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- PDB-2z46: Crystal Structure of Native-ORF134 -

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Basic information

Entry
Database: PDB / ID: 2z46
TitleCrystal Structure of Native-ORF134
ComponentsORF134
KeywordsCHAPERONE / helix bundle
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: 2.97 Å
AuthorsTomimoto, Y. / Ihara, K. / Onizuka, T. / Kanai, S. / Ashida, H. / Yokota, A. / Tanaka, S. / Miyasaka, H. / Yamada, Y. / Kato, R. / Wakatsuki, S.
CitationJournal: To be Published
Title: Crystal Structure of ORF134
Authors: Tomimoto, Y. / Ihara, K. / Onizuka, T. / Kanai, S. / Ashida, H. / Yokota, A. / Tanaka, S. / Miyasaka, H. / Yamada, Y. / Kato, R. / Wakatsuki, S.
History
DepositionJun 12, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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
C: ORF134
D: ORF134
E: ORF134
F: ORF134


Theoretical massNumber of molelcules
Total (without water)91,7056
Polymers91,7056
Non-polymers00
Water00
1
A: ORF134
B: ORF134


Theoretical massNumber of molelcules
Total (without water)30,5682
Polymers30,5682
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-32 kcal/mol
Surface area11810 Å2
MethodPISA
2
C: ORF134
D: ORF134


Theoretical massNumber of molelcules
Total (without water)30,5682
Polymers30,5682
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-35 kcal/mol
Surface area12090 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 area5160 Å2
ΔGint-39 kcal/mol
Surface area12340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.794, 93.794, 410.222
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
ORF134 / RbcX


Mass: 15284.084 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. (bacteria) / Strain: PCC7002 / Description: In vitro translation / Plasmid: pIVEX3.2 / 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: 4.92 Å3/Da / Density % sol: 74.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.4M Na acetate, 0.1M Na cacodylate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 1, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.97→50 Å / Num. obs: 37069 / % possible obs: 99.3 % / Biso Wilson estimate: 90.4 Å2 / Rmerge(I) obs: 0.088
Reflection shellResolution: 2.97→3.08 Å / Rmerge(I) obs: 0.726 / % possible all: 95.1

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Processing

Software
NameVersionClassification
REFMAC5.3.0034refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Z44

2z44


Resolution: 2.97→50 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.899 / SU B: 13.646 / SU ML: 0.252 / Cross valid method: THROUGHOUT / ESU R: 0.438 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27675 1955 5 %RANDOM
Rwork0.24814 ---
obs0.24961 37069 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 71.089 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20 Å2
2--0.44 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 2.97→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5347 0 0 0 5347
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225419
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2681.9847302
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4895652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.9924.672259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.309151081
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8921542
X-RAY DIFFRACTIONr_chiral_restr0.090.2852
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023944
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.22514
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.23775
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.2115
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5871.53369
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.06725302
X-RAY DIFFRACTIONr_scbond_it1.10532265
X-RAY DIFFRACTIONr_scangle_it2.0074.52000
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.97→3.047 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 145 -
Rwork0.423 2629 -
obs--98.06 %

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