[English] 日本語
Yorodumi
- PDB-1iwa: RUBISCO FROM GALDIERIA PARTITA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1iwa
TitleRUBISCO FROM GALDIERIA PARTITA
Components
  • ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
  • ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit
KeywordsLYASE / RUBISCO / PHOTOSYNTHESIS
Function / homology
Function and homology information


ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / chloroplast / monooxygenase activity / magnesium ion binding
Similarity search - Function
Ribulose bisphosphate carboxylase, small subunit / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase large subunit, type I ...Ribulose bisphosphate carboxylase, small subunit / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. / 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 large chain / Multifunctional fusion protein
Similarity search - Component
Biological speciesGaldieria partita (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsOkano, Y. / Mizohata, E. / Xie, Y. / Matsumura, H. / Sugawara, H. / Inoue, T. / Yokota, A. / Kai, Y.
Citation
Journal: FEBS LETT. / Year: 2002
Title: X-Ray Structure of Galdieria Rubisco Complexed with one sulfate ion per active site
Authors: Okano, Y. / Mizohata, E. / Xie, Y. / Matsumura, H. / Sugawara, H. / Inoue, T. / Yokota, A. / Kai, Y.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: The Transition between the Open and Closed States of Rubisco is triggered by the Inter-Phosphate Distance of the Bound Bisphosphate
Authors: Duff, A.P. / Andrews, T.J. / Curmi, P.M.
History
DepositionApr 30, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 30, 2003Provider: 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 / 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 large subunit
B: ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit
C: ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
D: ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit
E: ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
F: ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit
G: ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
H: ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit
I: ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
J: ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit
K: ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
L: ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit
M: ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
N: ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit
O: ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
P: ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)570,93024
Polymers570,16216
Non-polymers7698
Water56,0633112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area103890 Å2
ΔGint-501 kcal/mol
Surface area125760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)201.327, 146.988, 197.233
Angle α, β, γ (deg.)90.00, 99.79, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit


Mass: 55058.746 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Galdieria partita (eukaryote)
References: UniProt: O98949, ribulose-bisphosphate carboxylase
#2: Protein
ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit


Mass: 16211.486 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Galdieria partita (eukaryote)
References: UniProt: O98950, ribulose-bisphosphate carboxylase
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3112 / 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: 2.45 Å3/Da / Density % sol: 49.31 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
122.7 mg/mlprotein1drop
2100 mMHEPES-NaOH1reservoirpH7.5
312 %(w/v)PEG40001reservoir
45 %(w/v)MPD1reservoir
520 %(w/v)glycerol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionBiso Wilson estimate: 29.9 Å2
Reflection shellResolution: 2.6→40 Å
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 40.8 Å / Num. obs: 172258 / % possible obs: 98.9 % / Num. measured all: 895084 / Rmerge(I) obs: 0.103
Reflection shell
*PLUS
Lowest resolution: 2.76 Å / % possible obs: 97.4 % / Rmerge(I) obs: 0.306

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementResolution: 2.6→25.65 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.235 8610 5 %RANDOM
Rwork0.172 ---
obs0.172 171752 98.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.6045 Å2 / ksol: 0.38453 e/Å3
Displacement parametersBiso mean: 27.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0.47 Å2
2--0.68 Å20 Å2
3----0.71 Å2
Refine analyzeLuzzati coordinate error free: 0.33 Å / Luzzati sigma a free: 0.38 Å
Refinement stepCycle: LAST / Resolution: 2.6→25.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms38848 0 40 3112 42000
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.74
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.298 1417 5 %
Rwork0.219 26643 -
obs--97.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4CAP.PARAMCAP.TOP
X-RAY DIFFRACTION5KCX.PARAMKCX.TOP
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 40 Å / Num. reflection obs: 172258 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.34
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74
LS refinement shell
*PLUS
Highest resolution: 2.6 Å

+
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