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- PDB-2z44: Crystal Structure of Selenomethionine-labeled ORF134 -

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Basic information

Entry
Database: PDB / ID: 2z44
TitleCrystal Structure of Selenomethionine-labeled 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 / MAD / Resolution: 2.5 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 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ORF134


Theoretical massNumber of molelcules
Total (without water)15,4721
Polymers15,4721
Non-polymers00
Water61334
1
A: ORF134

A: ORF134


Theoretical massNumber of molelcules
Total (without water)30,9432
Polymers30,9432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,x-y,-z1
Buried area5220 Å2
ΔGint-39 kcal/mol
Surface area11670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.461, 56.461, 85.167
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11A-136-

HOH

21A-149-

HOH

31A-153-

HOH

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Components

#1: Protein ORF134 / RbcX


Mass: 15471.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. (bacteria) / Strain: PCC7002 / Description: In vitro translation / Plasmid: pIVEX2.3 / References: UniProt: Q44177
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.53 Å3/Da / Density % sol: 51.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50% PEG 200, 0.1M phosphate-citrate pH 4.2, 0.2M NaCl, 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: 0.97923, 0.97946, 0.96423
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 29, 2005
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979231
20.979461
30.964231
ReflectionResolution: 2.5→50 Å / Num. obs: 5247 / % possible obs: 98.7 % / Biso Wilson estimate: 64.2 Å2 / Rmerge(I) obs: 0.109
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.461 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.3.0034refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→48.8 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.899 / SU B: 12.048 / SU ML: 0.245 / Cross valid method: THROUGHOUT / ESU R: 0.406 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2805 248 4.5 %RANDOM
Rwork0.20452 ---
obs0.20823 5247 98.76 %-
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: 53.313 Å2
Baniso -1Baniso -2Baniso -3
1--2.27 Å2-1.14 Å20 Å2
2---2.27 Å20 Å2
3---3.41 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms895 0 0 34 929
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022907
X-RAY DIFFRACTIONr_bond_other_d0.0010.02630
X-RAY DIFFRACTIONr_angle_refined_deg1.4631.9831222
X-RAY DIFFRACTIONr_angle_other_deg0.91531543
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0235109
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.11424.77344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.94115181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.034157
X-RAY DIFFRACTIONr_chiral_restr0.0680.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02980
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02170
X-RAY DIFFRACTIONr_nbd_refined0.2040.2235
X-RAY DIFFRACTIONr_nbd_other0.1780.2603
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2441
X-RAY DIFFRACTIONr_nbtor_other0.0960.2482
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.224
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2680.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3240.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1191.5691
X-RAY DIFFRACTIONr_mcbond_other0.1431.5220
X-RAY DIFFRACTIONr_mcangle_it1.2882886
X-RAY DIFFRACTIONr_scbond_it1.883395
X-RAY DIFFRACTIONr_scangle_it2.9714.5336
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.498→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.439 18 -
Rwork0.268 391 -
obs--98.55 %

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