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- PDB-4f0k: UNACTIVATED RUBISCO with MAGNESIUM AND CARBON DIOXIDE BOUND -

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Basic information

Entry
Database: PDB / ID: 4f0k
TitleUNACTIVATED RUBISCO with MAGNESIUM AND CARBON DIOXIDE BOUND
Components(Ribulose bisphosphate carboxylase ...RuBisCO) x 2
KeywordsLYASE / ALPHA BETA DOMAIN / CATALYTIC DOMAIN TIM BARREL / CARBOXYLASE/OXYGENASE / NITROSYLATION / CHLOROPLAST
Function / homology
Function and homology information


ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / chloroplast / monooxygenase activity / magnesium ion binding
Similarity search - Function
Ribulose bisphosphate carboxylase, small subunit / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-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, small subunit / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-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
CARBON DIOXIDE / Ribulose bisphosphate carboxylase large chain / Ribulose bisphosphate carboxylase small subunit
Similarity search - Component
Biological speciesGaldieria sulphuraria (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsStec, B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural mechanism of RuBisCO activation by carbamylation of the active site lysine.
Authors: Stec, B.
History
DepositionMay 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_id / _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 bisphosphate carboxylase large chain
B: Ribulose bisphosphate carboxylase small chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7188
Polymers71,3382
Non-polymers3806
Water7,296405
1
A: Ribulose bisphosphate carboxylase large chain
B: Ribulose bisphosphate carboxylase small chain
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)573,74764
Polymers570,70616
Non-polymers3,04048
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_655-x+1,y,-z1
crystal symmetry operation6_565x,-y+1,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area110510 Å2
ΔGint-717 kcal/mol
Surface area125980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.136, 136.136, 121.287
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
11A-503-

GOL

21B-901-

CL

31A-1111-

HOH

41B-1081-

HOH

51B-1126-

HOH

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Components

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Ribulose bisphosphate carboxylase ... , 2 types, 2 molecules AB

#1: Protein Ribulose bisphosphate carboxylase large chain / RuBisCO large subunit


Mass: 55111.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Galdieria sulphuraria (eukaryote)
References: UniProt: P23755, ribulose-bisphosphate carboxylase
#2: Protein Ribulose bisphosphate carboxylase small chain / RuBisCO small subunit


Mass: 16226.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Galdieria sulphuraria (eukaryote)
References: UniProt: P23756, ribulose-bisphosphate carboxylase

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Non-polymers , 5 types, 411 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CO2 / CARBON DIOXIDE / Carbon dioxide


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 405 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 0.05 M potassium phosphate, 26% Ammonium Sulfate, pH 7.5, VAPOR DIFFUSION, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 21, 2004 / Details: confocal
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→96.23 Å / Num. all: 36145 / Num. obs: 35349 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 17.4
Reflection shellResolution: 2.05→2.11 Å / Rmerge(I) obs: 0.611 / % possible all: 94.3

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RUB

3rub


Resolution: 2.05→96.23 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.608 / SU ML: 0.142 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24109 1779 5 %RANDOM
Rwork0.17818 ---
obs0.18134 33570 97.93 %-
all-35349 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.879 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å20 Å2
2---0.45 Å20 Å2
3---0.89 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2.05→96.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4658 0 23 405 5086
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0224790
X-RAY DIFFRACTIONr_angle_refined_deg1.8421.9586474
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7675586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.06523.682220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.82715824
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7011533
X-RAY DIFFRACTIONr_chiral_restr0.1150.2702
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213619
X-RAY DIFFRACTIONr_mcbond_it2.55332917
X-RAY DIFFRACTIONr_mcangle_it3.87544689
X-RAY DIFFRACTIONr_scbond_it3.06631873
X-RAY DIFFRACTIONr_scangle_it4.24541785
LS refinement shellResolution: 2.047→2.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.438 130 -
Rwork0.383 2470 -
obs-2470 98.48 %

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