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- PDB-2pem: Crystal structure of RbcX in complex with substrate -

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Basic information

Entry
Database: PDB / ID: 2pem
TitleCrystal structure of RbcX in complex with substrate
Components
  • ORF134
  • RbcL
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: 2.95 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)92,6337
Polymers92,6337
Non-polymers00
Water28816
1
A: ORF134
B: ORF134
R: RbcL


Theoretical massNumber of molelcules
Total (without water)31,4963
Polymers31,4963
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6230 Å2
ΔGint-48 kcal/mol
Surface area11710 Å2
MethodPISA
2
C: ORF134
D: ORF134


Theoretical massNumber of molelcules
Total (without water)30,5682
Polymers30,5682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-35 kcal/mol
Surface area11440 Å2
MethodPISA
3
E: ORF134
F: ORF134


Theoretical massNumber of molelcules
Total (without water)30,5682
Polymers30,5682
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-37 kcal/mol
Surface area11790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.207, 93.207, 412.016
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).

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Components

#1: Protein
ORF134


Mass: 15284.084 Da / Num. of mol.: 6
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: Protein/peptide RbcL


Mass: 928.016 Da / Num. of mol.: 1 / Fragment: Residues 459-465 / Source method: obtained synthetically
Details: Synthetic peptide with the sequence based on Ribulose bisphosphate carboxylase large chain (RbcL) from Synechococcus sp. PCC 7002, UNP entry Q44176, RBL_SYNP2, residues 459-465
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 4.83 Å3/Da / Density % sol: 74.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.4 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: 0.976 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 22, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.95→103.142 Å / Num. obs: 37874 / % possible obs: 96.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 5.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.95-3.113.80.5361.42102655000.53697.6
3.11-3.33.80.3212.41968351690.32197.3
3.3-3.533.80.1714.31851048660.17197.4
3.53-3.813.80.1086.51726245580.10897.1
3.81-4.173.80.07491577141970.07496.7
4.17-4.663.80.05711.11432238150.05796.5
4.66-5.393.70.06691235833510.06696.2
5.39-6.63.60.0896.31043728870.08995.6
6.6-9.333.50.04811.1773722400.04894.5
9.33-93.253.30.0449.7428812910.04492.2

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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: 2.95→20 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.903 / SU B: 12.826 / SU ML: 0.237 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.424 / ESU R Free: 0.308 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1913 5.1 %RANDOM
Rwork0.235 ---
obs0.236 37701 95.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.682 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2---0.25 Å20 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5216 0 0 16 5232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225289
X-RAY DIFFRACTIONr_angle_refined_deg1.3881.9767163
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3945661
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.7124.262237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.15415947
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6821540
X-RAY DIFFRACTIONr_chiral_restr0.090.2854
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023900
X-RAY DIFFRACTIONr_nbd_refined0.2440.22634
X-RAY DIFFRACTIONr_nbtor_refined0.3140.23685
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2178
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.254
X-RAY DIFFRACTIONr_mcbond_it0.6881.53409
X-RAY DIFFRACTIONr_mcangle_it1.27225316
X-RAY DIFFRACTIONr_scbond_it1.59632073
X-RAY DIFFRACTIONr_scangle_it2.8174.51847
LS refinement shellResolution: 2.95→3.025 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 125 -
Rwork0.376 2596 -
obs-2721 97.01 %

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