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- PDB-2peq: Crystal structure of RbcX, crystal form II -

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Basic information

Entry
Database: PDB / ID: 2peq
TitleCrystal structure of RbcX, crystal form II
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: 1.9 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 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ORF134
B: ORF134


Theoretical massNumber of molelcules
Total (without water)30,5682
Polymers30,5682
Non-polymers00
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-40 kcal/mol
Surface area11640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.505, 69.339, 98.795
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-184-

HOH

21B-179-

HOH

31B-205-

HOH

DetailsThe biological unit is a dimer. There is 1 biological unit in the asymmetric unit.

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Components

#1: Protein ORF134


Mass: 15284.084 Da / Num. of mol.: 2
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.: 147 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 1.78 Å3/Da / Density % sol: 30.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350, 0.2 M KSCN, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: 1.9→56.796 Å / Num. obs: 17567 / % possible obs: 100 % / Redundancy: 4.2 % / Biso Wilson estimate: 24.103 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 5.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-24.30.5751.31085125300.575100
2-2.124.30.3492.21019923950.349100
2.12-2.274.20.2383.1952722530.238100
2.27-2.454.20.164.4887121100.16100
2.45-2.694.20.1146806919350.114100
2.69-34.20.0798.8731917600.079100
3-3.474.10.069.7638615740.06100
3.47-4.253.80.069.3514713430.06100
4.25-6.0140.0539.5421110500.053100
6.01-29.2440.03411.724596170.03499

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3 Å24.71 Å
Translation3 Å24.71 Å

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Processing

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

2pen


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.004 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.253 887 5.1 %RANDOM
Rwork0.197 ---
obs0.2 17551 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.31 Å20 Å20 Å2
2---0.48 Å20 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1744 0 0 147 1891
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221770
X-RAY DIFFRACTIONr_angle_refined_deg1.391.9842387
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6785216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.37224.56881
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.28215345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6241513
X-RAY DIFFRACTIONr_chiral_restr0.0930.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021287
X-RAY DIFFRACTIONr_nbd_refined0.2120.2885
X-RAY DIFFRACTIONr_nbtor_refined0.2960.21238
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2122
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2550.216
X-RAY DIFFRACTIONr_mcbond_it0.8631.51129
X-RAY DIFFRACTIONr_mcangle_it1.38721747
X-RAY DIFFRACTIONr_scbond_it2.4043723
X-RAY DIFFRACTIONr_scangle_it3.8414.5640
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 58 -
Rwork0.268 1228 -
obs-1286 100 %

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