[English] 日本語
Yorodumi
- PDB-1bxn: THE CRYSTAL STRUCTURE OF RUBISCO FROM ALCALIGENES EUTROPHUS TO 2.... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bxn
TitleTHE CRYSTAL STRUCTURE OF RUBISCO FROM ALCALIGENES EUTROPHUS TO 2.7 ANGSTROMS.
Components
  • PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)
  • PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN)
KeywordsLYASE / LYASE (CARBON-CARBON)
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, 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
PHOSPHATE ION / Ribulose bisphosphate carboxylase small subunit, chromosomal / Ribulose bisphosphate carboxylase large chain, chromosomal
Similarity search - Component
Biological speciesCupriavidus necator (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHansen, S. / Vollan, V.B. / Hough, E. / Andersen, K.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: The crystal structure of rubisco from Alcaligenes eutrophus reveals a novel central eight-stranded beta-barrel formed by beta-strands from four subunits.
Authors: Hansen, S. / Vollan, V.B. / Hough, E. / Andersen, K.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Purification, Crystallization and Preliminary X-Ray Studies of Two Isoforms of Rubisco from Alcaligenes Eutrophus
Authors: Hansen, S. / Hough, E. / Andersen, K.
History
DepositionOct 6, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 6, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)
I: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN)
C: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)
J: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN)
E: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)
K: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN)
G: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)
L: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)279,81116
Polymers279,0518
Non-polymers7608
Water00
1
A: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)
I: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN)
C: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)
J: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN)
E: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)
K: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN)
G: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)
L: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN)
hetero molecules

A: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)
I: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN)
C: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)
J: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN)
E: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)
K: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN)
G: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)
L: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)559,62232
Polymers558,10316
Non-polymers1,52016
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area95060 Å2
ΔGint-442 kcal/mol
Surface area121570 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)112.000, 112.000, 402.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.013, -0.987, 0.163), (1, 0.014, 0.001), (-0.003, 0.163, 0.987)93.962, 100.378, -16.079
2given(0.014, -0.986, 0.168), (1, 0.014, -0.001), (-0.001, 0.168, 0.986)93.52, 100.51, -16.493
3given(-0.987, 0.006, 0.16), (0.02, -0.987, 0.162), (0.159, 0.164, 0.974)-6.824, 196.01401, -15.705
4given(-0.986, 0.012, 0.165), (0.015, -0.987, 0.162), (0.165, 0.162, 0.973)-7.689, 196.035, -15.434
5given(0.004, 1), (-0.987, 0.004, 0.161), (0.161, -0.001, 0.987)-101.89, 95.244, 0.533
6given(0.008, 1, 0.002), (-0.986, 0.008, 0.166), (0.166, -0.004, 0.986)-102.032, 94.507, 0.958

-
Components

#1: Protein
PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN) / RUBISCO


Mass: 53703.910 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus necator (bacteria)
References: UniProt: P0C2C2*PLUS, ribulose-bisphosphate carboxylase
#2: Protein
PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN) / RUBISCO


Mass: 16058.934 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus necator (bacteria)
References: UniProt: P09658*PLUS, ribulose-bisphosphate carboxylase
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 45.8 %
Crystal growpH: 8.4 / Details: pH 8.40
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
140 mg/mlprotein1drop
220 mMHEPES1drop
30.7-0.8 M1reservoirK2HPO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.9117
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 11, 1997
RadiationMonochromator: YES / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9117 Å / Relative weight: 1
ReflectionResolution: 2.7→25 Å / Num. obs: 65785 / % possible obs: 88 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 1.5
Reflection
*PLUS
% possible obs: 87.5 %
Reflection shell
*PLUS
Highest resolution: 2.65 Å / Lowest resolution: 2.79 Å / % possible obs: 89.1 % / Redundancy: 4.3 % / Num. unique obs: 9546 / Rmerge(I) obs: 0.695

-
Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.8refinement
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AUS

1aus


Resolution: 2.7→15 Å / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.322 -10 %RANDOM
Rwork0.266 ---
obs0.266 65785 90 %-
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18104 0 40 0 18144
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.76
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.11
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.76
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.11

+
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