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- PDB-1rlc: CRYSTAL STRUCTURE OF THE UNACTIVATED RIBULOSE 1, 5-BISPHOSPHATE C... -

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Basic information

Entry
Database: PDB / ID: 1rlc
TitleCRYSTAL STRUCTURE OF THE UNACTIVATED RIBULOSE 1, 5-BISPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE COMPLEXED WITH A TRANSITION STATE ANALOG, 2-CARBOXY-D-ARABINITOL 1,5-BISPHOSPHATE
Components
  • RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE CHAIN)
  • RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (SMALL CHAIN)
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
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE / : / 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
AuthorsZhang, K.Y.J. / Cascio, D. / Eisenberg, D.
Citation
Journal: Protein Sci. / Year: 1994
Title: Crystal structure of the unactivated ribulose 1,5-bisphosphate carboxylase/oxygenase complexed with a transition state analog, 2-carboxy-D-arabinitol 1,5-bisphosphate.
Authors: Zhang, K.Y. / Cascio, D. / Eisenberg, D.
#1: Journal: J.Biol.Chem. / Year: 1992
Title: Crystal Structure of the Unactivated Form of Ribulose-1,5-Bisphosphate Carboxylase(Slash)Oxygenase from Tobacco Refined at 2.0 Angstroms Resolution
Authors: Curmi, P.M.G. / Cascio, D. / Sweet, R.M. / Eisenberg, D. / Schreuder, H.
#2: Journal: Science / Year: 1988
Title: Tertiary Structure of Plant Rubisco: Domains and Their Contacts
Authors: Chapman, M.S. / Suh, S.W. / Curmi, P.M.G. / Cascio, D. / Smith, W.W. / Eisenberg, D.
#3: Journal: Nature / Year: 1987
Title: Sliding-Layer Conformational Change Limited by the Quaternary Structure of Plant Rubisco
Authors: Chapman, M.S. / Suh, S.W. / Cascio, D. / Smith, W.W. / Eisenberg, D.
History
DepositionAug 4, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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 (LARGE CHAIN)
S: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (SMALL CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8973
Polymers67,5412
Non-polymers3561
Water00
1
L: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE CHAIN)
S: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (SMALL CHAIN)
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)543,17424
Polymers540,32516
Non-polymers2,8498
Water0
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 area92770 Å2
ΔGint-347 kcal/mol
Surface area121340 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)149.000, 149.000, 136.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Atom site foot note1: PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION GLN L 45 - PRO L 46 OMEGA ANGLE = 112.902
2: RESIDUES VAL L 90 - GLN L 96, THR L 330 - ASP L 340, AND PHE S 104 - VAL S 110 HAVE VERY HIGH TEMPERATURE FACTORS.
3: CIS PROLINE - PRO L 176

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Components

#1: Protein RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE CHAIN)


Mass: 52967.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana tabacum (common tobacco)
References: EMBL: Z00044, UniProt: P00876*PLUS, ribulose-bisphosphate carboxylase
#2: Protein RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (SMALL CHAIN)


Mass: 14573.587 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana tabacum (common tobacco)
References: UniProt: P69249, ribulose-bisphosphate carboxylase
#3: Sugar ChemComp-CAP / 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE


Type: saccharide / Mass: 356.115 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O13P2
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: 56.22 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.2 M1reservoirKH2PO4
20.3 Mammonium sulfate1reservoir
31 mM1reservoirNaN3
430-70 %(v/v)rubisco1drop
50.2 M1dropKH2PO4
60.3 Mammonium sulfate1drop
71 mM1dropNaN3

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.7 Å / Num. obs: 19091 / % possible obs: 92 % / Num. measured all: 69151 / Rmerge(I) obs: 0.092

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.196 / Rfactor obs: 0.196 / Highest resolution: 2.7 Å
Details: RESIDUES VAL L 90 - GLN L 96, THR L 330 - ASP L 340, AND PHE S 104 - VAL S 110 HAVE VERY HIGH TEMPERATURE FACTORS.
Refinement stepCycle: LAST / Highest resolution: 2.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4484 0 21 0 4505
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
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_deg3.63
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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