[English] 日本語
Yorodumi
- PDB-1rct: Crystal structure of Human purine nucleoside phosphorylase comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1rct
TitleCrystal structure of Human purine nucleoside phosphorylase complexed with INOSINE
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE / purine nucleoside phosphorylase / drug design / Synchrotron
Function / homology
Function and homology information


nicotinamide riboside catabolic process / Defective PNP disrupts phosphorolysis of (deoxy)guanosine and (deoxy)inosine / purine-containing compound salvage / deoxyinosine catabolic process / purine nucleobase binding / nucleotide biosynthetic process / deoxyadenosine catabolic process / dAMP catabolic process / inosine catabolic process / urate biosynthetic process ...nicotinamide riboside catabolic process / Defective PNP disrupts phosphorolysis of (deoxy)guanosine and (deoxy)inosine / purine-containing compound salvage / deoxyinosine catabolic process / purine nucleobase binding / nucleotide biosynthetic process / deoxyadenosine catabolic process / dAMP catabolic process / inosine catabolic process / urate biosynthetic process / IMP catabolic process / Ribavirin ADME / guanosine phosphorylase activity / nucleoside binding / Purine salvage / Purine catabolism / allantoin metabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / positive regulation of alpha-beta T cell differentiation / nucleobase-containing compound metabolic process / purine ribonucleoside salvage / phosphate ion binding / positive regulation of T cell proliferation / positive regulation of interleukin-2 production / secretory granule lumen / ficolin-1-rich granule lumen / immune response / response to xenobiotic stimulus / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / cytosol / 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
INOSINE / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsCanduri, F. / dos Santos, D.M. / Silva, R.G. / Mendes, M.A. / Palma, M.S. / de Azevedo Jr., W.F. / Basso, L.A. / Santos, D.S.
Citation
Journal: Biochem.Biophys.Res.Commun. / Year: 2004
Title: Structures of human purine nucleoside phosphorylase complexed with inosine and ddI
Authors: Canduri, F. / dos Santos, D.M. / Silva, R.G. / Mendes, M.A. / Basso, L.A. / Palma, M.S. / de Azevedo Jr., W.F. / Santos, D.S.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991
Title: Application of crystallographic and modeling methods in the design of purine nucleoside phosphorylase inhibitors
Authors: Ealick, S.E. / Babu, Y.S. / Bugg, C.E. / Erion, M.D. / Guida, W.C. / Montgomery, J.A. / Secrist III, J.A.
History
DepositionNov 4, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6105
Polymers32,0541
Non-polymers5564
Water81145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Purine nucleoside phosphorylase
hetero molecules

E: Purine nucleoside phosphorylase
hetero molecules

E: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,83015
Polymers96,1613
Non-polymers1,66912
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area10790 Å2
ΔGint-179 kcal/mol
Surface area30070 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)140.990, 140.990, 161.130
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

-
Components

#1: Protein Purine nucleoside phosphorylase / Inosine phosphorylase / PNP


Mass: 32053.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET-23A+ / Production host: Escherichia coli (E. coli)
References: UniProt: P00491, purine-nucleoside phosphorylase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NOS / INOSINE


Mass: 268.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N4O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.825 Å3/Da / Density % sol: 71 %
Crystal growpH: 5.3 / Details: pH 5.30
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 7.1 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 mg/mlprotein1drop
210 mMpotassium phosphate1droppH7.1
319 %(v/v)satammonium sulfate1reservoir
40.05 Mcitrate1reservoirpH5.3

-
Data collection

DiffractionMean temperature: 104 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.431 / Wavelength: 1.431 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 19, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.4311
21.4311
ReflectionResolution: 2.8→56.79 Å / Num. all: 109144 / Num. obs: 15363 / % possible obs: 93.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Rmerge(I) obs: 0.072
Reflection shellResolution: 2.8→2.95 Å / Rmerge(I) obs: 0.216 / % possible all: 95.7
Reflection
*PLUS
Redundancy: 5.5 %
Reflection shell
*PLUS
% possible obs: 95.7 % / Rmerge(I) obs: 0.268

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PWY

1pwy


Resolution: 2.8→8 Å / Data cutoff high absF: 2 / Data cutoff low absF: 2 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.29 1443 10 %RANDOM
Rwork0.208 ---
all0.213 15363 --
obs0.208 15363 99.99 %-
Displacement parametersBiso mean: 43.07 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å / Luzzati d res low obs: 8 Å
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2251 0 34 45 2330
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_angle_deg2
X-RAY DIFFRACTIONx_dihedral_angle_d25.25
X-RAY DIFFRACTIONx_improper_angle_d1.7
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 8 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.29
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.25
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.7

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more