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- PDB-4rub: A CRYSTAL FORM OF RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE(SLASH)OXY... -

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Basic information

Entry
Database: PDB / ID: 4rub
TitleA CRYSTAL FORM OF RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE FROM NICOTIANA TABACUM IN THE ACTIVATED STATE
Components(RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (FORM IV)) x 2
KeywordsLYASE(CARBON-CARBON)
Function / homology
Function and homology information


photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / plasmodesma / reductive pentose-phosphate cycle / chloroplast / monooxygenase activity / defense response to virus / magnesium ion binding
Similarity search - Function
Ribulose-1,5-bisphosphate carboxylase small subunit, N-terminal / Ribulose-1,5-bisphosphate carboxylase small subunit / 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-1,5-bisphosphate carboxylase small subunit, N-terminal / Ribulose-1,5-bisphosphate carboxylase small subunit / 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 / FORMIC ACID / Ribulose bisphosphate carboxylase large chain / Ribulose bisphosphate carboxylase small subunit, chloroplastic
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsSchreuder, H. / Cascio, D. / Curmi, P.M.G. / Eisenberg, D.
CitationJournal: J.Mol.Biol. / Year: 1987
Title: A crystal form of ribulose-1,5-bisphosphate carboxylase/oxygenase from Nicotiana tabacum in the activated state.
Authors: Suh, S.W. / Cascio, D. / Chapman, M.S. / Eisenberg, D.
History
DepositionMay 25, 1990Processing site: BNL
Revision 1.0Oct 15, 1992Provider: 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 / pdbx_struct_conn_angle / 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 / _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.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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 (FORM IV)
S: RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (FORM IV)
B: RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (FORM IV)
T: RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (FORM IV)
C: RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (FORM IV)
U: RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (FORM IV)
D: RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (FORM IV)
V: RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (FORM IV)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)271,58020
Polymers269,8748
Non-polymers1,70612
Water00
1
A: RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (FORM IV)
S: RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (FORM IV)
B: RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (FORM IV)
T: RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (FORM IV)
C: RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (FORM IV)
U: RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (FORM IV)
D: RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (FORM IV)
V: RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (FORM IV)
hetero molecules

A: RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (FORM IV)
S: RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (FORM IV)
B: RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (FORM IV)
T: RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (FORM IV)
C: RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (FORM IV)
U: RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (FORM IV)
D: RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (FORM IV)
V: RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (FORM IV)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)543,16040
Polymers539,74916
Non-polymers3,41224
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area110320 Å2
ΔGint-528 kcal/mol
Surface area117040 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)204.600, 204.600, 117.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Atom site foot note1: PRO 176 IN EACH OF THE LARGE CHAINS IS A CIS PROLINE.
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-1), (-0.8131, 0.5821), (0.5821, 0.8131)154, -22.78, 7.31
2given(-1), (-0.5821, -0.8131), (-0.8131, 0.5821)154, 31.82, 16.36
DetailsTHE FOLLOWING TRANSFORMATION GENERATES APPROXIMATE COORDINATES OF LARGE CHAIN *B* WHEN APPLIED TO CHAIN *A* AND THE SMALL CHAIN *T* WHEN APPLIED TO CHAIN *S*: 1.0 0.0 0.0 0.0 0.0 0.0 1.0 + -39.13 0.0 -1.0 0.0 39.13 THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS EIGHT LARGE AND EIGHT SMALL SUBUNITS. COORDINATES ARE PRESENTED IN THIS ENTRY FOR FOUR LARGE SUBUNITS WITH CHAIN IDENTIFIERS *A*-*D* AND FOUR SMALL SUBUNITS WITH CHAIN IDENTIFIERS *S*-*V*. THE FOLLOWING TRANSFORMATION GENERATES THE COORDINATES OF THE REMAINING HALF-MOLECULE FROM THE COORDINATES OF THE HALF-MOLECULE PRESENTED IN THIS ENTRY. 1.0 0.0 0.0 0.0 0.0 -1.0 0.0 + 0.0 0.0 0.0 -1.0 78.27 THE TRANSFORMATION PRESENTED IN MTRIX 1 RECORDS GENERATES THE LARGE SUBUNIT *C* WHEN APPLIED TO CHAIN *A* AND GENERATES THE SMALL SUBUNIT *U* WHEN APPLIED TO CHAIN *S*. THE TRANSFORMATION PRESENTED IN MTRIX 2 RECORDS GENERATES THE LARGE SUBUNIT *D* WHEN APPLIED TO CHAIN *A* AND GENERATES THE SMALL SUBUNIT *V* WHEN APPLIED TO CHAIN *S*.

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Components

#1: Protein
RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (FORM IV)


Mass: 52967.090 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana tabacum (common tobacco)
References: UniProt: P00876, ribulose-bisphosphate carboxylase
#2: Protein
RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (FORM IV)


Mass: 14501.524 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana tabacum (common tobacco)
References: UniProt: P69249, 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: saccharide / Mass: 356.115 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O13P2
#5: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
Compound detailsTHE FOLLOWING SALT BRIDGES EXIST BETWEEN ATOMS WITH COORDINATES IN THE ATOM RECORDS PRESENTED IN ...THE FOLLOWING SALT BRIDGES EXIST BETWEEN ATOMS WITH COORDINATES IN THE ATOM RECORDS PRESENTED IN THIS ENTRY AND ATOMS IN THE SYMMETRY RELATED MOLECULES, WHERE THE SYMMETRY TRANSFORMATION IS GIVEN IN REMARK 7 ABOVE. THE SYMMETRY RELATED CHAIN INDICATOR IS INDICATED WITH '*'. OE2 GLU A 110 NZ LYS C* 146 OE2 GLU C 110 NZ LYS A* 146 NZ LYS A 161 OD1 ASP B* 216 NZ LYS C 161 OD1 ASP D* 216 NZ LYS B 252 OD1 ASP A* 286 NZ LYS D 252 OD1 ASP C* 286 NH1 ARG A 258 OE2 GLU B* 259 NH1 ARG C 258 OE2 GLU D* 259

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.18 %
Crystal grow
*PLUS
pH: 8.3 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
114.8 mg/mlenzyme 1drop
233.8 mMTris-HCl1drop
347.5 mM1dropNaCl
49.5 mM1dropMgCl2
518 mM1dropNaHCO3
60.95 mM1dropNaN3
74.9 %(w/v)PEG80001drop
80.5 %(w/v)beta-octyl glucoside1drop
912.8-13.0 %(w/v)PEG80001reservoir
1050 mMTris-HCl1reservoir
1150 mM1reservoirNaCl
1210 mM1reservoirMgCl2
1320 mM1reservoirNaHCO3
141 mM1reservoirNaN3

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementRfactor obs: 0.202 / Highest resolution: 2.7 Å
Refinement stepCycle: LAST / Highest resolution: 2.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18608 0 100 0 18708
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.019
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg3.2
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

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