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- PDB-5efo: X-ray structure uridine phosphorylase from Vibrio cholerae in com... -

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Basic information

Entry
Database: PDB / ID: 5efo
TitleX-ray structure uridine phosphorylase from Vibrio cholerae in complex with cytidine and cytosine at 1.63A.
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / Rossmann Fold
Function / homology
Function and homology information


uridine phosphorylase / nucleotide catabolic process / UMP salvage / uridine catabolic process / uridine phosphorylase activity / purine-nucleoside phosphorylase activity / purine nucleoside catabolic process / metal ion binding / 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
4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE / 6-AMINOPYRIMIDIN-2(1H)-ONE / DI(HYDROXYETHYL)ETHER / Uridine phosphorylase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.63 Å
AuthorsProkofev, I.I. / Lashkov, A.A. / Gabdoulkhakov, A.G. / Betzel, C. / Mikhailov, A.M.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
RFBR14-04-00952a Russian Federation
CitationJournal: To Be Published
Title: X-ray structure uridine phosphorylase from Vibrio cholerae in complex with uridine at 2.24 A resolution
Authors: Prokofev, I.I. / Lashkov, A.A. / Gabdoulkhakov, A.G. / Betzel, C. / Mikhailov, A.M.
History
DepositionOct 24, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,65926
Polymers162,6546
Non-polymers2,00520
Water27,1851509
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26610 Å2
ΔGint-115 kcal/mol
Surface area46090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.949, 76.336, 89.694
Angle α, β, γ (deg.)67.540, 73.740, 84.920
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Uridine phosphorylase


Mass: 27108.994 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: udp, udp_1, DN30_1909, EN12_05055, ERS013138_02408, ERS013140_00580, ERS013186_00327, ERS013199_00063, ERS013201_00032, ERS013202_00369, ERS013206_00377
Production host: Escherichia coli (E. coli) / References: UniProt: Q9K4U1, uridine phosphorylase

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Non-polymers , 8 types, 1529 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CYT / 6-AMINOPYRIMIDIN-2(1H)-ONE / CYTOSINE


Mass: 111.102 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H5N3O
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-CTN / 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE / CYTIDINE


Mass: 243.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N3O5
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1509 / 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: 2.24 Å3/Da / Density % sol: 45.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG4000, 0.1M TRIS-HCl, 0.2M MgCl2x6H2O

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97989 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 15, 2015
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97989 Å / Relative weight: 1
ReflectionResolution: 1.63→45.157 Å / Num. all: 164109 / Num. obs: 164109 / % possible obs: 93.2 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.053 / Rrim(I) all: 0.096 / Net I/av σ(I): 6.835 / Net I/σ(I): 10.5 / Num. measured all: 533373
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.63-1.723.20.4281.768525216790.2810.4282.584.2
1.72-1.823.40.3222.379292233020.2040.3223.695.6
1.82-1.953.10.2722.665480212780.1880.2724.393.1
1.95-2.13.40.1464.869384204040.0930.1467.796.1
2.1-2.313.10.1225.655069180280.0850.122991.8
2.31-2.583.40.0837.157416170950.0540.08313.896.6
2.58-2.983.30.0668.449352150690.0440.0661796.6
2.98-3.643.30.051141723125620.0330.0523.195.4
3.64-5.153.20.03914.92963994070.0260.03927.192.3
5.15-45.1573.30.03414.41749352850.0220.03426.294.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
MOLREPphasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LWZ

4lwz


Resolution: 1.63→19.97 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.941 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2073 8011 4.9 %RANDOM
Rwork0.163 ---
obs0.1652 154258 92.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.46 Å2 / Biso mean: 20.75 Å2 / Biso min: 5.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0.17 Å20.04 Å2
2---0.07 Å2-0.11 Å2
3---0.13 Å2
Refinement stepCycle: final / Resolution: 1.63→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11262 0 78 1518 12858
Biso mean--32.13 35.09 -
Num. residues----1513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01912133
X-RAY DIFFRACTIONr_angle_refined_deg1.1911.96816533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.42751654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.25223.74500
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.038152072
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1761591
X-RAY DIFFRACTIONr_chiral_restr0.0780.21944
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219120
X-RAY DIFFRACTIONr_mcbond_it2.5151.7016184
X-RAY DIFFRACTIONr_mcangle_it3.3112.5547761
X-RAY DIFFRACTIONr_scbond_it3.0691.9975949
X-RAY DIFFRACTIONr_rigid_bond_restr3.09312133
X-RAY DIFFRACTIONr_sphericity_free37.6845445
X-RAY DIFFRACTIONr_sphericity_bonded19.343512951
LS refinement shellResolution: 1.63→1.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 466 -
Rwork0.286 9068 -
all-9534 -
obs--73.86 %

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