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- PDB-1brw: THE CRYSTAL STRUCTURE OF PYRIMIDINE NUCLEOSIDE PHOSPHORYLASE IN A... -

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Basic information

Entry
Database: PDB / ID: 1brw
TitleTHE CRYSTAL STRUCTURE OF PYRIMIDINE NUCLEOSIDE PHOSPHORYLASE IN A CLOSED CONFORMATION
ComponentsPROTEIN (PYRIMIDINE NUCLEOSIDE PHOSPHORYLASE)
KeywordsTRANSFERASE / NUCLEOSIDE PHOSPHORYLASE / DOMAIN MOVEMENT
Function / homology
Function and homology information


pyrimidine-nucleoside phosphorylase / pyrimidine nucleoside metabolic process / thymidine phosphorylase activity / pyrimidine nucleobase metabolic process / 1,4-alpha-oligoglucan phosphorylase activity / deoxyuridine phosphorylase activity / uridine phosphorylase activity / metal ion binding / cytosol
Similarity search - Function
Pyrimidine-nucleoside phosphorylase, bacterial/eukaryotic / Pyrimidine nucleoside phosphorylase-like, C-terminal domain / Thymidine/pyrimidine-nucleoside phosphorylase / Pyrimidine nucleoside phosphorylase, C-terminal / Pyrimidine-nucleoside phosphorylase, conserved site / Pyrimidine nucleoside phosphorylase-like, C-terminal domain superfamily / Pyrimidine nucleoside phosphorylase C-terminal domain / Thymidine and pyrimidine-nucleoside phosphorylases signature. / Pyrimidine nucleoside phosphorylase C-terminal domain / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C ...Pyrimidine-nucleoside phosphorylase, bacterial/eukaryotic / Pyrimidine nucleoside phosphorylase-like, C-terminal domain / Thymidine/pyrimidine-nucleoside phosphorylase / Pyrimidine nucleoside phosphorylase, C-terminal / Pyrimidine-nucleoside phosphorylase, conserved site / Pyrimidine nucleoside phosphorylase-like, C-terminal domain superfamily / Pyrimidine nucleoside phosphorylase C-terminal domain / Thymidine and pyrimidine-nucleoside phosphorylases signature. / Pyrimidine nucleoside phosphorylase C-terminal domain / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 / Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2 / Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain / Glycosyl transferase family 3, N-terminal domain / Glycosyl transferase family 3, N-terminal domain superfamily / Glycosyl transferase family, helical bundle domain / Glycosyl transferase, family 3 / Glycosyl transferase family, a/b domain / Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain superfamily / Aldehyde Oxidoreductase; domain 3 / Alpha-Beta Complex / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / URACIL / Pyrimidine-nucleoside phosphorylase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPugmire, M.J. / Ealick, S.E.
CitationJournal: Structure / Year: 1998
Title: The crystal structure of pyrimidine nucleoside phosphorylase in a closed conformation.
Authors: Pugmire, M.J. / Ealick, S.E.
History
DepositionAug 25, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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_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: PROTEIN (PYRIMIDINE NUCLEOSIDE PHOSPHORYLASE)
B: PROTEIN (PYRIMIDINE NUCLEOSIDE PHOSPHORYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8999
Polymers92,1262
Non-polymers7737
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.570, 70.450, 122.780
Angle α, β, γ (deg.)90.00, 98.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein PROTEIN (PYRIMIDINE NUCLEOSIDE PHOSPHORYLASE) / EC 2.4.2.2 TRANSFERASE / PYNP


Mass: 46063.184 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Geobacillus stearothermophilus (bacteria)
References: UniProt: P77836, pyrimidine-nucleoside phosphorylase

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Non-polymers , 5 types, 117 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-URA / URACIL


Mass: 112.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4N2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.57 Å3/Da / Density % sol: 52 %
Crystal growpH: 6
Details: 0.1 M MES PH 6.0-6.2 25% PEG 6000 PSEUDOURIDINE AT 10X PROTEIN CONCENTRATION
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop / Details: Zhou, M., (1998) Acta Cryst., D55, 287.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mMpotassium phosphate1drop
210 mg/mlprotein1drop
315 %ammonium sulfate1reservoir
450 mMcitrate1reservoir
54 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.91
DetectorType: ADSC / Detector: CCD / Date: Feb 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 55716 / % possible obs: 88.4 % / Redundancy: 2.9 % / Rsym value: 0.067
Reflection
*PLUS
Num. measured all: 396276 / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.07 Å / % possible obs: 41.7 % / Redundancy: 1.6 % / Rmerge(I) obs: 0.232

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2TPT

2tpt


Resolution: 2.1→30 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.276 2431 5 %RANDOM
Rwork0.232 ---
obs0.232 54378 82.9 %-
Displacement parametersBiso mean: 26.9 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6438 0 44 110 6592
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_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.2
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
LS refinement shellResolution: 2.1→2.2 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3677 209 8.6 %
Rwork0.3171 4220 -
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 30 Å / σ(F): 2 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 26.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.2
LS refinement shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.2 Å / % reflection Rfree: 8.6 %

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