[English] 日本語
Yorodumi
- PDB-1u9y: Crystal Structure of Phosphoribosyl Diphosphate Synthase from Met... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1u9y
TitleCrystal Structure of Phosphoribosyl Diphosphate Synthase from Methanocaldococcus jannaschii
ComponentsRibose-phosphate pyrophosphokinase
KeywordsTRANSFERASE / PRPP synthase
Function / homology
Function and homology information


ribose phosphate diphosphokinase complex / ribose-phosphate diphosphokinase / ribose phosphate diphosphokinase activity / ribonucleoside monophosphate biosynthetic process / 5-phosphoribose 1-diphosphate biosynthetic process / purine nucleotide biosynthetic process / kinase activity / phosphorylation / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Ribose-phosphate pyrophosphokinase, archaea / N-terminal domain of ribose phosphate pyrophosphokinase / Ribose-phosphate pyrophosphokinase / Ribose-phosphate pyrophosphokinase, N-terminal domain / N-terminal domain of ribose phosphate pyrophosphokinase / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold ...Ribose-phosphate pyrophosphokinase, archaea / N-terminal domain of ribose phosphate pyrophosphokinase / Ribose-phosphate pyrophosphokinase / Ribose-phosphate pyrophosphokinase, N-terminal domain / N-terminal domain of ribose phosphate pyrophosphokinase / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribose-phosphate pyrophosphokinase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsKadziola, A. / Johansson, E. / Jepsen, C.H. / McGuire, J. / Larsen, S. / Hove-Jensen, B.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Novel class III phosphoribosyl diphosphate synthase: structure and properties of the tetrameric, phosphate-activated, non-allosterically inhibited enzyme from Methanocaldococcus jannaschii
Authors: Kadziola, A. / Jepsen, C.H. / Johansson, E. / McGuire, J. / Larsen, S. / Hove-Jensen, B.
History
DepositionAug 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_database_related
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_related.db_name
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ribose-phosphate pyrophosphokinase
B: Ribose-phosphate pyrophosphokinase
C: Ribose-phosphate pyrophosphokinase
D: Ribose-phosphate pyrophosphokinase


Theoretical massNumber of molelcules
Total (without water)125,7334
Polymers125,7334
Non-polymers00
Water10,557586
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11520 Å2
ΔGint-23 kcal/mol
Surface area40860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.011, 138.280, 138.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

-
Components

#1: Protein
Ribose-phosphate pyrophosphokinase / E.C.2.7.6.1 / Phosphoribosyl Diphosphate Synthase / RPPK / Phosphoribosyl pyrophosphate synthetase / P-Rib-PP ...Phosphoribosyl Diphosphate Synthase / RPPK / Phosphoribosyl pyrophosphate synthetase / P-Rib-PP synthetase / PRPP synthetase


Mass: 31433.258 Da / Num. of mol.: 4 / Fragment: Phosphoribosyl Diphosphate Synthase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: prs / Production host: Escherichia coli (E. coli)
References: UniProt: Q58761, ribose-phosphate diphosphokinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 586 / 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: 2.66 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9794 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 7, 2002
RadiationMonochromator: Silicon (111) crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.65→20 Å / Num. all: 40242 / Num. obs: 40242 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.081 / Net I/σ(I): 20.7
Reflection shellResolution: 2.65→2.7 Å / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 4.1 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
CNS0.9refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Bacillus subtilis PRPP synthase

Resolution: 2.65→20 Å
Isotropic thermal model: Neigbour restrained B-factor optimization
Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2017 5 %random
Rwork0.22 ---
all0.221 40242 --
obs0.221 40242 99.8 %-
Displacement parametersBiso mean: 33.9 Å2
Refinement stepCycle: LAST / Resolution: 2.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8524 0 0 586 9110
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008381
X-RAY DIFFRACTIONc_angle_deg1.33562

+
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