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- PDB-1geh: CRYSTAL STRUCTURE OF ARCHAEAL RUBISCO (RIBULOSE 1,5-BISPHOSPHATE ... -

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Basic information

Entry
Database: PDB / ID: 1geh
TitleCRYSTAL STRUCTURE OF ARCHAEAL RUBISCO (RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE)
ComponentsRIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
KeywordsLYASE / Pentagonal toroid decamer / RUBISCO
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 speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.8 Å
AuthorsKitano, K. / Maeda, N. / Fukui, T. / Atomi, H. / Imanaka, T. / Miki, K.
Citation
Journal: Structure / Year: 2001
Title: Crystal Structure of a Novel-Type Archaeal Rubisco with Pentagonal Symmetry
Authors: Kitano, K. / Maeda, N. / Fukui, T. / Atomi, H. / Imanaka, T. / Miki, K.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: Ribulose Bisphosphate Carboxylase/oxygenase from Hyperthermophilic Archaeon Pyrococcus kodakaraensis KOD1 is Composed Solely of Large Subunits and Forms a Pentagonal Structure
Authors: Maeda, N. / Kitano, K. / Fukui, T. / Ezaki, S. / Atomi, H. / Miki, K. / Imanaka, T.
History
DepositionNov 13, 2000Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
B: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
C: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
D: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
E: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,84315
Polymers248,8825
Non-polymers96110
Water0
1
A: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
B: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
C: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
D: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
E: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
hetero molecules

A: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
B: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
C: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
D: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
E: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)499,68630
Polymers497,76510
Non-polymers1,92120
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)233.75, 233.75, 93.26
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is a decamer generated from the pentamer in the asymmetric unit by the operations: y, x, -z.

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Components

#1: Protein
RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE


Mass: 49776.480 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: KOD1 / Production host: Escherichia coli (E. coli)
References: UniProt: O93627, ribulose-bisphosphate carboxylase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 9
Details: Ammoinum sulfate, pH 9.0, VAPOR DIFFUSION, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / Details: Maeda, N., (1999) J.Mol.Biol., 293, 57.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
21.8 Mammonium sulfate1drop
310 mM1dropMgCl2
4100 mMCHES-NaOH1droppH9.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-6A11
SYNCHROTRONPhoton Factory BL-6B21
Detector
TypeIDDetector
FUJI1IMAGE PLATE
FUJI2IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→100 Å / Num. obs: 64453 / % possible obs: 89.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 12.1 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 11.8
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.335 / % possible all: 65.5
Reflection
*PLUS
Lowest resolution: 100 Å / Num. measured all: 784332
Reflection shell
*PLUS
% possible obs: 65.5 % / Mean I/σ(I) obs: 3.4

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.8→100 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 11437229 / Data cutoff low absF: 0 / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 6530 10.1 %RANDOM
Rwork0.224 ---
all-64453 --
obs-64453 --
Solvent computationSolvent model: FLAT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16890 0 50 0 16940
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it10.051.5
X-RAY DIFFRACTIONc_mcangle_it15.582
X-RAY DIFFRACTIONc_scbond_it13.932
X-RAY DIFFRACTIONc_scangle_it19.712.5
LS refinement shellHighest resolution: 2.8 Å / Total num. of bins used: 6 /
Num. reflection% reflection
Rwork7222 -
Rfree-10.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 100 Å / σ(F): 1 / % reflection Rfree: 10.1 % / Rfactor obs: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.404
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87
X-RAY DIFFRACTIONc_mcbond_it10.051.5
X-RAY DIFFRACTIONc_scbond_it13.932
X-RAY DIFFRACTIONc_mcangle_it15.582
X-RAY DIFFRACTIONc_scangle_it19.712.5
LS refinement shell
*PLUS
% reflection Rfree: 10.1 %

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