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- PDB-1ej7: CRYSTAL STRUCTURE OF UNACTIVATED TOBACCO RUBISCO WITH BOUND PHOSP... -

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Basic information

Entry
Database: PDB / ID: 1ej7
TitleCRYSTAL STRUCTURE OF UNACTIVATED TOBACCO RUBISCO WITH BOUND PHOSPHATE IONS
Components
  • RUBISCO (LARGE SUBUNIT)
  • RUBISCO (SMALL SUBUNIT)
KeywordsLYASE / TIM Barrel / alpha/beta barrel
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
PHOSPHATE ION / Ribulose bisphosphate carboxylase large chain / Ribulose bisphosphate carboxylase small subunit, chloroplastic
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / Resolution: 2.45 Å
AuthorsDuff, A.P. / Andrews, T.J. / Curmi, P.M.G.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: The transition between the open and closed states of rubisco is triggered by the inter-phosphate distance of the bound bisphosphate.
Authors: Duff, A.P. / Andrews, T.J. / Curmi, P.M.G.
History
DepositionMar 1, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _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
L: RUBISCO (LARGE SUBUNIT)
S: RUBISCO (SMALL SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5935
Polymers67,3082
Non-polymers2853
Water3,009167
1
L: RUBISCO (LARGE SUBUNIT)
S: RUBISCO (SMALL SUBUNIT)
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)540,74640
Polymers538,46716
Non-polymers2,27924
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 area97740 Å2
ΔGint-508 kcal/mol
Surface area128690 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)149.180, 149.180, 138.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11L-750-

HOH

21L-864-

HOH

31L-873-

HOH

DetailsRubisco is comprised of eight large subunits and eight small subunits. The asymmetric unit contains one large subunit and one small subunit. The other subunits can be obtained by applying crystallographic symmetries on the asymmetric unit. Rubisco is comprised of eight large subunits and eight small subunits. The asymmetric unit contains one large subunit and one small subunit.

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Components

#1: Protein RUBISCO (LARGE SUBUNIT)


Mass: 52734.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / Organ: LEAF / Variant: WISCONSIN-38
References: UniProt: P00876, ribulose-bisphosphate carboxylase
#2: Protein RUBISCO (SMALL SUBUNIT)


Mass: 14573.587 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / Organ: LEAF / Variant: WISCONSIN-38
References: UniProt: P69249, ribulose-bisphosphate carboxylase
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 56.96 %
Crystal growTemperature: 295 K / Method: liquid diffusion / pH: 5.2
Details: 10microL of (tobacco rubisco 20-50mg/ml in (tris-Cl 50mm pH 7.4 at 4degC, MgCl2 20mM, NaHCO3 20mM, EDTA 0.1mM, beta-mercaptoethanol 50mM)) and 35 microL of (K2HPO4 200mM, NH4K2PO4 300mM, ...Details: 10microL of (tobacco rubisco 20-50mg/ml in (tris-Cl 50mm pH 7.4 at 4degC, MgCl2 20mM, NaHCO3 20mM, EDTA 0.1mM, beta-mercaptoethanol 50mM)) and 35 microL of (K2HPO4 200mM, NH4K2PO4 300mM, NaN3, plus HCl to pH 5.2 at 24degC) is sealed, in contact, in a 7mm glass capillary, LIQUID DIFFUSION, temperature 295K
Crystal grow
*PLUS
Temperature: 25 ℃ / Method: liquid-liquid diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.2 M11K2HPO4
20.3 M11NH4H2PO4
4389 mMphosphate11
311NaOH

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12951
22951
32951
42951
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 2.54
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: May 25, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.54 Å / Relative weight: 1
ReflectionResolution: 2.45→20 Å / Num. all: 28862 / Num. obs: 27448 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Redundancy: 3.45 % / Biso Wilson estimate: 35.7 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 12
Reflection shellResolution: 2.45→2.54 Å / Rmerge(I) obs: 0.339 / % possible all: 92.2
Reflection shell
*PLUS
% possible obs: 92.2 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.843refinement
X-PLORphasing
RefinementResolution: 2.45→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.197 1372 Random
Rwork0.149 --
all-28862 -
obs-27448 -
Refinement stepCycle: LAST / Resolution: 2.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4608 0 15 167 4790
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 35.7 Å2
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scangle_it

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