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- PDB-2peo: Crystal structure of RbcX from Anabaena CA -

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Basic information

Entry
Database: PDB / ID: 2peo
TitleCrystal structure of RbcX from Anabaena CA
ComponentsRbcX protein
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 speciesAnabaena sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RbcX protein
B: RbcX protein


Theoretical massNumber of molelcules
Total (without water)35,3902
Polymers35,3902
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-42 kcal/mol
Surface area12780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.021, 69.021, 113.805
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
DetailsThe biological unit of RbcX is a dimer. There is 1 biological unit in the asymmetric unit.

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Components

#1: Protein RbcX protein


Mass: 17694.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena sp. (bacteria) / Strain: CA / Gene: rbcX / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q44212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.21 Å3/Da / Density % sol: 44.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1.0 M Ammonium phosphate, 0.1 M Sodium citrate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.072 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 18, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.4→59.774 Å / Num. obs: 11805 / % possible obs: 98.1 % / Redundancy: 3.6 % / Biso Wilson estimate: 41.512 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 8.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.4-2.532.90.4441.7444215420.44488.2
2.53-2.683.40.3362.3553916450.33699.9
2.68-2.873.80.3082.4592215630.30899.9
2.87-3.13.80.2013.6552214500.201100
3.1-3.393.80.126.2506013310.12100
3.39-3.793.80.0759463912130.07599.9
3.79-4.383.80.04714.7409410690.04799.9
4.38-5.373.80.03915.135099140.03999.9
5.37-7.593.80.05112.226606990.05199.8
7.59-59.763.80.02719.314273790.02796.6

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
MAR345CCDdata collection
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2PEN

2pen


Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.876 / SU B: 11.201 / SU ML: 0.257 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.467 / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.298 502 4.7 %RANDOM
Rwork0.241 ---
obs0.244 10630 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.152 Å2
Baniso -1Baniso -2Baniso -3
1-2.31 Å21.16 Å20 Å2
2--2.31 Å20 Å2
3----3.47 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1755 0 0 14 1769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221782
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.9672412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5715221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.73524.62580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.53315316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.0051511
X-RAY DIFFRACTIONr_chiral_restr0.0960.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021315
X-RAY DIFFRACTIONr_nbd_refined0.2460.2857
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21240
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.266
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.23
X-RAY DIFFRACTIONr_mcbond_it0.7261.51164
X-RAY DIFFRACTIONr_mcangle_it1.25921789
X-RAY DIFFRACTIONr_scbond_it2.0673699
X-RAY DIFFRACTIONr_scangle_it3.4324.5623
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 42 -
Rwork0.257 736 -
obs-778 98.86 %

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