[English] 日本語
Yorodumi
- PDB-5bs2: Crystal structure of RbcX-IIa from Chlamydomonas reinhardtii in c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5bs2
TitleCrystal structure of RbcX-IIa from Chlamydomonas reinhardtii in complex with RbcL C-terminal tail
Components
  • Ribulose bisphosphate carboxylase large chain
  • Ribulose bisphosphate carboxylase large chain,CrRbcX-IIa
KeywordsCHAPERONE / RbcX
Function / homology
Function and homology information


ribulose bisphosphate carboxylase complex assembly / photorespiration / ribulose-bisphosphate carboxylase / carbon fixation / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / protein folding chaperone / photosynthesis / chloroplast / monooxygenase activity / magnesium ion binding
Similarity search - Function
Chaperonin-like RbcX / Chaperonin-like RbcX superfamily / RbcX protein / Chaperonin-like RbcX / 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 ...Chaperonin-like RbcX / Chaperonin-like RbcX superfamily / RbcX protein / Chaperonin-like RbcX / 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 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Predicted protein / Ribulose bisphosphate carboxylase large chain
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.97 Å
AuthorsBracher, A. / Hauser, T. / Liu, C. / Hartl, F.U. / Hayer-Hartl, M.
CitationJournal: Plos One / Year: 2015
Title: Structural Analysis of the Rubisco-Assembly Chaperone RbcX-II from Chlamydomonas reinhardtii.
Authors: Bracher, A. / Hauser, T. / Liu, C. / Hartl, F.U. / Hayer-Hartl, M.
History
DepositionJun 1, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ribulose bisphosphate carboxylase large chain,CrRbcX-IIa
B: Ribulose bisphosphate carboxylase large chain,CrRbcX-IIa
R: Ribulose bisphosphate carboxylase large chain


Theoretical massNumber of molelcules
Total (without water)30,6883
Polymers30,6883
Non-polymers00
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-37 kcal/mol
Surface area12550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.217, 38.525, 50.355
Angle α, β, γ (deg.)88.470, 81.530, 67.920
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: MET / End label comp-ID: MET / Refine code: 0 / Auth seq-ID: 44 - 156 / Label seq-ID: 20 - 132

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Ribulose bisphosphate carboxylase large chain,CrRbcX-IIa / RuBisCO large subunit


Mass: 14917.970 Da / Num. of mol.: 2 / Fragment: UNP residues 462-473,UNP residues 44-156
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: rbcL, CGL41, CHLREDRAFT_162607 / Plasmid: pHue / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P00877, UniProt: A8HQH2, ribulose-bisphosphate carboxylase
#2: Protein/peptide Ribulose bisphosphate carboxylase large chain / RuBisCO large subunit


Mass: 852.030 Da / Num. of mol.: 1 / Fragment: UNP residues 462-467
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: rbcL / Plasmid: pHue / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P00877, ribulose-bisphosphate carboxylase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.32 Å3/Da / Density % sol: 46.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris-HCl pH 8.5, 25% PEG2000 MME / PH range: 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99988 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99988 Å / Relative weight: 1
ReflectionResolution: 1.97→49.781 Å / Num. all: 15820 / Num. obs: 15820 / % possible obs: 94.2 % / Redundancy: 2.4 % / Rpim(I) all: 0.06 / Rrim(I) all: 0.102 / Rsym value: 0.081 / Net I/av σ(I): 6.511 / Net I/σ(I): 10.4 / Num. measured all: 38750
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.97-2.072.20.4941.6481821520.3940.494287.9
2.07-2.22.50.3032.2541821930.230.3033.994.8
2.2-2.352.40.2252.7509020880.1680.2255.495.9
2.35-2.542.30.163.7453119440.1190.167.495.2
2.54-2.782.60.134.2471118170.0910.1310.197.1
2.78-3.112.50.0985.6419216540.070.09812.997.4
3.11-3.592.50.0629.1360014220.0440.06217.995.8
3.59-4.42.60.04313.7299311680.030.04323.593.4
4.4-6.222.40.03914.721698940.0290.03923.792.7
6.22-35.6832.50.03412.812284880.0280.03426.591

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
MOLREPphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BS1

5bs1


Resolution: 1.97→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.2156 / WRfactor Rwork: 0.197 / FOM work R set: 0.8017 / SU B: 11.071 / SU ML: 0.138 / SU R Cruickshank DPI: 0.2048 / SU Rfree: 0.1606 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.205 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2219 810 5.1 %RANDOM
Rwork0.1996 ---
obs0.2007 15009 94.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.7 Å2 / Biso mean: 30.375 Å2 / Biso min: 16.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.97 Å20.57 Å22.89 Å2
2--4.42 Å2-1.71 Å2
3----3.84 Å2
Refinement stepCycle: final / Resolution: 1.97→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1800 0 0 87 1887
Biso mean---36.99 -
Num. residues----232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191832
X-RAY DIFFRACTIONr_bond_other_d0.0050.021740
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.9612471
X-RAY DIFFRACTIONr_angle_other_deg1.09233975
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3525229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.93723.17685
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.44415314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.0631518
X-RAY DIFFRACTIONr_chiral_restr0.0750.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022090
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02428
Refine LS restraints NCS

Ens-ID: 1 / Number: 5742 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.966→2.017 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 66 -
Rwork0.382 1022 -
all-1088 -
obs--84.6 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6145-0.964-1.66331.88752.9226.73180.0056-0.05210.0746-0.1170.1778-0.0984-0.17250.2534-0.18340.0509-0.038-0.06660.0340.02910.22656.2187-3.9168-7.9377
20.7516-1.2293-1.05143.50522.87983.2952-0.04840.0502-0.02990.0351-0.03570.09630.0209-0.23990.08410.0291-0.0144-0.06720.0570.03320.1902-6.62356.04566.9631
318.3691-14.3247-7.23211.22035.63762.88690.05521.0665-1.09390.0897-0.66440.81890.0042-0.35520.60920.33210.156-0.08430.41510.07340.4353-14.040415.02611.5303
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A44 - 156
2X-RAY DIFFRACTION1D1 - 27
3X-RAY DIFFRACTION2B44 - 156
4X-RAY DIFFRACTION2E1 - 39
5X-RAY DIFFRACTION3R462 - 467

+
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