854.66470.0390.0830.6812-0.31020.1885-0.0876-0.43160.22680.03010.3588-0.060.02510.2174-0.01610.234527.891410.622-18.9506
92.58850.170.1010.8445-0.82523.1348-0.03910.6553-0.7278-0.5294-0.1060.23940.3195-0.48560.11190.2614-0.0175-0.02050.3695-0.14540.337310.3798-7.018-29.5047
101.47110.06760.63540.5440.35064.38370.17730.07410.1052-0.1377-0.05850.0364-0.6869-0.74360.00380.25520.1027-0.02580.3421-0.02710.23385.36199.7249-10.1349
115.3701-1.4461-0.27371.2280.7231.8519-0.1456-0.0704-0.0722-0.10480.123-0.11510.02750.10050.04110.20010.00620.0030.1781-0.03890.177717.49641.1454-21.1801
123.254-0.52770.18453.25980.32891.978-0.097-0.0877-0.730.2490.08430.41410.4581-0.20150.04570.2376-0.01880.0040.23420.02380.2919.573-11.3556-19.616
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 148 )
2X-RAY DIFFRACTION2chain 'A' and (resid 149 through 178 )
3X-RAY DIFFRACTION3chain 'A' and (resid 179 through 225 )
4X-RAY DIFFRACTION4chain 'A' and (resid 226 through 296 )
5X-RAY DIFFRACTION5chain 'B' and (resid 7 through 24 )
6X-RAY DIFFRACTION6chain 'B' and (resid 25 through 83 )
7X-RAY DIFFRACTION7chain 'B' and (resid 84 through 148 )
8X-RAY DIFFRACTION8chain 'B' and (resid 149 through 162 )
9X-RAY DIFFRACTION9chain 'B' and (resid 163 through 193 )
10X-RAY DIFFRACTION10chain 'B' and (resid 194 through 225 )
11X-RAY DIFFRACTION11chain 'B' and (resid 226 through 245 )
12X-RAY DIFFRACTION12chain 'B' and (resid 246 through 294 )

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