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- PDB-3rub: CRYSTAL STRUCTURE OF THE UNACTIVATED FORM OF RIBULOSE-1,5-BISPHOS... -

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Entry
Database: PDB / ID: 3rub
TitleCRYSTAL STRUCTURE OF THE UNACTIVATED FORM OF RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE FROM TOBACCO REFINED AT 2.0-ANGSTROMS RESOLUTION
Components(RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE, FORM III) x 2
KeywordsLYASE(CARBON-CARBON)
Function / homology
Function and homology information


photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / plasmodesma / 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 / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / 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 / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase, large subunit, C-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
ASPARAGINE / Ribulose bisphosphate carboxylase large chain / Ribulose bisphosphate carboxylase small subunit, chloroplastic
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsSchreuder, H. / Cascio, D. / Curmi, P.M.G. / Chapman, M.S. / Suh, S.W. / Eisenberg, D.S.
Citation
Journal: J.Biol.Chem. / Year: 1992
Title: Crystal structure of the unactivated form of ribulose-1,5-bisphosphate carboxylase/oxygenase from tobacco refined at 2.0-A resolution.
Authors: Curmi, P.M. / Cascio, D. / Sweet, R.M. / Eisenberg, D. / Schreuder, H.
#1: Journal: To be Published
Title: Crystal Structure of the Inactive Form of Ribulose-1,5-Bisphosphate Carboxylase(Slash)Oxygenase (Rubis/Co): Disulfide Bonds and Active Site Region
Authors: Schreuder, H. / Curmi, P.M.G. / Cascio, D. / Eisenberg, D.
#2: Journal: Science / Year: 1988
Title: Tertiary Structure of Plant Rubis/Co: Domains and Their Contacts
Authors: Chapman, M.S. / Suh, S.W. / Curmi, P.M.G. / Cascio, D. / Smith, W.W. / Eisenberg, D.S.
#3: Journal: Nature / Year: 1987
Title: Sliding-Layer Conformational Change Limited by the Quaternary Structure of Plant Rubis/Co
Authors: Chapman, M.S. / Suh, S.W. / Cascio, D. / Smith, W.W. / 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 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE, FORM III
S: RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE, FORM III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0356
Polymers67,6152
Non-polymers4204
Water3,891216
1
L: RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE, FORM III
S: RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE, FORM III
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)544,28148
Polymers540,91916
Non-polymers3,36232
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_656-x+1,y,-z+11
crystal symmetry operation6_566x,-y+1,-z+11
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area95280 Å2
ΔGint-696 kcal/mol
Surface area120450 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)148.700, 148.700, 137.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Atom site foot note1: PRO L 176 IS A CIS PROLINE.
2: RESIDUES 90 - 96 AND 330 - 340 OF THE LARGE SUBUNIT AND RESIDUES 104 - 110 OF THE SMALL SUBUNIT HAVE VERY HIGH TEMPERATURE FACTORS.
3: MET L 405 WAS MODELED AS GLY, THEREFORE NO SIDECHAIN COORDINATES ARE PRESENTED FOR THIS RESIDUE.
Components on special symmetry positions
IDModelComponents
11L-514-

HOH

21L-518-

HOH

31L-539-

HOH

41L-604-

HOH

51L-665-

HOH

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Components

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


Mass: 53041.234 Da / Num. of mol.: 1
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 III


Mass: 14573.587 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
References: UniProt: P69249, ribulose-bisphosphate carboxylase
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ASN / ASPARAGINE


Type: L-peptide linking / Mass: 132.118 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8N2O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHERE ARE SALT BRIDGES BETWEEN THE FOLLOWING ATOMS AND SYMMETRY RELATED ATOMS. (THE 'A' AND 'D' ...THERE ARE SALT BRIDGES BETWEEN THE FOLLOWING ATOMS AND SYMMETRY RELATED ATOMS. (THE 'A' AND 'D' DENOTE ACCEPTOR AND DONOR RESPECTIVELY). ATOM 1 ATOM 2 OE1 GLU L 109 (A) NH1 ARG S 53 (D) OE1 GLU L 110 (A) NH1 ARG L 213 (D) THE COORDINATES OF THIS SYMMETRY RELATED ATOM 2 CAN BE OBTAINED FROM THE COORDINATES IN THIS ENTRY BY THE FOLLOWING TRANSFORMATION: 0 1 0 0 1 0 0 + 0 0 0 -1 137.5 ATOM 1 ATOM 2 OE2 GLU L 110 NZ LYS L 146 THE COORDINATES OF THIS SYMMETRY RELATED ATOM 2 CAN BE OBTAINED FROM THE COORDINATES IN THIS ENTRY BY THE FOLLOWING TRANSFORMATION: -1 0 0 148.7 0 1 0 + 0 0 0 -1 137.5 ATOM 1 ATOM 2 NZ LYS L 161 (D) OD1 ASP L 216 (A) NH1 ARG L 258 (D) OE1 GLU L 59 (A) THE COORDINATES OF THIS SYMMETRY RELATED ATOM 2 CAN BE OBTAINED FROM THE COORDINATES IN THIS ENTRY BY THE FOLLOWING TRANSFORMATION: 0 -1 0 148.7 1 0 0 + 0 0 0 1 0 ATOM 1 ATOM 2 NH1 ARG L 187 (D) OE1 GLU S 43 (A) OE1 GLU L 223 (A) NH2 ARG S 65 (D) NZ LYS L 252 (D) OD2 ASP L 286 (A) THE COORDINATES OF THIS SYMMETRY RELATED ATOM 2 CAN BE OBTAINED FROM THE COORDINATES IN THIS ENTRY BY THE FOLLOWING TRANSFORMATION: 1 0 0 0 0 -1 0 + 148.7 0 0 1 0
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.21 %
Crystal grow
*PLUS
pH: 7.2 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
250 mMphosphate1drop
30.5 mMEDTA1drop
40.1 mMazide1drop
50.2 Mphosphate1reservoir
60.3 M1reservoir(NH4)2SO4
71 mMazide1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 43733 / % possible obs: 84.1 % / Rmerge(I) obs: 0.088
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.1 Å / Rmerge(I) obs: 0.214

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementResolution: 2→8 Å
Details: RESIDUES 64-68 OF THE LARGE SUBUNIT ARE COMPLETELY DISORDERED. NO COORDINATES ARE PRESENTED FOR THESE RESIDUES. RESIDUES 90 - 96 AND 330 - 340 OF THE LARGE SUBUNIT AND RESIDUES 104 - 110 OF ...Details: RESIDUES 64-68 OF THE LARGE SUBUNIT ARE COMPLETELY DISORDERED. NO COORDINATES ARE PRESENTED FOR THESE RESIDUES. RESIDUES 90 - 96 AND 330 - 340 OF THE LARGE SUBUNIT AND RESIDUES 104 - 110 OF THE SMALL SUBUNIT HAVE VERY HIGH TEMPERATURE FACTORS.
RfactorNum. reflection
all0.194 47792
obs0.171 43088
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4484 0 16 216 4716
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.019
X-RAY DIFFRACTIONp_angle_deg3.2
Refinement
*PLUS
σ(I): 1 / Rfactor all: 0.194 / Rfactor obs: 0.171
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.030.045
X-RAY DIFFRACTIONp_planar_d0.040.054
X-RAY DIFFRACTIONp_plane_restr0.020.016
X-RAY DIFFRACTIONp_chiral_restr0.150.165
X-RAY DIFFRACTIONp_mcbond_it11.569
X-RAY DIFFRACTIONp_scbond_it24.445
X-RAY DIFFRACTIONp_mcangle_it1.52.669
X-RAY DIFFRACTIONp_scangle_it36.975

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