[English] 日本語
Yorodumi
- PDB-1vdm: Crystal structure of purine phosphoribosyltransferase from Pyroco... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vdm
TitleCrystal structure of purine phosphoribosyltransferase from Pyrococcus horikoshii Ot3
Componentspurine phosphoribosyltransferase
KeywordsTRANSFERASE / purine phosphoribosyltransferase / Pyrococcus horikoshii / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


nucleoside metabolic process / glycosyltransferase activity
Similarity search - Function
Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
153aa long hypothetical purine phosphoribosyltransferase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å
AuthorsSugahara, M. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of purine phosphoribosyltransferase from Pyrococcus horikoshii Ot3
Authors: Sugahara, M. / Kunishima, N.
History
DepositionMar 23, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 24, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: purine phosphoribosyltransferase
B: purine phosphoribosyltransferase
C: purine phosphoribosyltransferase
D: purine phosphoribosyltransferase
E: purine phosphoribosyltransferase
F: purine phosphoribosyltransferase
G: purine phosphoribosyltransferase
H: purine phosphoribosyltransferase
I: purine phosphoribosyltransferase
J: purine phosphoribosyltransferase
K: purine phosphoribosyltransferase
L: purine phosphoribosyltransferase


Theoretical massNumber of molelcules
Total (without water)211,22112
Polymers211,22112
Non-polymers00
Water13,493749
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.603, 157.350, 170.631
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dodecamer in the asymmetric unit.

-
Components

#1: Protein
purine phosphoribosyltransferase


Mass: 17601.727 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET11a / Production host: Escherichia coli (E. coli)
References: UniProt: O57827, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 749 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 3.36 Å3/Da / Density % sol: 63.35 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 4.4 / Details: NaCl, pH 4.4, microbatch, temperature 291K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONSPring-8 BL26B111
SYNCHROTRONSPring-8 BL26B121.0081
ROTATING ANODERIGAKU31.54178
Detector
TypeIDDetectorDate
RIGAKU RAXIS V1IMAGE PLATESep 25, 2003
RIGAKU JUPITER2CCDSep 26, 2003
RIGAKU RAXIS V3IMAGE PLATESep 28, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.00811
31.541781
ReflectionResolution: 2.5→40 Å / Num. all: 99412 / Num. obs: 99412 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 50.611 Å2 / Rmerge(I) obs: 0.129 / Rsym value: 0.123 / Net I/σ(I): 8
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.785 / Mean I/σ(I) obs: 3.23 / Num. unique all: 9841 / Rsym value: 0.731 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MIR / Resolution: 2.5→39.55 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 4939 -random
Rwork0.209 ---
all0.211 98798 --
obs0.211 98798 100 %-
Displacement parametersBiso mean: 46.4 Å2
Baniso -1Baniso -2Baniso -3
1-8.61 Å20 Å20 Å2
2---6.62 Å20 Å2
3----2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.5→39.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14432 0 0 749 15181
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.008
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.014
RfactorNum. reflection% reflection
Rfree0.313 493 -
Rwork0.298 --
obs-9270 100 %

+
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://pdbjlvh1.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