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- PDB-3pnp: THE HIGH RESOLUTION CRYSTAL STRUCTURE OF BOVINE SPLEEN PURINE NUC... -

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Basic information

Entry
Database: PDB / ID: 3pnp
TitleTHE HIGH RESOLUTION CRYSTAL STRUCTURE OF BOVINE SPLEEN PURINE NUCLEOSIDE PHOSPHORYLASE IN COMPLEX FORMS WITH PHOSPHATE AND 9-DEAZAINOSINE
ComponentsPURINE NUCLEOSIDE PHOSPHORYLASE
KeywordsPHOSPHORYLASE / SALVAGE PATHWAY / TRANSFERASE
Function / homology
Function and homology information


guanosine phosphorylase activity / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / purine ribonucleoside salvage / cytoplasm
Similarity search - Function
Purine nucleoside phosphorylase I, inosine/guanosine-specific / Purine phosphorylase, family 2, conserved site / Purine and other phosphorylases family 2 signature. / Purine nucleoside phosphorylase / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsPugmire, M.J. / Mao, C. / Ealick, S.E.
CitationJournal: To be Published
Title: The High Resolution Crystal Structure of Bovine Spleen Purine Nucleoside Phosphorylase in Complex Forms with Phosphate and 9-Deazainosine
Authors: Pugmire, M.J. / Mao, C. / Ealick, S.E.
History
DepositionMar 27, 1998Processing site: BNL
Revision 1.0Mar 30, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / 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 / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: PURINE NUCLEOSIDE PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1283
Polymers32,0081
Non-polymers1192
Water1,78399
1
A: PURINE NUCLEOSIDE PHOSPHORYLASE
hetero molecules

A: PURINE NUCLEOSIDE PHOSPHORYLASE
hetero molecules

A: PURINE NUCLEOSIDE PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3839
Polymers96,0253
Non-polymers3586
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_656-z+1,x+1/2,-y+3/21
crystal symmetry operation11_466y-1/2,-z+3/2,-x+11
Buried area7050 Å2
ΔGint-76 kcal/mol
Surface area27490 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)93.000, 93.000, 93.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-384-

HOH

21A-390-

HOH

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Components

#1: Protein PURINE NUCLEOSIDE PHOSPHORYLASE / / PNP


Mass: 32008.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: SPLEEN
References: UniProt: P55859, purine-nucleoside phosphorylase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.24 %
Crystal growpH: 8 / Details: pH 8.0

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Data collection

DiffractionMean temperature: 133 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1
DetectorDetector: CCD / Date: Feb 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.55 Å / Num. obs: 37524 / % possible obs: 96 % / Rsym value: 0.056

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→8 Å / Data cutoff high absF: 10000000 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1526 5 %RANDOM
Rwork0.208 ---
obs0.208 30671 96 %-
Displacement parametersBiso mean: 20.7 Å2
Refinement stepCycle: LAST / Resolution: 1.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 6 99 2159
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.399
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.19
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.192
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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