[English] 日本語
Yorodumi
- PDB-4twb: Sulfolobus solfataricus ribose-phosphate pyrophosphokinase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4twb
TitleSulfolobus solfataricus ribose-phosphate pyrophosphokinase
ComponentsRibose-phosphate pyrophosphokinase
KeywordsTRANSFERASE
Function / homology
Function and homology information


ribose phosphate diphosphokinase complex / ribose-phosphate diphosphokinase / ribose phosphate diphosphokinase activity / 5-phosphoribose 1-diphosphate biosynthetic process / purine nucleotide biosynthetic process / kinase activity / 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
ADENOSINE MONOPHOSPHATE / Ribose-phosphate pyrophosphokinase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.802 Å
AuthorsKadziola, A.
CitationJournal: Extremophiles / Year: 2015
Title: Structure of dimeric, recombinant Sulfolobus solfataricus phosphoribosyl diphosphate synthase: a bent dimer defining the adenine specificity of the substrate ATP.
Authors: Andersen, R.W. / Leggio, L.L. / Hove-Jensen, B. / Kadziola, A.
History
DepositionJun 30, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Mar 4, 2015Group: Database references
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Feb 14, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.pdbx_collection_date
Revision 1.5Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
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
E: Ribose-phosphate pyrophosphokinase
F: Ribose-phosphate pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,99918
Polymers193,3396
Non-polymers2,66012
Water43224
1
A: Ribose-phosphate pyrophosphokinase
B: Ribose-phosphate pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3336
Polymers64,4462
Non-polymers8874
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-49 kcal/mol
Surface area22740 Å2
MethodPISA
2
C: Ribose-phosphate pyrophosphokinase
D: Ribose-phosphate pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3336
Polymers64,4462
Non-polymers8874
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-29 kcal/mol
Surface area22710 Å2
MethodPISA
3
E: Ribose-phosphate pyrophosphokinase
F: Ribose-phosphate pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3336
Polymers64,4462
Non-polymers8874
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-28 kcal/mol
Surface area22740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.217, 92.846, 138.338
Angle α, β, γ (deg.)90.00, 90.91, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 1:190 or resseq 204:291 or resseq 301:302 or resseq 402:405 )
211chain B and (resseq 1:190 or resseq 204:291 or resseq 301:302 or resseq 402:405 )
112chain A and (resseq 1:190 or resseq 204:291 or resseq 301:302 or resseq 402:405 )
212chain C and (resseq 1:190 or resseq 204:291 or resseq 301:302 or resseq 402:405 )
113chain A and (resseq 1:190 or resseq 204:291 or resseq 301:302 or resseq 402:405 )
213chain D and (resseq 1:190 or resseq 204:291 or resseq 301:302 or resseq 402:405 )
114chain A and (resseq 1:190 or resseq 204:291 or resseq 301:302 or resseq 402:405 )
214chain E and (resseq 1:190 or resseq 204:291 or resseq 301:302 or resseq 402:405 )
115chain A and (resseq 1:190 or resseq 204:291 or resseq 301:302 or resseq 402:405 )
215chain F and (resseq 1:190 or resseq 204:291 or resseq 301:302 or resseq 402:405 )

NCS ensembles :
ID
1
2
3
4
5

-
Components

#1: Protein
Ribose-phosphate pyrophosphokinase / RPPK / Phosphoribosyl pyrophosphate synthase / PRPP synthase


Mass: 32223.221 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Production host: Escherichia coli (E. coli)
References: UniProt: Q97Z86, ribose-phosphate diphosphokinase
#2: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.83 % / Description: 350*100*100 um3
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5
Details: Protein: 12.7 mg/mL 50 mM Tris/HCl pH 7.6 10 mM AMP 10 mM ribose 5-phosphate Buffer: 0.2 M diammonium citrate pH 5.0 Precipitant: 14 % PEG10000

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.03908 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03908 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 48432 / Num. obs: 48432 / % possible obs: 97.9 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 14
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.4 / % possible all: 98.1

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX(phenix.refine)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U9Y

1u9y


Resolution: 2.802→19.984 Å / SU ML: 1.1 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2647 2406 4.97 %5 % random selection
Rwork0.2346 ---
obs0.2361 48382 97.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.012 Å2 / ksol: 0.308 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.7424 Å20 Å2-16.2902 Å2
2---0.312 Å20 Å2
3----6.4304 Å2
Refinement stepCycle: LAST / Resolution: 2.802→19.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13002 0 168 24 13194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913350
X-RAY DIFFRACTIONf_angle_d1.30618102
X-RAY DIFFRACTIONf_dihedral_angle_d18.7555022
X-RAY DIFFRACTIONf_chiral_restr0.0822208
X-RAY DIFFRACTIONf_plane_restr0.0042256
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2199X-RAY DIFFRACTIONPOSITIONAL
12B2199X-RAY DIFFRACTIONPOSITIONAL0.05
21A2199X-RAY DIFFRACTIONPOSITIONAL
22C2199X-RAY DIFFRACTIONPOSITIONAL0.061
31A2199X-RAY DIFFRACTIONPOSITIONAL
32D2199X-RAY DIFFRACTIONPOSITIONAL0.067
41A2199X-RAY DIFFRACTIONPOSITIONAL
42E2199X-RAY DIFFRACTIONPOSITIONAL0.058
51A2199X-RAY DIFFRACTIONPOSITIONAL
52F2199X-RAY DIFFRACTIONPOSITIONAL0.056
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8015-2.85860.38561100.31122587X-RAY DIFFRACTION47
2.8586-2.92050.37231570.28472718X-RAY DIFFRACTION50
2.9205-2.98830.28981380.28242746X-RAY DIFFRACTION50
2.9883-3.06270.36341480.28072689X-RAY DIFFRACTION50
3.0627-3.14520.34461560.26972719X-RAY DIFFRACTION50
3.1452-3.23740.26391600.26122704X-RAY DIFFRACTION50
3.2374-3.34140.35011490.26042739X-RAY DIFFRACTION50
3.3414-3.46030.29731390.26382722X-RAY DIFFRACTION50
3.4603-3.59810.38181170.31042545X-RAY DIFFRACTION46
3.5981-3.76080.39191220.33532599X-RAY DIFFRACTION47
3.7608-3.95760.26741340.23952701X-RAY DIFFRACTION49
3.9576-4.20340.2491470.19762671X-RAY DIFFRACTION49
4.2034-4.52450.19431400.17522758X-RAY DIFFRACTION50
4.5245-4.97340.18871380.16422744X-RAY DIFFRACTION50
4.9734-5.67860.16751510.16812766X-RAY DIFFRACTION51
5.6786-7.10070.20611490.19362784X-RAY DIFFRACTION51
7.1007-19.98490.18721510.17332784X-RAY DIFFRACTION51

+
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