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- PDB-4mch: Crystal structure of uridine phosphorylase from vibrio fischeri e... -

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Basic information

Entry
Database: PDB / ID: 4mch
TitleCrystal structure of uridine phosphorylase from vibrio fischeri es114 complexed with 6-hydroxy-1-naphthoic acid, NYSGRC Target 029520.
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NYSGRC / PSI-Biology / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


uridine phosphorylase / nucleoside metabolic process / uridine phosphorylase activity
Similarity search - Function
Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
6-hydroxynaphthalene-1-carboxylic acid / Uridine phosphorylase
Similarity search - Component
Biological speciesVibrio fischeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.73 Å
AuthorsMalashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. ...Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Love, J. / Fiser, A. / Khafizov, K. / Seidel, R. / Bonanno, J.B. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of uridine phosphorylase from vibrio fischeri es114 complexed with 6-hydroxy-1-naphthoic acid, NYSGRC Target 029520.
Authors: Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. ...Authors: Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Love, J. / Fiser, A. / Khafizov, K. / Seidel, R. / Bonanno, J.B. / Almo, S.C.
History
DepositionAug 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 1.2Dec 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,20817
Polymers29,8291
Non-polymers1,37816
Water2,810156
1
A: Uridine phosphorylase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)187,245102
Polymers178,9776
Non-polymers8,26996
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area33690 Å2
ΔGint-53 kcal/mol
Surface area52950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.975, 163.975, 58.355
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-610-

HOH

21A-614-

HOH

31A-664-

HOH

41A-686-

HOH

Detailshexameric

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Components

#1: Protein Uridine phosphorylase


Mass: 29829.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio fischeri (bacteria) / Strain: ES114 / Gene: 3280420, VF_A0530 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q5E046, uridine phosphorylase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-61N / 6-hydroxynaphthalene-1-carboxylic acid / 6-HYDROXY-1-NAPHTHOIC ACID


Mass: 188.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H8O3
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.53 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M AMMONIUM SULFATE, 0.1 M HEPES:NAOH, PH 8.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9791 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Aug 13, 2013
RadiationProtocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.73→19.753 Å / Num. obs: 31147 / % possible obs: 99.6 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 7.9
Reflection shell

Rmerge(I) obs: 0.015 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.73-1.827.10.53216645581.502100
1.82-1.937.10.83033442970.878100
1.93-2.077.11.62842840210.466100
2.07-2.237.22.72698637730.276100
2.23-2.457.33.92518434650.184100
2.45-2.747.44.92335631460.134100
2.74-3.167.44.92063127770.121100
3.16-3.877.46.11765023750.094100
3.87-5.477.412.21336218170.04899.1
5.47-19.7537.11865229180.03688.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.2.5data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4LNH

4lnh


Resolution: 1.73→19.16 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.2157 / WRfactor Rwork: 0.1871 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9078 / SU B: 3.152 / SU ML: 0.047 / SU R Cruickshank DPI: 0.0204 / SU Rfree: 0.0196 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.02 / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1962 1570 5 %RANDOM
Rwork0.1729 ---
obs0.1741 31134 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 111.25 Å2 / Biso mean: 34.5311 Å2 / Biso min: 19.47 Å2
Baniso -1Baniso -2Baniso -3
1--9.21 Å2-0 Å2-0 Å2
2---9.21 Å2-0 Å2
3---18.42 Å2
Refinement stepCycle: LAST / Resolution: 1.73→19.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1886 0 75 156 2117
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191977
X-RAY DIFFRACTIONr_angle_refined_deg1.1961.9942660
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9425241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09624.88990
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.90215310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0721510
X-RAY DIFFRACTIONr_chiral_restr0.0830.2309
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021457
X-RAY DIFFRACTIONr_mcbond_it1.5374.302970
X-RAY DIFFRACTIONr_mcangle_it2.46657.8091209
X-RAY DIFFRACTIONr_scbond_it2.495.1511006
LS refinement shellResolution: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 111 -
Rwork0.305 2166 -
all-2277 -
obs--99.48 %
Refinement TLS params.Method: refined / Origin x: 1.4853 Å / Origin y: 29.7345 Å / Origin z: 27.326 Å
111213212223313233
T0.0609 Å20.0065 Å20.0024 Å2-0.0177 Å20.0047 Å2--0.006 Å2
L0.3796 °20.1254 °20.0466 °2-0.7518 °20.0381 °2--0.4037 °2
S0.0102 Å °0.0063 Å °0.0115 Å °-0.0039 Å °0.004 Å °0.06 Å °-0.1178 Å °-0.0494 Å °-0.0143 Å °

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