[English] 日本語
Yorodumi
- PDB-1rks: E. COLI RIBOKINASE IN COMPLEX WITH D-RIBOSE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1rks
TitleE. COLI RIBOKINASE IN COMPLEX WITH D-RIBOSE
ComponentsPROTEIN (RIBOKINASE)
KeywordsTRANSFERASE / CARBOHYDRATE KINASE / RIBOSE / INDUCED FIT
Function / homology
Function and homology information


ribokinase / ribokinase activity / D-ribose catabolic process / protein homodimerization activity / ATP binding / metal ion binding / cytosol
Similarity search - Function
Ribokinase / Ribokinase/fructokinase / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / alpha-D-ribofuranose / Ribokinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.4 Å
AuthorsSigrell, J.A. / Cameron, A.D. / Mowbray, S.L.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Induced fit on sugar binding activates ribokinase.
Authors: Sigrell, J.A. / Cameron, A.D. / Mowbray, S.L.
#1: Journal: Structure / Year: 1998
Title: Structure of Escherichia Coli Ribokinase in Complex with Ribose and Nucleotide Determined to 1.8 A Resolution: Insights Into a New Family of Kinase Structures
Authors: Sigrell, J.A. / Cameron, A.D. / Jones, T.A. / Mowbray, S.L.
#2: Journal: Protein Sci. / Year: 1997
Title: Purification, Characterization, and Crystallization of Escherichia Coli Ribokinase
Authors: Sigrell, J.A. / Cameron, A.D. / Jones, T.A. / Mowbray, S.L.
#3: Journal: J.Biol.Chem. / Year: 1986
Title: Ribokinase from Escherichia Coli K12. Nucleotide Sequence and Overexpression of the Rbsk Gene and Purification of Ribokinase
Authors: Hope, J.N. / Bell, A.W. / Hermodson, M.A. / Groarke, J.M.
History
DepositionMay 17, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 31, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_special_symmetry / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (RIBOKINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6604
Polymers32,3201
Non-polymers3403
Water1,60389
1
A: PROTEIN (RIBOKINASE)
hetero molecules

A: PROTEIN (RIBOKINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3218
Polymers64,6412
Non-polymers6806
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z+2/31
Buried area3660 Å2
ΔGint-33 kcal/mol
Surface area23600 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)95.210, 95.210, 154.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Cell settinghexagonal
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-313-

PO4

-
Components

#1: Protein PROTEIN (RIBOKINASE) / E.C.2.7.1.15


Mass: 32320.393 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Description: THE RBSK GENE WAS CLONED BEHIND AURCE 11 TRP-PROMOTER, FORMING THE PLASMID PJGK10
Cellular location: CYTOPLASM / Gene: RBSK / Plasmid: PJGK10 / Production host: Escherichia coli (E. coli) / Strain (production host): MRI240 / References: UniProt: P0A9J6, ribokinase
#2: Sugar ChemComp-RIB / alpha-D-ribofuranose / alpha-D-ribose / D-ribose / ribose / Ribose


Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DRibfaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-ribofuranoseCOMMON NAMEGMML 1.0
a-D-RibfIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RibSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE SUGAR IS IN THE ALPHA-FURANOSE FORM AND HAS THE UNCOMMON O4'-ENDO PUCKERING.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 48.7 % / Description: RIGIDBODY REFINEMENT FROM 1RKD
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.4
Details: 5 MM RIBOSE, 10 MM MGCL2 IN THE DROP, 0.1 M TRIS-HCL BUFFER, PH 8.4 WITH 2.1-2.4 M NH4H2PO4 AS PRECIPITANT, VAPOR DIFFUSION, HANGING DROP CRYO-SOLUTION: MOTHER LIQUOR CONTAINING 20% GLYCEROL. ...Details: 5 MM RIBOSE, 10 MM MGCL2 IN THE DROP, 0.1 M TRIS-HCL BUFFER, PH 8.4 WITH 2.1-2.4 M NH4H2PO4 AS PRECIPITANT, VAPOR DIFFUSION, HANGING DROP CRYO-SOLUTION: MOTHER LIQUOR CONTAINING 20% GLYCEROL. SOAK-TIME: 2-3 MINUTES.
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mMribose1reservoir
210 mMADP1reservoir
30.05 mM1reservoirAlF3
415 mM1reservoirNaF
50.1 Msodium acetate1reservoir
60.25 M1reservoirMgCl2
720 %(v/v)MPD1reservoir
88.8-15 %(w/v)PEG40001reservoir
93-3.5 mg/mlribokinase1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Nov 15, 1997 / Details: MSC MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→29 Å / Num. obs: 16814 / % possible obs: 99.9 % / Redundancy: 10.5 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 30.2
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 5.8 / % possible all: 99.8
Reflection
*PLUS
Num. measured all: 134333
Reflection shell
*PLUS
% possible obs: 99.8 %

-
Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.4→15 Å / SU B: 7.72 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.37 / ESU R Free: 0.28 / Details: BULK SOLVENT CORRECTION APPLIED
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1668 11.1 %RANDOM
Rwork0.229 ---
obs0.231 16740 99.9 %-
Displacement parametersBiso mean: 45.3 Å2
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2236 0 20 89 2345
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.0320.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0360.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.7531
X-RAY DIFFRACTIONp_mcangle_it1.3422
X-RAY DIFFRACTIONp_scbond_it2.8763
X-RAY DIFFRACTIONp_scangle_it3.9825
X-RAY DIFFRACTIONp_plane_restr0.0210.03
X-RAY DIFFRACTIONp_chiral_restr0.1130.15
X-RAY DIFFRACTIONp_singtor_nbd0.1880.3
X-RAY DIFFRACTIONp_multtor_nbd0.260.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1670.3
X-RAY DIFFRACTIONp_planar_tor3.97
X-RAY DIFFRACTIONp_staggered_tor1415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor31.220
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / σ(F): 0 / % reflection Rfree: 11.1 % / Rfactor all: 0.231 / Rfactor obs: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 45.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.04
X-RAY DIFFRACTIONp_planar_d0.05
X-RAY DIFFRACTIONp_plane_restr0.03
X-RAY DIFFRACTIONp_chiral_restr0.15
X-RAY DIFFRACTIONp_mcbond_it1
X-RAY DIFFRACTIONp_scbond_it3
X-RAY DIFFRACTIONp_mcangle_it2
X-RAY DIFFRACTIONp_scangle_it5

+
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