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- PDB-3kdn: Crystal structure of Type III Rubisco SP4 mutant complexed with 2-CABP -

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Basic information

Entry
Database: PDB / ID: 3kdn
TitleCrystal structure of Type III Rubisco SP4 mutant complexed with 2-CABP
ComponentsRibulose bisphosphate carboxylase
KeywordsLYASE / ribulose-1 / 5-bisphosphate carboxylase/oxygenase / Rubisco / Carbon dioxide fixation / Magnesium / Metal-binding / Monooxygenase
Function / homology
Function and homology information


AMP catabolic process / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / carbon fixation / oxidoreductase activity / magnesium ion binding
Similarity search - Function
Ribulose bisphosphate carboxylase, type III / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / 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 ...Ribulose bisphosphate carboxylase, type III / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / 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
Similarity search - Component
Biological speciesThermococcus kodakaraensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsNishitani, Y. / Fujihashi, M. / Doi, T. / Yoshida, S. / Atomi, H. / Imanaka, T. / Miki, K.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structure-based catalytic optimization of a type III Rubisco from a hyperthermophile
Authors: Nishitani, Y. / Yoshida, S. / Fujihashi, M. / Kitagawa, K. / Doi, T. / Atomi, H. / Imanaka, T. / Miki, K.
History
DepositionOct 23, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_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_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribulose bisphosphate carboxylase
B: Ribulose bisphosphate carboxylase
C: Ribulose bisphosphate carboxylase
D: Ribulose bisphosphate carboxylase
E: Ribulose bisphosphate carboxylase
F: Ribulose bisphosphate carboxylase
G: Ribulose bisphosphate carboxylase
H: Ribulose bisphosphate carboxylase
I: Ribulose bisphosphate carboxylase
J: Ribulose bisphosphate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)502,28930
Polymers498,48510
Non-polymers3,80420
Water47,7762652
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area62460 Å2
ΔGint-386 kcal/mol
Surface area125400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.474, 246.241, 133.080
Angle α, β, γ (deg.)90.00, 104.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ribulose bisphosphate carboxylase / RuBisCO


Mass: 49848.477 Da / Num. of mol.: 10 / Mutation: G326E, K327R, W328D, D329I, V330T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakaraensis (archaea) / Strain: KOD1 / Gene: rbcL, TK2290 / Plasmid: pET-21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS
References: UniProt: O93627, ribulose-bisphosphate carboxylase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#3: Sugar
ChemComp-CAP / 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE


Type: saccharide / Mass: 356.115 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H14O13P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2652 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M Acetate, 80mM CaCl2, 6% PEG6000, 10% MPD, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 3, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 345208 / % possible obs: 96.5 % / Rsym value: 0.071 / Net I/σ(I): 15.4
Reflection shellResolution: 2.09→2.13 Å / Mean I/σ(I) obs: 2.3 / Rsym value: 0.384 / % possible all: 70.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0066refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GEH

1geh


Resolution: 2.09→42.86 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.905 / SU B: 4.808 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25286 17388 5 %RANDOM
Rwork0.21261 ---
obs0.21463 327701 96.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.249 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20 Å2-2.43 Å2
2---1.66 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 2.09→42.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34127 0 220 2652 36999
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.02235203
X-RAY DIFFRACTIONr_angle_refined_deg0.7681.96147816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.69654361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.02123.4411607
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.054155593
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.06415229
X-RAY DIFFRACTIONr_chiral_restr0.0530.25093
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02127095
X-RAY DIFFRACTIONr_mcbond_it0.2941.521685
X-RAY DIFFRACTIONr_mcangle_it0.562234534
X-RAY DIFFRACTIONr_scbond_it0.786313518
X-RAY DIFFRACTIONr_scangle_it1.3444.513282
LS refinement shellResolution: 2.09→2.144 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 954 -
Rwork0.298 17951 -
obs--71.73 %

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