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- PDB-1wdd: Crystal Structure of Activated Rice Rubisco Complexed with 2-Carb... -

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Basic information

Entry
Database: PDB / ID: 1wdd
TitleCrystal Structure of Activated Rice Rubisco Complexed with 2-Carboxyarabinitol-1,5-bisphosphate
Components(Ribulose bisphosphate carboxylase ...RuBisCO) x 2
KeywordsLYASE / Rubisco / Photosynthesis / alpha/beta barrel / N-methylmethionine / Post-translational modification
Function / homology
Function and homology information


photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / plastid / chloroplast / monooxygenase activity / nucleotide binding / 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 / 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-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 / 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
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE / Ribulose bisphosphate carboxylase large chain / Ribulose bisphosphate carboxylase small subunit, chloroplastic 1
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsMizohata, E. / Matsumura, H. / Ueno, T. / Ishida, H. / Inoue, T. / Makino, A. / Mae, T. / Kai, Y.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Crystal structure of rice Rubisco and implications for activation induced by positive effectors NADPH and 6-phosphogluconate
Authors: Matsumura, H. / Mizohata, E. / Ishida, H. / Kogami, A. / Ueno, T. / Makino, A. / Inoue, T. / Yokota, A. / Mae, T. / Kai, Y.
History
DepositionMay 13, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 13, 2012Group: Database references
Revision 1.4Jun 5, 2013Group: Database references
Revision 1.5Oct 25, 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 / 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_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.conn_type_id / _struct_conn.id / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 15, 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 large chain
S: Ribulose bisphosphate carboxylase small chain C
E: Ribulose bisphosphate carboxylase large chain
W: Ribulose bisphosphate carboxylase small chain C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,27325
Polymers135,9474
Non-polymers2,32621
Water17,997999
1
A: Ribulose bisphosphate carboxylase large chain
S: Ribulose bisphosphate carboxylase small chain C
E: Ribulose bisphosphate carboxylase large chain
W: Ribulose bisphosphate carboxylase small chain C
hetero molecules

A: Ribulose bisphosphate carboxylase large chain
S: Ribulose bisphosphate carboxylase small chain C
E: Ribulose bisphosphate carboxylase large chain
W: Ribulose bisphosphate carboxylase small chain C
hetero molecules

A: Ribulose bisphosphate carboxylase large chain
S: Ribulose bisphosphate carboxylase small chain C
E: Ribulose bisphosphate carboxylase large chain
W: Ribulose bisphosphate carboxylase small chain C
hetero molecules

A: Ribulose bisphosphate carboxylase large chain
S: Ribulose bisphosphate carboxylase small chain C
E: Ribulose bisphosphate carboxylase large chain
W: Ribulose bisphosphate carboxylase small chain C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)553,092100
Polymers543,78716
Non-polymers9,30684
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
Buried area131610 Å2
ΔGint-549 kcal/mol
Surface area111360 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)111.713, 111.713, 196.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11S-247-

HOH

21W-937-

HOH

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Components

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Ribulose bisphosphate carboxylase ... , 2 types, 4 molecules AESW

#1: Protein Ribulose bisphosphate carboxylase large chain / Large Subunit of Ribulose-1 / 5-bisphosphate Carboxylase/Oxygenase / RuBisCO large subunit


Mass: 52993.031 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
Tissue: leaves
References: UniProt: P0C512, ribulose-bisphosphate carboxylase
#2: Protein Ribulose bisphosphate carboxylase small chain C / Small Subunit of Ribulose-1 / 5-bisphosphate Carboxylase/Oxygenase / RuBisCO small subunit C


Mass: 14980.304 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
Tissue: leaves
References: UniProt: Q0INY7, ribulose-bisphosphate carboxylase

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Sugars , 1 types, 2 molecules

#4: Sugar ChemComp-CAP / 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE


Type: saccharideCarbohydrate / Mass: 356.115 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O13P2

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Non-polymers , 3 types, 1018 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 999 / 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: 2.26 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Mar 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionBiso Wilson estimate: 17.7 Å2

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IR1

1ir1


Resolution: 1.35→22.32 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 3255293.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.182 12745 5 %RANDOM
Rwork0.16 ---
obs0.16 255778 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 88.9832 Å2 / ksol: 0.413068 e/Å3
Displacement parametersBiso mean: 21.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.24 Å20 Å20 Å2
2--1.24 Å20 Å2
3----2.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.35→22.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9303 0 146 999 10448
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.022
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.43
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.35→1.43 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.338 1825 4.9 %
Rwork0.328 35111 -
obs--84.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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