[English] 日本語
Yorodumi
- PDB-7t1j: Crystal structure of RUBISCO from Rhodospirillaceae bacterium BRH_c57 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7t1j
TitleCrystal structure of RUBISCO from Rhodospirillaceae bacterium BRH_c57
ComponentsRibulose bisphosphate carboxylase
KeywordsLYASE / Ribulose-1 / 5-bisphosphate carboxylase-oxygenase
Function / homology
Function and homology information


ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / magnesium ion binding
Similarity search - Function
Ribulose bisphosphate carboxylase large subunit, type II / 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
Similarity search - Domain/homology
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE / Ribulose bisphosphate carboxylase
Similarity search - Component
Biological speciesRhodospirillaceae bacterium BRH_c57 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsPereira, J.H. / Liu, A.K. / Shih, P.M. / Adams, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Sci Adv / Year: 2022
Title: Structural plasticity enables evolution and innovation of RuBisCO assemblies.
Authors: Liu, A.K. / Pereira, J.H. / Kehl, A.J. / Rosenberg, D.J. / Orr, D.J. / Chu, S.K.S. / Banda, D.M. / Hammel, M. / Adams, P.D. / Siegel, J.B. / Shih, P.M.
History
DepositionDec 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ribulose bisphosphate carboxylase
B: Ribulose bisphosphate carboxylase
C: Ribulose bisphosphate carboxylase
D: Ribulose bisphosphate carboxylase
E: Ribulose bisphosphate carboxylase
F: Ribulose bisphosphate carboxylase
G: Ribulose bisphosphate carboxylase
H: Ribulose bisphosphate carboxylase
I: Ribulose bisphosphate carboxylase
J: Ribulose bisphosphate carboxylase
K: Ribulose bisphosphate carboxylase
L: Ribulose bisphosphate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)610,37236
Polymers605,80712
Non-polymers4,56524
Water80,2214453
1
A: Ribulose bisphosphate carboxylase
B: Ribulose bisphosphate carboxylase
C: Ribulose bisphosphate carboxylase
D: Ribulose bisphosphate carboxylase
G: Ribulose bisphosphate carboxylase
H: Ribulose bisphosphate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)305,18618
Polymers302,9046
Non-polymers2,28312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Ribulose bisphosphate carboxylase
F: Ribulose bisphosphate carboxylase
I: Ribulose bisphosphate carboxylase
J: Ribulose bisphosphate carboxylase
K: Ribulose bisphosphate carboxylase
L: Ribulose bisphosphate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)305,18618
Polymers302,9046
Non-polymers2,28312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.807, 104.978, 369.611
Angle α, β, γ (deg.)90.000, 93.040, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein
Ribulose bisphosphate carboxylase / RuBisCO


Mass: 50483.938 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillaceae bacterium BRH_c57 (bacteria)
Gene: cbbM, VR70_18855 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0F2R9T6, ribulose-bisphosphate carboxylase
#2: Sugar
ChemComp-CAP / 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE


Type: saccharide / Mass: 356.115 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C6H14O13P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4453 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Magnesium Formate pH 5.9, 20 % PEG 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X17B1 / Wavelength: 0.907936 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.907936 Å / Relative weight: 1
ReflectionResolution: 1.96→29.52 Å / Num. obs: 399609 / % possible obs: 98.2 % / Redundancy: 1.9 % / Biso Wilson estimate: 27.13 Å2 / CC1/2: 0.982 / Net I/σ(I): 4.81
Reflection shellResolution: 1.96→2.03 Å / Num. unique obs: 35839 / CC1/2: 0.41

-
Processing

Software
NameVersionClassification
phenix.refine1.20.1_4487refinement
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9rub

9rub


Resolution: 1.96→29.52 Å / SU ML: 0.2501 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.7648
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2354 2001 0.5 %0.5
Rwork0.1957 397361 --
obs0.1959 399362 98.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.02 Å2
Refinement stepCycle: LAST / Resolution: 1.96→29.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms42016 0 264 4453 46733
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004743288
X-RAY DIFFRACTIONf_angle_d0.619658631
X-RAY DIFFRACTIONf_chiral_restr0.04226097
X-RAY DIFFRACTIONf_plane_restr0.00437782
X-RAY DIFFRACTIONf_dihedral_angle_d14.846615619
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.010.32721230.286624048X-RAY DIFFRACTION83.41
2.01-2.070.31541440.267428661X-RAY DIFFRACTION99.87
2.07-2.130.29381400.253628687X-RAY DIFFRACTION99.87
2.13-2.20.27571550.238428825X-RAY DIFFRACTION99.91
2.2-2.270.26711420.229428724X-RAY DIFFRACTION99.75
2.27-2.370.25441370.220728666X-RAY DIFFRACTION99.86
2.37-2.470.27531480.218528852X-RAY DIFFRACTION99.87
2.47-2.60.26491420.213828745X-RAY DIFFRACTION99.82
2.6-2.770.27631470.214328847X-RAY DIFFRACTION99.63
2.77-2.980.27291450.209128465X-RAY DIFFRACTION98.74
2.98-3.280.23171390.194428518X-RAY DIFFRACTION98.74
3.28-3.750.21191410.172528776X-RAY DIFFRACTION99.24
3.75-4.730.19111480.146428669X-RAY DIFFRACTION98.72
4.73-29.520.18331500.174128878X-RAY DIFFRACTION98.21

+
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