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- PDB-2cxe: Crystal structure of octameric ribulose-1,5-bisphosphate carboxyl... -

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Basic information

Entry
Database: PDB / ID: 2cxe
TitleCrystal structure of octameric ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) from Pyrococcus horikoshii OT3 (form-2 crystal)
ComponentsRibulose bisphosphate carboxylaseRuBisCO
KeywordsLYASE / structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


AMP catabolic process / ribulose-bisphosphate carboxylase / carbon fixation / ribulose-bisphosphate carboxylase activity / oxidoreductase activity / magnesium ion binding
Similarity search - Function
Ribulose bisphosphate carboxylase, type III / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase large chain, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal / RuBisCO / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily / RuBisCO large subunit, N-terminal domain superfamily / Ribulose bisphosphate carboxylase large chain, catalytic domain ...Ribulose bisphosphate carboxylase, type III / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase large chain, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal / RuBisCO / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily / RuBisCO large subunit, N-terminal domain superfamily / Ribulose bisphosphate carboxylase large chain, catalytic domain / Alpha-Beta Plaits / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribulose bisphosphate carboxylase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMizohata, E. / Mishima, C. / Akasaka, R. / Uda, H. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of octameric ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) from Pyrococcus horikoshii OT3 (form-2 crystal)
Authors: Mizohata, E. / Mishima, C. / Akasaka, R. / Uda, H. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionJun 28, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 28, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Ribulose bisphosphate carboxylase
B: Ribulose bisphosphate carboxylase
C: Ribulose bisphosphate carboxylase
D: Ribulose bisphosphate carboxylase


Theoretical massNumber of molelcules
Total (without water)193,2504
Polymers193,2504
Non-polymers00
Water3,675204
1
A: Ribulose bisphosphate carboxylase
B: Ribulose bisphosphate carboxylase
C: Ribulose bisphosphate carboxylase
D: Ribulose bisphosphate carboxylase

A: Ribulose bisphosphate carboxylase
B: Ribulose bisphosphate carboxylase
C: Ribulose bisphosphate carboxylase
D: Ribulose bisphosphate carboxylase


Theoretical massNumber of molelcules
Total (without water)386,5018
Polymers386,5018
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
MethodPQS
2
A: Ribulose bisphosphate carboxylase

A: Ribulose bisphosphate carboxylase


Theoretical massNumber of molelcules
Total (without water)96,6252
Polymers96,6252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7010 Å2
ΔGint-35 kcal/mol
Surface area29610 Å2
MethodPISA
3
B: Ribulose bisphosphate carboxylase
C: Ribulose bisphosphate carboxylase


Theoretical massNumber of molelcules
Total (without water)96,6252
Polymers96,6252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-35 kcal/mol
Surface area29670 Å2
MethodPISA
4
D: Ribulose bisphosphate carboxylase

D: Ribulose bisphosphate carboxylase


Theoretical massNumber of molelcules
Total (without water)96,6252
Polymers96,6252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6900 Å2
ΔGint-35 kcal/mol
Surface area29750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.478, 149.207, 107.461
Angle α, β, γ (deg.)90.00, 127.37, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-436-

HOH

21D-437-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.25005, 0.86374, -0.43752), (-0.86642, -0.0021, -0.49931), (-0.43219, 0.50393, 0.74784)-30.09503, 34.80614, -17.49799
3given(-0.25073, 0.86432, 0.43599), (0.86839, 0.00177, 0.49589), (0.42783, 0.50294, -0.751)-30.10256, 34.89288, -17.44243
4given(-0.4928, 0.00535, -0.87012), (0.00024, -0.99998, -0.00628), (-0.87014, -0.0033, 0.49279)-0.05093, 69.6814, -0.0297
DetailsThe biological assembly is the octamer. Although the present asymmetic unit is tetramer, NCS constraint is applied to produce monomer (segment id A). The second, third, and fourth part in the asymmetric unit is generated by MTRIX in the PDB file. Biological assembly is generated from the asymmetric component by operator -x, y, -z.

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Components

#1: Protein
Ribulose bisphosphate carboxylase / RuBisCO / ribulose-1 / 5-bisphosphate carboxylase/oxygenase / RuBisCO


Mass: 48312.602 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O58677, ribulose-bisphosphate carboxylase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.83 Å3/Da / Density % sol: 55.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: magnesium chloride, sodium chloride, sodium acetate, PEG6000, Tris, pH 5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM / Detector: CCD / Date: May 17, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 39367

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→46.72 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 416476.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.328 1838 5 %RANDOM
Rwork0.295 ---
obs0.295 36882 85.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.2828 Å2 / ksol: 0.307086 e/Å3
Displacement parametersBiso mean: 88.3 Å2
Baniso -1Baniso -2Baniso -3
1-11.96 Å20 Å246.05 Å2
2---43.61 Å20 Å2
3---31.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.74 Å0.68 Å
Luzzati d res low-5 Å
Luzzati sigma a1.45 Å1.4 Å
Refinement stepCycle: LAST / Resolution: 3→46.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13144 0 0 204 13348
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.074
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg5.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d3.11
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.606 290 5.3 %
Rwork0.58 5162 -
obs--76.3 %

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