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- PDB-1gk8: Rubisco from Chlamydomonas reinhardtii -

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Basic information

Entry
Database: PDB / ID: 1gk8
TitleRubisco from Chlamydomonas reinhardtii
Components
  • RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1
  • RIBULOSE-1,5 BISPHOSPHATE CARBOXYLASE LARGE CHAIN
KeywordsLYASE / RUBISCO / PHOTOSYNTHESIS
Function / homology
Function and homology information


photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / chloroplast / monooxygenase activity / magnesium ion binding
Similarity search - Function
Ribulose bisphosphate carboxylase, small subunit / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase large subunit, type I ...Ribulose bisphosphate carboxylase, small subunit / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. / 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
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE / Ribulose bisphosphate carboxylase small subunit, chloroplastic 1 / Ribulose bisphosphate carboxylase large chain
Similarity search - Component
Biological speciesCHLAMYDOMONAS REINHARDTII (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsTaylor, T.C.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: First Crystal Structure of Rubisco from a Green Alga, Chlamydomonas Reinhardtii.
Authors: Taylor, T.C. / Backlund, A. / Bjorhall, K. / Spreitzer, R.J. / Andersson, I.
History
DepositionAug 9, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_struct_special_symmetry / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 LARGE CHAIN
C: RIBULOSE-1,5 BISPHOSPHATE CARBOXYLASE LARGE CHAIN
E: RIBULOSE-1,5 BISPHOSPHATE CARBOXYLASE LARGE CHAIN
G: RIBULOSE-1,5 BISPHOSPHATE CARBOXYLASE LARGE CHAIN
I: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1
K: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1
M: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1
O: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)279,49349
Polymers275,9238
Non-polymers3,57041
Water46,0462556
1
A: RIBULOSE-1,5 BISPHOSPHATE CARBOXYLASE LARGE CHAIN
C: RIBULOSE-1,5 BISPHOSPHATE CARBOXYLASE LARGE CHAIN
E: RIBULOSE-1,5 BISPHOSPHATE CARBOXYLASE LARGE CHAIN
G: RIBULOSE-1,5 BISPHOSPHATE CARBOXYLASE LARGE CHAIN
I: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1
K: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1
M: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1
O: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1
hetero molecules

A: RIBULOSE-1,5 BISPHOSPHATE CARBOXYLASE LARGE CHAIN
C: RIBULOSE-1,5 BISPHOSPHATE CARBOXYLASE LARGE CHAIN
E: RIBULOSE-1,5 BISPHOSPHATE CARBOXYLASE LARGE CHAIN
G: RIBULOSE-1,5 BISPHOSPHATE CARBOXYLASE LARGE CHAIN
I: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1
K: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1
M: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1
O: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)558,98598
Polymers551,84516
Non-polymers7,14082
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)171.375, 142.638, 124.717
Angle α, β, γ (deg.)90.00, 124.13, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-2282-

HOH

21E-2311-

HOH

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Components

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Protein , 2 types, 8 molecules ACEGIKMO

#1: Protein
RIBULOSE-1,5 BISPHOSPHATE CARBOXYLASE LARGE CHAIN / RUBISCO LARGE SUBUNIT


Mass: 52696.840 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) CHLAMYDOMONAS REINHARDTII (plant)
References: UniProt: P00877, ribulose-bisphosphate carboxylase
#2: Protein
RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1 / RUBISCO SMALL SUBUNIT 1


Mass: 16283.806 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) CHLAMYDOMONAS REINHARDTII (plant)
References: UniProt: P00873, ribulose-bisphosphate carboxylase

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Sugars , 1 types, 4 molecules

#4: Sugar
ChemComp-CAP / 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE


Type: saccharide / Mass: 356.115 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O13P2

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Non-polymers , 3 types, 2593 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2556 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsRESIDUE 46 IN THE LARGE SUBUNITS (CHAIN A C E G) WAS FOUND TO BE PRO AFTER INSPECTION OF THE ...RESIDUE 46 IN THE LARGE SUBUNITS (CHAIN A C E G) WAS FOUND TO BE PRO AFTER INSPECTION OF THE ELECTRON DENSITY MAPS.

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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: 2.3 Å3/Da / Density % sol: 46.21 %
Crystal growTemperature: 291 K / pH: 7.5
Details: 50 MM HEPES PH 7.5, 8-12% PEG 4000, 50 MM NAHCO3, 5 MM MGCL2, 50 UM 2-CABP, 18 DEG C, 10-15 MG/ML PROTEIN
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-15 mg/mlprotein1drop
250 mMHEPES1reservoir
38-12 %PEG40001reservoir
450 mM1reservoirNaHCO3
55 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorDate: Jun 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.4→100 Å / Num. obs: 469880 / % possible obs: 97 % / Redundancy: 4 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 21.7
Reflection shellResolution: 1.4→1.43 Å / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 2.6 / % possible all: 94
Reflection
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 100 Å / Num. obs: 30387 / % possible obs: 97 % / Num. measured all: 469880
Reflection shell
*PLUS
Highest resolution: 1.4 Å / % possible obs: 94 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 8RUC

8ruc


Resolution: 1.4→20 Å / SU B: 9.7 / SU ML: 0.38 / Cross valid method: THROUGHOUT / ESU R Free: 0.05
Details: CONTRIBUTION FOR RIDING HYDROGENS ADDED DURING LAST CYCLE. THE SMALL SUBUNIT C TERMINUS IS DISORDERED BEYOND RESIDUE 126. THE LARGE SUBUNIT N-TERMINI ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.162 23546 5 %RANDOM
Rwork0.149 ---
obs0.149 467822 97 %-
Refinement stepCycle: LAST / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18687 0 220 2556 21463
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 13.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.007
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.3

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