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

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Basic information

Entry
Database: PDB / ID: 5epu
TitleX-ray structure uridine phosphorylase from Vibrio cholerae in complex with cytosine at 1.06A.
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / Rossmann Fold
Function / homology
Function and homology information


nucleotide catabolic process / uridine phosphorylase / nucleoside catabolic process / uridine phosphorylase activity / UMP salvage / 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
6-AMINOPYRIMIDIN-2(1H)-ONE / Uridine phosphorylase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.06 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 cytosine at 1.06A.
Authors: Prokofev, I.I. / Lashkov, A.A. / Gabdoulkhakov, A.G. / Betzel, C. / Mikhailov, A.M.
History
DepositionNov 12, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 23, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry

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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)164,61435
Polymers162,6546
Non-polymers1,96029
Water38,1742119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27180 Å2
ΔGint-169 kcal/mol
Surface area45650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.848, 96.715, 92.890
Angle α, β, γ (deg.)90.000, 119.960, 90.000
Int Tables number4
Space group name H-MP1211

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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, udp_2, DN30_1909, EN12_05055, ERS013138_02408, ERS013140_00580, ERS013160_01327, ERS013186_00327, ERS013199_00063, ERS013201_00032, ERS013202_00369, ERS013206_00377, ERS013212_00480
Production host: Escherichia coli (E. coli) / References: UniProt: Q9K4U1, uridine phosphorylase

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Non-polymers , 8 types, 2148 molecules

#2: Chemical
ChemComp-CYT / 6-AMINOPYRIMIDIN-2(1H)-ONE / CYTOSINE


Mass: 111.102 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H5N3O
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2119 / 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: 2.22 Å3/Da / Density % sol: 44.63 %
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 16, 2015
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97989 Å / Relative weight: 1
ReflectionResolution: 1.06→46.461 Å / Num. obs: 615831 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 11.28 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 16.26
Reflection shellResolution: 1.06→1.12 Å / Rmerge(I) obs: 0.608 / Mean I/σ(I) obs: 2.54 / Rejects: 0 / % possible all: 83.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K6O

4k6o


Resolution: 1.06→46.46 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.982 / WRfactor Rfree: 0.1135 / WRfactor Rwork: 0.099 / FOM work R set: 0.9237 / SU B: 0.594 / SU ML: 0.013 / SU R Cruickshank DPI: 0.0215 / SU Rfree: 0.0217 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.021 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.122 30490 5 %RANDOM
Rwork0.105 ---
obs0.106 585343 95.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 133.93 Å2 / Biso mean: 11.75 Å2 / Biso min: 2.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å2-0.26 Å2
2--0.94 Å20 Å2
3----0.24 Å2
Refinement stepCycle: final / Resolution: 1.06→46.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11299 0 306 2207 13812
Biso mean--11.52 28.26 -
Num. residues----1509
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01913408
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213287
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.97118459
X-RAY DIFFRACTIONr_angle_other_deg0.974330816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.00551954
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.28623.292565
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.223152462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.51815123
X-RAY DIFFRACTIONr_chiral_restr0.0920.22161
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215678
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023073
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2290.8566693
X-RAY DIFFRACTIONr_mcbond_other1.2280.8566690
X-RAY DIFFRACTIONr_mcangle_it1.6331.298506
X-RAY DIFFRACTIONMAIN-CHAIN ANGLE OTHER ATOMS (A**2)
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONSIDE-CHAIN BOND OTHER ATOMS (A**2)
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONSIDE-CHAIN ANGLE OTHER ATOMS (A**2)
X-RAY DIFFRACTIONLONG RANGE B REFINED ATOMS (A**2)
X-RAY DIFFRACTIONLONG RANGE B OTHER ATOMS (A**2)
X-RAY DIFFRACTIONr_rigid_bond_restr3.736326695
X-RAY DIFFRACTIONr_sphericity_free33.4545460
X-RAY DIFFRACTIONr_sphericity_bonded9.785528041
LS refinement shellResolution: 1.06→1.09 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 1750 -
Rwork0.239 31808 -
all-33558 -
obs--70.51 %

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