[English] 日本語
Yorodumi
- PDB-1geh: CRYSTAL STRUCTURE OF ARCHAEAL RUBISCO (RIBULOSE 1,5-BISPHOSPHATE ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1geh
TitleCRYSTAL STRUCTURE OF ARCHAEAL RUBISCO (RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE)
ComponentsRIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
KeywordsLYASE / Pentagonal toroid decamer / RUBISCO
Function / homology
Function and homology information


AMP catabolic process / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / carbon fixation / oxidoreductase activity / magnesium ion binding
Similarity search - Function
Ribulose bisphosphate carboxylase, type III / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase large chain, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal / RuBisCO / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily / RuBisCO large subunit, N-terminal domain superfamily / Ribulose bisphosphate carboxylase large chain, catalytic domain ...Ribulose bisphosphate carboxylase, type III / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase large chain, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal / RuBisCO / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily / RuBisCO large subunit, N-terminal domain superfamily / Ribulose bisphosphate carboxylase large chain, catalytic domain / Alpha-Beta Plaits / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribulose bisphosphate carboxylase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.8 Å
AuthorsKitano, K. / Maeda, N. / Fukui, T. / Atomi, H. / Imanaka, T. / Miki, K.
Citation
Journal: Structure / Year: 2001
Title: Crystal Structure of a Novel-Type Archaeal Rubisco with Pentagonal Symmetry
Authors: Kitano, K. / Maeda, N. / Fukui, T. / Atomi, H. / Imanaka, T. / Miki, K.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: Ribulose Bisphosphate Carboxylase/oxygenase from Hyperthermophilic Archaeon Pyrococcus kodakaraensis KOD1 is Composed Solely of Large Subunits and Forms a Pentagonal Structure
Authors: Maeda, N. / Kitano, K. / Fukui, T. / Ezaki, S. / Atomi, H. / Miki, K. / Imanaka, T.
History
DepositionNov 13, 2000Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
A: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
B: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
C: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
D: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
E: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,84315
Polymers248,8825
Non-polymers96110
Water00
1
A: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
B: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
C: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
D: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
E: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
hetero molecules

A: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
B: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
C: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
D: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
E: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)499,68630
Polymers497,76510
Non-polymers1,92120
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)233.75, 233.75, 93.26
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is a decamer generated from the pentamer in the asymmetric unit by the operations: y, x, -z.

-
Components

#1: Protein
RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE


Mass: 49776.480 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: KOD1 / Production host: Escherichia coli (E. coli)
References: UniProt: O93627, ribulose-bisphosphate carboxylase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

-
Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 9
Details: Ammoinum sulfate, pH 9.0, VAPOR DIFFUSION, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / Details: Maeda, N., (1999) J.Mol.Biol., 293, 57.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
21.8 Mammonium sulfate1drop
310 mM1dropMgCl2
4100 mMCHES-NaOH1droppH9.0

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-6A11
SYNCHROTRONPhoton Factory BL-6B21
Detector
TypeIDDetector
FUJI1IMAGE PLATE
FUJI2IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→100 Å / Num. obs: 64453 / % possible obs: 89.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 12.1 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 11.8
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.335 / % possible all: 65.5
Reflection
*PLUS
Lowest resolution: 100 Å / Num. measured all: 784332
Reflection shell
*PLUS
% possible obs: 65.5 % / Mean I/σ(I) obs: 3.4

-
Processing

Software
NameVersionClassification
MLPHAREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.8→100 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 11437229 / Data cutoff low absF: 0 / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 6530 10.1 %RANDOM
Rwork0.224 ---
all-64453 --
obs-64453 --
Solvent computationSolvent model: FLAT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16890 0 50 0 16940
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it10.051.5
X-RAY DIFFRACTIONc_mcangle_it15.582
X-RAY DIFFRACTIONc_scbond_it13.932
X-RAY DIFFRACTIONc_scangle_it19.712.5
LS refinement shellHighest resolution: 2.8 Å / Total num. of bins used: 6 /
Num. reflection% reflection
Rwork7222 -
Rfree-10.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 100 Å / σ(F): 1 / % reflection Rfree: 10.1 % / Rfactor obs: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.404
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87
X-RAY DIFFRACTIONc_mcbond_it10.051.5
X-RAY DIFFRACTIONc_scbond_it13.932
X-RAY DIFFRACTIONc_mcangle_it15.582
X-RAY DIFFRACTIONc_scangle_it19.712.5
LS refinement shell
*PLUS
% reflection Rfree: 10.1 %

+
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