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- PDB-1vhw: Crystal structure of purine nucleoside phosphorylase with adenosine -

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Basic information

Entry
Database: PDB / ID: 1vhw
TitleCrystal structure of purine nucleoside phosphorylase with adenosine
Componentspurine nucleoside phosphorylase
KeywordsTRANSFERASE / structural genomics
Function / homology
Function and homology information


purine nucleoside catabolic process / purine-nucleoside phosphorylase activity / purine-nucleoside phosphorylase / cytosol
Similarity search - Function
Purine nucleoside phosphorylase DeoD-type / 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
ADENOSINE / Purine nucleoside phosphorylase DeoD-type 1
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsStructural GenomiX
CitationJournal: Proteins / Year: 2005
Title: Structural analysis of a set of proteins resulting from a bacterial genomics project
Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / ...Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / Feil, I. / Furlong, E.B. / Gajiwala, K.S. / Gao, X. / He, D. / Hendle, J. / Huber, A. / Hoda, K. / Kearins, P. / Kissinger, C. / Laubert, B. / Lewis, H.A. / Lin, J. / Loomis, K. / Lorimer, D. / Louie, G. / Maletic, M. / Marsh, C.D. / Miller, I. / Molinari, J. / Muller-Dieckmann, H.J. / Newman, J.M. / Noland, B.W. / Pagarigan, B. / Park, F. / Peat, T.S. / Post, K.W. / Radojicic, S. / Ramos, A. / Romero, R. / Rutter, M.E. / Sanderson, W.E. / Schwinn, K.D. / Tresser, J. / Winhoven, J. / Wright, T.A. / Wu, L. / Xu, J. / Harris, T.J.
History
DepositionDec 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: purine nucleoside phosphorylase
B: purine nucleoside phosphorylase
C: purine nucleoside phosphorylase
D: purine nucleoside phosphorylase
E: purine nucleoside phosphorylase
F: purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,84612
Polymers165,2436
Non-polymers1,6036
Water29,1301617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24980 Å2
ΔGint-111 kcal/mol
Surface area43440 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)46.601, 152.720, 96.717
Angle α, β, γ (deg.)90.00, 103.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
purine nucleoside phosphorylase


Mass: 27540.436 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: Q9KPM0, purine-nucleoside phosphorylase
#2: Chemical
ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1617 / 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: 2.02 Å3/Da / Density % sol: 39.16 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMHEPES1droppH7.5
2150 mM1dropNaCl
310 mMmethionine1drop
410 %glycerol1drop
55 mMdithiothreitol1drop
610 mg/mlprotein1drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.9795 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.54→33.52 Å / Num. all: 181396 / Num. obs: 181396 / % possible obs: 94.1 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 12.9
Reflection shellResolution: 1.54→1.62 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.145 / Mean I/σ(I) obs: 6.4 / % possible all: 86
Reflection shell
*PLUS
% possible obs: 86 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata reduction
REFMAC4refinement
CCP4(SCALAdata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→33.52 Å / σ(F): 0
RfactorNum. reflection
Rfree0.193 9090
Rwork0.162 -
obs-181394
Solvent computationSolvent model: Babinet bulk solvent correction / Bsol: 367.02 Å2 / ksol: 0.999 e/Å3
Displacement parametersBiso mean: 16.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.697 Å20 Å2-0.103 Å2
2---0.676 Å20 Å2
3----0.07 Å2
Refine Biso Class: all / Treatment: isotropic
Refinement stepCycle: LAST / Resolution: 1.54→33.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10579 0 114 1617 12310
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_d2.056
X-RAY DIFFRACTIONp_planar_tor2.698
X-RAY DIFFRACTIONp_chiral_restr0.124
X-RAY DIFFRACTIONp_plane_restr0.01
X-RAY DIFFRACTIONp_mcbond_it1.104
X-RAY DIFFRACTIONp_mcangle_it1.919
X-RAY DIFFRACTIONp_scbond_it2.027
X-RAY DIFFRACTIONp_scangle_it3.158
Software
*PLUS
Version: 4 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.1

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