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- PDB-9rub: CRYSTAL STRUCTURE OF ACTIVATED RIBULOSE-1,5-BISPHOSPHATE CARBOXYL... -

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Basic information

Entry
Database: PDB / ID: 9rub
TitleCRYSTAL STRUCTURE OF ACTIVATED RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE COMPLEXED WITH ITS SUBSTRATE, RIBULOSE-1,5-BISPHOSPHATE
ComponentsRIBULOSE-1,5-BISPHOSPHATE CARBOXYLASERuBisCO
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 / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-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 / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-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
FORMIC ACID / RIBULOSE-1,5-DIPHOSPHATE / Ribulose bisphosphate carboxylase
Similarity search - Component
Biological speciesRhodospirillum rubrum (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsLundqvist, T. / Schneider, G.
Citation
Journal: J.Biol.Chem. / Year: 1991
Title: Crystal structure of activated ribulose-1,5-bisphosphate carboxylase complexed with its substrate, ribulose-1,5-bisphosphate.
Authors: Lundqvist, T. / Schneider, G.
#1: Journal: Embo J. / Year: 1990
Title: Comparison of the Crystal Structures of L2 and L8S8 Rubisco Suggests a Functional Role for the Small Subunit
Authors: Schneider, G. / Knight, S. / Andersson, I. / Lindqvist, Y. / Lundqvist, T. / Branden, C.-I.
#2: Journal: J.Mol.Biol. / Year: 1990
Title: Crystallographic Refinement and Structure of Ribulose-1,5-Bisphosphate Carboxylase from Rhodospirillum Rubrum at 1.7 Angstroms Resolution
Authors: Schneider, G. / Lindqvist, Y. / Lundqvist, T.
#3: 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.
#4: Journal: J.Biol.Chem. / Year: 1989
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
DepositionNov 28, 1990Processing site: BNL
Revision 1.0Jan 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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 1.4Feb 24, 2021Group: Advisory / Database references / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_close_contact ...pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_ref_seq_dif / struct_site
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET SHEETS *ACT* AND *BCT* PRESENTED BELOW ARE ACTUALLY EIGHT-STRANDED BETA/ALPHA BARRELS. THESE ...SHEET SHEETS *ACT* AND *BCT* PRESENTED BELOW ARE ACTUALLY EIGHT-STRANDED BETA/ALPHA BARRELS. THESE ARE REPRESENTED AS NINE-STRANDED SHEETS 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: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE
B: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,8398
Polymers101,0782
Non-polymers7616
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8750 Å2
ΔGint-61 kcal/mol
Surface area33330 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 B 167 ARE CIS PROLINES.
2: RESIDUES LYS A 191 AND LYS B 191 ARE CARBAMYLATED AT THE EPSILON-AMINO GROUP.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.37374, -0.056007, 0.940855), (-0.0734, -0.9968, -0.033512), (0.909789, -0.054363, -0.37674)
Vector: 6.14161, 17.878, -7.57091)
DetailsTHE TRANSFORMATION GIVEN ON THE *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO COORDINATES OF CHAIN *B*. RESIDUES 422 - 450 WERE OMITTED WHEN GENERATING THIS TRANSFORMATION MATRIX.

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Components

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


Mass: 50538.918 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: Sugar ChemComp-RUB / RIBULOSE-1,5-DIPHOSPHATE / Ribulose 1,5-bisphosphate


Type: saccharideCarbohydrate / Mass: 310.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H12O11P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.29 %
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: 2.6 Å / Num. obs: 25502 / % possible obs: 82 % / Num. measured all: 47847 / Rmerge(I) obs: 0.083

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.199 / Highest resolution: 2.6 Å
Details: RESIDUES A 191 AND B 191 ARE MODIFIED LYSINES WHICH ARE CARBAMYLATED AT THE EPSILON-AMINO GROUP. THE CARBAMYL GROUPS ARE PRESENTED AS HET GROUPS *CBX* AT THE END OF CHAINS *A* AND *B*.
Refinement stepCycle: LAST / Highest resolution: 2.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7000 0 44 0 7044
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.6
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: X-PLOR/PROLSQ / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / Rfactor obs: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_angle_d / Dev ideal: 2.6

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