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- PDB-4h1t: X-RAY Structure of the Complex VchUPh with Phosphate ion at 1.92A... -

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Basic information

Entry
Database: PDB / ID: 4h1t
TitleX-RAY Structure of the Complex VchUPh with Phosphate ion at 1.92A Resolution.
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / Rossmann Fold / Nucleoside / Phosphorylation
Function / homology
Function and homology information


uridine phosphorylase / nucleotide catabolic process / uridine phosphorylase activity / UMP salvage / nucleoside catabolic process / metal ion binding / cytoplasm
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
ETHANOL / : / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Uridine phosphorylase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.924 Å
AuthorsProkofev, I.I. / Lashkov, A.A. / Gabdoulkhakov, A.G. / Sotnichenko, S.E. / Betzel, C. / Mikhailov, A.M.
CitationJournal: TO BE PUBLISHED
Title: X-RAY Structure of the Complex VchUPh with Phosphate ion at 1.92A Resolution.
Authors: Prokofev, I.I. / Lashkov, A.A. / Gabdoulkhakov, A.G. / Sotnichenko, S.E. / Betzel, C. / Mikhailov, A.M.
History
DepositionSep 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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_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.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_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.value / _struct_conn.pdbx_dist_value / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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)169,77999
Polymers162,6546
Non-polymers7,12593
Water22,1581230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38340 Å2
ΔGint-97 kcal/mol
Surface area46010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.691, 71.080, 87.937
Angle α, β, γ (deg.)69.620, 72.560, 85.740
Int Tables number1
Space group name H-MP1
DetailsBiological Assembly is asymmetric unit cell.

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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) / Strain: 569B / Gene: udp / Plasmid: pMZ21 / Production host: Escherichia coli (E. coli) / Strain (production host): AM201 / References: UniProt: Q9K4U1, uridine phosphorylase

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Non-polymers , 9 types, 1323 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 43 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-EOH / ETHANOL / Ethanol


Mass: 46.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O
#5: Chemical...
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#7: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#9: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1230 / 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: 2.19 Å3/Da / Density % sol: 43.77 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Ammonium sulfate 0.5 M di-Sodium phosphate 0.5 M di-Potassium phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.81 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 11, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 1.924→78.817 Å / Num. all: 102754 / Num. obs: 102754 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 10.747 Å2 / Rsym value: 0.037 / Net I/σ(I): 30
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.92-2.033.70.111754208146470.11196.3
2.03-2.1540.089.756715142450.0898
2.15-2.33.80.05812.950230133260.05898
2.3-2.4840.05214.849459124190.05298.4
2.48-2.7240.04417.345574114490.04498.8
2.72-3.0440.03322.641484104260.03398.9
3.04-3.5140.023303666792160.02399.1
3.51-4.33.90.02132.92990177570.02199.3
4.3-6.0840.01933.42387760190.01999.6
6.08-29.3623.90.01636.71279632500.01698.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASERphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O6V

3o6v


Resolution: 1.924→26.272 Å / Occupancy max: 1 / Occupancy min: 0.06 / FOM work R set: 0.8803 / SU ML: 0.23 / σ(F): 1.97 / Phase error: 19.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2171 5129 5 %RANDOM
Rwork0.1771 ---
all0.1812 103696 --
obs0.1791 102659 98.24 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.85 Å2 / ksol: 0.381 e/Å3
Displacement parametersBiso max: 88.66 Å2 / Biso mean: 13.4436 Å2 / Biso min: 1.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.0479 Å2-0.0825 Å2-0.0778 Å2
2---0.1072 Å20.0373 Å2
3---0.0593 Å2
Refinement stepCycle: LAST / Resolution: 1.924→26.272 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11257 0 445 1230 12932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812085
X-RAY DIFFRACTIONf_angle_d0.84316285
X-RAY DIFFRACTIONf_chiral_restr0.0561889
X-RAY DIFFRACTIONf_plane_restr0.0032078
X-RAY DIFFRACTIONf_dihedral_angle_d12.7614481
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9243-1.94620.28881470.23042977312491
1.9462-1.96910.25751800.20293217339798
1.9691-1.99310.26221690.18243301347097
1.9931-2.01830.2481700.17883209337998
2.0183-2.04480.20491770.16113262343997
2.0448-2.07280.20861810.15573177335898
2.0728-2.10240.25491630.16073289345298
2.1024-2.13380.21651760.16693242341898
2.1338-2.16710.18371700.15073204337499
2.1671-2.20260.21691580.19173299345798
2.2026-2.24060.50041730.42973265343897
2.2406-2.28130.26361700.19713206337699
2.2813-2.32520.20541640.16653213337798
2.3252-2.37260.20361760.16373347352398
2.3726-2.42420.21921680.15813235340398
2.4242-2.48050.21511650.15843273343898
2.4805-2.54250.22061710.16663276344799
2.5425-2.61120.21131460.17193287343399
2.6112-2.6880.23181820.17253223340599
2.688-2.77460.19351720.15943289346199
2.7746-2.87370.18911730.17043255342899
2.8737-2.98860.22661770.1783290346799
2.9886-3.12440.20451780.16633250342899
3.1244-3.28880.19161940.16373290348499
3.2888-3.49440.18511830.15733225340899
3.4944-3.76350.2031740.1783320349499
3.7635-4.14090.17131740.14533269344399
4.1409-4.73710.15171900.12743304349499
4.7371-5.95680.18561690.161432853454100
5.9568-26.27470.15471390.15753251339097

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