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- PDB-5rub: CRYSTALLOGRAPHIC REFINEMENT AND STRUCTURE OF RIBULOSE-1,5-BISPHOS... -

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Basic information

Entry
Database: PDB / ID: 5rub
TitleCRYSTALLOGRAPHIC REFINEMENT AND STRUCTURE OF RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE FROM RHODOSPIRILLUM RUBRUM AT 1.7 ANGSTROMS RESOLUTION
ComponentsRUBISCO (RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE)
KeywordsLYASE(CARBON-CARBON)
Function / homology
Function and homology information


ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / magnesium ion binding
Similarity search - Function
Ribulose bisphosphate carboxylase large subunit, type II / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / 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 ...Ribulose bisphosphate carboxylase large subunit, type II / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / 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
Ribulose bisphosphate carboxylase
Similarity search - Component
Biological speciesRhodospirillum rubrum (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsSchneider, G. / Lindqvist, Y. / Lundqvist, T.
Citation
Journal: J.Mol.Biol. / Year: 1990
Title: Crystallographic refinement and structure of ribulose-1,5-bisphosphate carboxylase from Rhodospirillum rubrum at 1.7 A resolution.
Authors: Schneider, G. / Lindqvist, Y. / Lundqvist, T.
#1: Journal: Biochemistry / Year: 1991
Title: Crystal Structure of the Ternary Complex of Ribulose-1,5-Bisphosphate Carboxylase, Mg(II), and Activator Co2 at 2.3-Angstroms Resolution
Authors: Lundqvist, T. / Schneider, G.
#2: Journal: J.Biol.Chem. / Year: 1989
Title: Crystal Structure of the Complex of Ribulose-1,5-Bisphosphate Carboxylase and a Transition State Analogue, 2-Carboxy-D-Arabinitol 1,5-Bisphosphate
Authors: Lundqvist, T. / Schneider, G.
#3: 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.
#4: Journal: J.Biol.Chem. / Year: 1988
Title: Crystal Structure of the Binary Complex of Ribulose-1,5-Bisphosphate Carboxylase and its Product, 3-Phospho-D-Glycerate
Authors: Lundqvist, T. / Schneider, G.
#5: Journal: Embo J. / Year: 1986
Title: Three-Dimensional Structure of Ribulose-1,5-Bisphosphate Carboxylase(Slash)Oxygenase from Rhodospirillum Rubrum at 2.9 Angstroms Resolution
Authors: Schneider, G. / Lindqvist, Y. / Branden, C.-I. / Lorimer, G.
History
DepositionMay 29, 1990Processing site: BNL
SupersessionOct 15, 1991ID: 2RUB
Revision 1.0Oct 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Mar 6, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 700SHEET THE SHEETS PRESENTED AS *ACT* AND *BCT* ON SHEET RECORDS BELOW ARE ACTUALLY EIGHT-STRANDED ...SHEET THE SHEETS PRESENTED AS *ACT* AND *BCT* ON SHEET RECORDS BELOW ARE ACTUALLY EIGHT-STRANDED BETA-BARRELS. THIS IS REPRESENTED BY A NINE-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RUBISCO (RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE)
B: RUBISCO (RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE)


Theoretical massNumber of molelcules
Total (without water)106,5382
Polymers106,5382
Non-polymers00
Water13,259736
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-26 kcal/mol
Surface area29990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.500, 70.600, 104.100
Angle α, β, γ (deg.)90.00, 92.10, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUES PRO A 167 AND PRO B 167 ARE CIS PROLINES.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.37374, -0.056207, 0.940855), (-0.0734, -0.9968, -0.033512), (0.909789, -0.054363, -0.37674)
Vector: 6.14161, 17.878, -7.57091)

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Components

#1: Protein RUBISCO (RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE)


Mass: 53268.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (bacteria)
References: UniProt: P04718, ribulose-bisphosphate carboxylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 736 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.49 %
Crystal grow
*PLUS
Temperature: 4,20 ℃ / Method: microdialysis / PH range low: 5.8 / PH range high: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.05 MMES11
210 mM11Mg2+
31 mMdithiothreitol11
40.1 mMEDTA11

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Data collection

Reflection
*PLUS
Highest resolution: 1.7 Å / Num. obs: 76719 / Num. measured all: 183490 / Rmerge(I) obs: 0.083

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.7→5.5 Å / σ(F): 0 /
RfactorNum. reflection
obs0.18 76452
Refinement stepCycle: LAST / Resolution: 1.7→5.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6641 0 0 736 7377
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.02
X-RAY DIFFRACTIONp_angle_d0.0470.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.050.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.9581
X-RAY DIFFRACTIONp_mcangle_it1.6821.5
X-RAY DIFFRACTIONp_scbond_it0.9441
X-RAY DIFFRACTIONp_scangle_it1.6471.5
X-RAY DIFFRACTIONp_plane_restr0.0130.02
X-RAY DIFFRACTIONp_chiral_restr0.1630.15
X-RAY DIFFRACTIONp_singtor_nbd0.1960.5
X-RAY DIFFRACTIONp_multtor_nbd0.2560.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2830.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.33
X-RAY DIFFRACTIONp_staggered_tor19.915
X-RAY DIFFRACTIONp_orthonormal_tor31.820
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 5.5 Å / Num. reflection obs: 76452 / σ(F): 1 / Rfactor obs: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 45.9 Å2

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