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- PDB-2pej: Crystal structure of RbcX point mutant Y17A/Y20L -

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Basic information

Entry
Database: PDB / ID: 2pej
TitleCrystal structure of RbcX point mutant Y17A/Y20L
ComponentsORF134
KeywordsCHAPERONE / helix bundle / protein complex assembly
Function / homology
Function and homology information


ribulose bisphosphate carboxylase complex assembly / carboxysome / carbon fixation / protein folding chaperone / photosynthesis / protein homodimerization activity / cytoplasm
Similarity search - Function
RuBisCO chaperone RbcX / Chaperonin-like 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: 3.4 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)90,8526
Polymers90,8526
Non-polymers00
Water00
1
A: ORF134
B: ORF134


Theoretical massNumber of molelcules
Total (without water)30,2842
Polymers30,2842
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-38 kcal/mol
Surface area10960 Å2
MethodPISA
2
C: ORF134
D: ORF134


Theoretical massNumber of molelcules
Total (without water)30,2842
Polymers30,2842
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-32 kcal/mol
Surface area11080 Å2
MethodPISA
3
E: ORF134
F: ORF134


Theoretical massNumber of molelcules
Total (without water)30,2842
Polymers30,2842
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-37 kcal/mol
Surface area11400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.446, 93.446, 411.544
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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).

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Components

#1: Protein
ORF134


Mass: 15141.973 Da / Num. of mol.: 6 / Mutation: Y17A, Y20L
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

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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: 4.94 Å3/Da / Density % sol: 75.11 %
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

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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: 3.4→103.142 Å / Num. obs: 26126 / % possible obs: 99.6 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 3.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.4-3.583.60.5031.51333837420.50399.8
3.58-3.83.50.2772.71242535120.27799.6
3.8-4.063.50.1734.11175633340.17399.6
4.06-4.393.50.11261081230970.11299.6
4.39-4.813.50.0896.9997828820.08999.6
4.81-5.383.40.0857898026330.08599.6
5.38-6.213.30.0956.5790323640.09599.8
6.21-7.63.20.0776.9645120010.07799.5
7.6-10.753.10.0666.7490315910.06699
10.75-93.2530.0667.429259700.06698.8

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Processing

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

2pen


Resolution: 3.4→20 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.916 / SU B: 20.589 / SU ML: 0.342 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.799 / ESU R Free: 0.447 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.294 1319 5.1 %RANDOM
Rwork0.253 ---
obs0.255 25915 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 106.428 Å2
Baniso -1Baniso -2Baniso -3
1--1.79 Å20 Å20 Å2
2---1.79 Å20 Å2
3---3.57 Å2
Refinement stepCycle: LAST / Resolution: 3.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4727 0 0 0 4727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0214782
X-RAY DIFFRACTIONr_angle_refined_deg1.3191.9746517
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8375646
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.85124.326178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.2815752
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6081532
X-RAY DIFFRACTIONr_chiral_restr0.0830.2820
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023523
X-RAY DIFFRACTIONr_nbd_refined0.2560.22443
X-RAY DIFFRACTIONr_nbtor_refined0.3070.23325
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2203
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.22
X-RAY DIFFRACTIONr_mcbond_it0.541.53307
X-RAY DIFFRACTIONr_mcangle_it1.01225097
X-RAY DIFFRACTIONr_scbond_it1.29531589
X-RAY DIFFRACTIONr_scangle_it2.4044.51420
LS refinement shellResolution: 3.4→3.486 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 100 -
Rwork0.276 1761 -
obs-1861 99.41 %

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