[English] 日本語
Yorodumi
- PDB-2pek: Crystal structure of RbcX point mutant Q29A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2pek
TitleCrystal structure of RbcX point mutant Q29A
ComponentsORF134
KeywordsCHAPERONE / helix bundle / protein complex assembly
Function / homology
Function and homology information


ribulose bisphosphate carboxylase complex assembly / carboxysome / carbon fixation / photosynthesis / protein folding chaperone / protein homodimerization activity / cytoplasm
Similarity search - Function
Chaperonin-like RbcX / RuBisCO chaperone RbcX / Chaperonin-like RbcX superfamily / RbcX protein / Chaperonin-like RbcX / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
RuBisCO chaperone RbcX
Similarity search - Component
Biological speciesSynechococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsSaschenbrecker, S. / Bracher, A. / Vasudeva Rao, K. / Vasudeva Rao, B. / Hartl, F.U. / Hayer-Hartl, M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2007
Title: Structure and Function of RbcX, an Assembly Chaperone for Hexadecameric Rubisco.
Authors: Saschenbrecker, S. / Bracher, A. / Rao, K.V. / Rao, B.V. / Hartl, F.U. / Hayer-Hartl, M.
History
DepositionApr 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ORF134
B: ORF134
C: ORF134
D: ORF134
E: ORF134
F: ORF134


Theoretical massNumber of molelcules
Total (without water)91,3626
Polymers91,3626
Non-polymers00
Water1086
1
A: ORF134
B: ORF134


Theoretical massNumber of molelcules
Total (without water)30,4542
Polymers30,4542
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-38 kcal/mol
Surface area11120 Å2
MethodPISA
2
C: ORF134
D: ORF134


Theoretical massNumber of molelcules
Total (without water)30,4542
Polymers30,4542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-35 kcal/mol
Surface area11280 Å2
MethodPISA
3
E: ORF134
F: ORF134


Theoretical massNumber of molelcules
Total (without water)30,4542
Polymers30,4542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-38 kcal/mol
Surface area11130 Å2
MethodPISA
4
C: ORF134
D: ORF134

E: ORF134
F: ORF134


Theoretical massNumber of molelcules
Total (without water)60,9084
Polymers60,9084
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_445-y-1/2,x-1/2,z+1/41
Buried area10440 Å2
ΔGint-85 kcal/mol
Surface area21180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.996, 92.996, 413.724
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
DetailsThe biological unit of RbcX is a dimer. There are 3 biological units in the asymmetric unit (chains A & B, chains C & D and chains E & F).

-
Components

#1: Protein
ORF134


Mass: 15227.033 Da / Num. of mol.: 6 / Mutation: Q29A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. (bacteria) / Strain: PCC 7002 / Gene: RbcX / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q44177
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 4.89 Å3/Da / Density % sol: 74.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5-2.5 M Sodium acetate, 0.1 M HEPES-NaOH pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 26, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→103.695 Å / Num. obs: 34180 / % possible obs: 99.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 6.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.1-3.273.60.4851.61730448240.48599.9
3.27-3.473.60.2712.81661146560.27199.9
3.47-3.713.60.1534.91550143570.153100
3.71-43.50.1047.11439140640.10499.8
4-4.383.50.06810.21320537860.068100
4.38-4.93.50.059111194534560.059100
4.9-5.663.40.0689.41031730590.06899.9
5.66-6.933.30.0827.1862326370.08299.7
6.93-9.83.20.047.8665120830.0499.6
9.8-933.10.03314.4388812580.03399.4

-
Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2PEN

2pen


Resolution: 3.1→20 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.903 / SU B: 13.08 / SU ML: 0.234 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.464 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1726 5.1 %RANDOM
Rwork0.231 ---
obs0.233 33963 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å20 Å2
2--0.57 Å20 Å2
3----1.14 Å2
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4970 0 0 6 4976
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0215041
X-RAY DIFFRACTIONr_angle_refined_deg1.2731.9766854
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1545651
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.424.126206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.50415840
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8371534
X-RAY DIFFRACTIONr_chiral_restr0.080.2837
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023717
X-RAY DIFFRACTIONr_nbd_refined0.2380.22558
X-RAY DIFFRACTIONr_nbtor_refined0.310.23534
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2172
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.21
X-RAY DIFFRACTIONr_mcbond_it0.541.53347
X-RAY DIFFRACTIONr_mcangle_it0.97725188
X-RAY DIFFRACTIONr_scbond_it1.34731886
X-RAY DIFFRACTIONr_scangle_it2.4024.51666
LS refinement shellResolution: 3.1→3.179 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 128 -
Rwork0.337 2233 -
obs-2361 99.79 %

+
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