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- PDB-8ruc: ACTIVATED SPINACH RUBISCO COMPLEXED WITH 2-CARBOXYARABINITOL BISP... -

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Basic information

Entry
Database: PDB / ID: 8ruc
TitleACTIVATED SPINACH RUBISCO COMPLEXED WITH 2-CARBOXYARABINITOL BISPHOSPHATE
Components(RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE) x 2
KeywordsLYASE (CARBON-CARBON) / PHOTOSYNTHESIS / CARBON DIOXIDE FIXATION / PHOTORESPIRATION / LYASE / OXIDOREDUCTASE / MONOOXYGENASE / CHLOROPLAST
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, small subunit / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-terminal domain / 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, small subunit / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-terminal domain / 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 speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR STARTING MODEL FOR MOLECULAR REPLACEMENT: NULL / Resolution: 1.6 Å
AuthorsAndersson, I. / Knight, S. / Branden, C.-I.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Large structures at high resolution: the 1.6 A crystal structure of spinach ribulose-1,5-bisphosphate carboxylase/oxygenase complexed with 2-carboxyarabinitol bisphosphate.
Authors: Andersson, I.
#1: Journal: J.Mol.Biol. / Year: 1990
Title: Crystallographic Analysis of Ribulose 1,5-Bisphosphate Carboxylase from Spinach at 2.4 A Resolution
Authors: Knight, S. / Andersson, I. / Branden, C.I.
#2: Journal: Nature / Year: 1989
Title: Crystal Structure of the Active Site of Ribulose-Bisphosphate Carboxylase
Authors: Andersson, I. / Knight, S. / Schneider, G. / Lindqvist, Y. / Lundqvist, T. / Branden, C.-I. / Lorimer, G.H.
#3: Journal: Science / Year: 1989
Title: Reexamination of the Three-Dimensional Structure of the Small Subunit of Rubisco from Higher Plants
Authors: Knight, S. / Andersson, I. / Branden, C.-I.
History
DepositionFeb 22, 1996Processing site: BNL
SupersessionAug 1, 1996ID: 8RUB
Revision 1.0Aug 1, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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_ref_seq_dif.details / _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
C: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
E: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
G: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
I: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
J: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
K: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
L: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)271,47516
Polymers269,9548
Non-polymers1,5228
Water27,3831520
1
A: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
C: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
E: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
G: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
I: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
J: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
K: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
L: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
hetero molecules

A: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
C: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
E: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
G: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
I: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
J: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
K: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
L: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)542,95132
Polymers539,90716
Non-polymers3,04316
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area112250 Å2
ΔGint-537 kcal/mol
Surface area120020 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)157.200, 157.200, 201.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsTHE ENZYME IS A HEXADECAMER L8S8 OF EIGHT L (LARGE) SUBUNIT AND 8 S (SMALL) SUBUNITS. THE L SUBUNIT HAS BEEN ASSIGNED CHAIN IDENTIFIERS A, B, C, D, E, F, G, AND H. THE S SUBUNIT HAS BEEN ASSIGNED CHAIN IDENTIFIERS I, J, K, L, M, N, O, AND P. IN THE CATALYTICALLY COMPETENT MOLECULE, DIMERS OF THE LARGE SUBUNITS FORM FUNCTIONAL UNITS. IN REFERENCE 1 THESE DIMERS ARE DESIGNATED *AB*, *CD*, *EF*, AND *GH*. THIS ENTRY PRESENTS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONTAINS HALF THE MOLECULE: FOUR L AND FOUR S SUBUNITS RELATED BY A FOUR-FOLD AXIS THROUGH THE MOLECULAR CENTER AT X=0, Y=1/4, Z=1/4. THE FOUR L CHAINS PRESENT ARE A, C, E, G AND THE FOUR S CHAINS PRESENT ARE I, J, K, L. ALSO INCLUDED ARE FOUR MAGNESIUM IONS, FOUR INHIBITOR MOLECULES (CAP) AND 1520 WATERS.

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Components

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


Mass: 52849.742 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / Organ: LEAF
References: UniProt: P00875, ribulose-bisphosphate carboxylase
#2: Protein
RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE / RUBISCO


Mass: 14638.671 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / Organ: LEAF
References: UniProt: P00870, ribulose-bisphosphate carboxylase
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Sugar
ChemComp-CAP / 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE


Type: saccharideCarbohydrate / Mass: 356.115 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O13P2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1520 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRESIDUE 201 OF THE L SUBUNITS IS A MODIFIED ACTIVATOR LYSINE WHICH IS CARBAMYLATED AT THE EPSILON- ...RESIDUE 201 OF THE L SUBUNITS IS A MODIFIED ACTIVATOR LYSINE WHICH IS CARBAMYLATED AT THE EPSILON-AMINO GROUP. THE MODIFIED LYSINES WITH THEIR CARBAMYL ACTIVATOR GROUP ARE PRESENTED AS HET GROUPS *KCX* OF L CHAINS A, C, E, G.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 40 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Andersson, I., (1983) J. Biol. Chem., 258, 14088. / PH range low: 6 / PH range high: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
20.05 M1dropKH2PO4
38-15 %PEG60001drop
40.05 M1reservoirKH2PO4
58-15 %PEG60001reservoir
60.1 M1reservoirNaCl
1protein1drop

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1.04
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 7, 1990
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 277449 / Redundancy: 4 % / Rmerge(I) obs: 0.069
Reflection shellResolution: 1.6→1.67 Å / % possible all: 49
Reflection
*PLUS
Num. measured all: 1131480

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
WEISdata reduction
SCALEdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR STARTING MODEL FOR MOLECULAR REPLACEMENT: NULL
Resolution: 1.6→7 Å / σ(F): 0
Details: NO ELECTRON DENSITY IS OBSERVED FOR THE FIRST EIGHT RESIDUES OF THE LARGE SUBUNIT. NO COORDINATES ARE PRESENTED FOR THESE RESIDUES. THE ELECTRON DENSITY FOR RESIDUES ALA 9, SER 10 AND VAL 11 ...Details: NO ELECTRON DENSITY IS OBSERVED FOR THE FIRST EIGHT RESIDUES OF THE LARGE SUBUNIT. NO COORDINATES ARE PRESENTED FOR THESE RESIDUES. THE ELECTRON DENSITY FOR RESIDUES ALA 9, SER 10 AND VAL 11 OF THE L SUBUNITS IS WEAK.
RfactorNum. reflection% reflection
Rwork0.211 --
obs0.211 261995 81.7 %
Displacement parametersBiso mean: 15.2 Å2
Refinement stepCycle: LAST / Resolution: 1.6→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18760 0 88 1520 20368
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it13.5
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it15.2
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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