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- PDB-4r31: Crystal structure of a putative uridine phosphorylase from Actino... -

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Basic information

Entry
Database: PDB / ID: 4r31
TitleCrystal structure of a putative uridine phosphorylase from Actinobacillus succinogenes 130Z (Target NYSGRC-029667 )
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / phosphorylase / uridine / Structural genomics / NYSGRC / PSI-Biology / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


uridine phosphorylase / nucleotide catabolic process / uridine phosphorylase activity / UMP salvage / nucleoside metabolic process / 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
Uridine phosphorylase
Similarity search - Component
Biological speciesActinobacillus succinogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsSampathkumar, P. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: to be published
Title: Crystal structure of a putative uridine phosphorylase from Actinobacillus succinogenes 130Z (Target NYSGRC-029667 )
Authors: Sampathkumar, P. / Ahmed, M. / Attonito, J. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Fiser, A. / Glenn, A.S. / Hammonds, J. / Himmel, D.M. / Hillerich, B. / Khafizov, K. / ...Authors: Sampathkumar, P. / Ahmed, M. / Attonito, J. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Fiser, A. / Glenn, A.S. / Hammonds, J. / Himmel, D.M. / Hillerich, B. / Khafizov, K. / Lafleur, J. / Love, J.D. / Stead, M. / Seidel, R. / Toro, R. / Morisco, L.L. / Sojitra, S.S. / Wasserman, S.R. / Schramm, V.L. / Almo, S.C. / New York Structural Genomics Research Consortium
History
DepositionAug 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name

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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)183,57117
Polymers182,5586
Non-polymers1,01311
Water14,466803
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23220 Å2
ΔGint-159 kcal/mol
Surface area48490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.422, 120.595, 176.879
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Uridine phosphorylase /


Mass: 30426.283 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinobacillus succinogenes (bacteria) / Strain: 130Z / Gene: Asuc_0427 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon-PlusRIL / References: UniProt: A6VLF7, uridine phosphorylase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 803 / 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: 2.52 Å3/Da / Density % sol: 51.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: Protein (20mM HEPES pH7.5, 150mM NaCl, 5% glycerol, and 5mM DTT); Reservoir (MCSG1 #81: 0.2 M sodium formate, 20% (w/v) PEG 3350); Cryoprotection (33% glycerol), 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: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 3, 2013 / Details: MIRRORS
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 126139 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.6 % / Biso Wilson estimate: 30.7 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 13.18
Reflection shellResolution: 2→2.03 Å / Redundancy: 12.5 % / Mean I/σ(I) obs: 1.23 / Num. unique all: 6175 / % possible all: 98.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0073refinement
PDB_EXTRACT3.14data extraction
HKL-3000data reduction
SCALEPACKdata scaling
SHELXCphasing
SHELXDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.986 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2081 6187 4.9 %RANDOM
Rwork0.1694 ---
obs0.1713 125108 99.88 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 121.46 Å2 / Biso mean: 33.385 Å2 / Biso min: 13.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å20 Å2
2--0.64 Å2-0 Å2
3----1.27 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11431 0 66 803 12300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01911846
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211397
X-RAY DIFFRACTIONr_angle_refined_deg1.3441.97916112
X-RAY DIFFRACTIONr_angle_other_deg0.766326221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.90851559
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.94623.94467
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.467151792
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.741571
X-RAY DIFFRACTIONr_chiral_restr0.0740.21873
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02113514
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022617
X-RAY DIFFRACTIONr_mcbond_it1.6193.1276129
X-RAY DIFFRACTIONr_mcbond_other1.6183.1266128
X-RAY DIFFRACTIONr_mcangle_it2.5534.6797663
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 436 -
Rwork0.259 8696 -
all-9132 -
obs-8696 99.97 %

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