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- PDB-5wsk: Structure of Ribulose-1,5-bisphosphate carboxylase/oxygenase from... -

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Basic information

Entry
Database: PDB / ID: 5wsk
TitleStructure of Ribulose-1,5-bisphosphate carboxylase/oxygenase from wheat
Components
  • Ribulose bisphosphate carboxylase large chain
  • Ribulose bisphosphate carboxylase small chain
KeywordsLYASE / Activited Rubisco / wheat
Function / homology
Function and homology information


photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / chloroplast / monooxygenase activity / 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
Ribulose bisphosphate carboxylase large chain / Ribulose bisphosphate carboxylase small chain
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.781 Å
AuthorsMa, Y. / Liu, C.
CitationJournal: To Be Published
Title: Structure of Ribulose-1,5-bisphosphate carboxylase/oxygenase from wheat
Authors: Ma, Y. / Liu, C.
History
DepositionDec 7, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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
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.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
Revision 1.2Nov 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

Downloads & links

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Assembly

Deposited unit
A: Ribulose bisphosphate carboxylase large chain
B: Ribulose bisphosphate carboxylase large chain
C: Ribulose bisphosphate carboxylase large chain
D: Ribulose bisphosphate carboxylase large chain
E: Ribulose bisphosphate carboxylase small chain
F: Ribulose bisphosphate carboxylase small chain
H: Ribulose bisphosphate carboxylase small chain
G: Ribulose bisphosphate carboxylase small chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)289,99512
Polymers289,8988
Non-polymers974
Water31,2021732
1
A: Ribulose bisphosphate carboxylase large chain
B: Ribulose bisphosphate carboxylase large chain
E: Ribulose bisphosphate carboxylase small chain
F: Ribulose bisphosphate carboxylase small chain
hetero molecules

A: Ribulose bisphosphate carboxylase large chain
B: Ribulose bisphosphate carboxylase large chain
E: Ribulose bisphosphate carboxylase small chain
F: Ribulose bisphosphate carboxylase small chain
hetero molecules

A: Ribulose bisphosphate carboxylase large chain
B: Ribulose bisphosphate carboxylase large chain
E: Ribulose bisphosphate carboxylase small chain
F: Ribulose bisphosphate carboxylase small chain
hetero molecules

A: Ribulose bisphosphate carboxylase large chain
B: Ribulose bisphosphate carboxylase large chain
E: Ribulose bisphosphate carboxylase small chain
F: Ribulose bisphosphate carboxylase small chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)579,99024
Polymers579,79616
Non-polymers1948
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area95260 Å2
ΔGint-413 kcal/mol
Surface area119860 Å2
MethodPISA
2
C: Ribulose bisphosphate carboxylase large chain
D: Ribulose bisphosphate carboxylase large chain
H: Ribulose bisphosphate carboxylase small chain
G: Ribulose bisphosphate carboxylase small chain
hetero molecules

C: Ribulose bisphosphate carboxylase large chain
D: Ribulose bisphosphate carboxylase large chain
H: Ribulose bisphosphate carboxylase small chain
G: Ribulose bisphosphate carboxylase small chain
hetero molecules

C: Ribulose bisphosphate carboxylase large chain
D: Ribulose bisphosphate carboxylase large chain
H: Ribulose bisphosphate carboxylase small chain
G: Ribulose bisphosphate carboxylase small chain
hetero molecules

C: Ribulose bisphosphate carboxylase large chain
D: Ribulose bisphosphate carboxylase large chain
H: Ribulose bisphosphate carboxylase small chain
G: Ribulose bisphosphate carboxylase small chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)579,99024
Polymers579,79616
Non-polymers1948
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 area94720 Å2
ΔGint-434 kcal/mol
Surface area119900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.720, 110.720, 200.956
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

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Components

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


Mass: 52963.020 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
References: UniProt: P11383, ribulose-bisphosphate carboxylase
#2: Protein
Ribulose bisphosphate carboxylase small chain


Mass: 19511.484 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
References: UniProt: W5F0E6, ribulose-bisphosphate carboxylase
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1732 / 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: 2.13 Å3/Da / Density % sol: 42.24 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M Tris-HCl, pH 8.5, 12.5% PEG 3350

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Nov 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.78→44.415 Å / Num. obs: 226185 / % possible obs: 98.39 % / Redundancy: 1 % / Net I/σ(I): 1.34

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UZH

1uzh


Resolution: 1.781→44.415 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1874 11328 5.01 %
Rwork0.1545 --
obs0.1562 226185 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.781→44.415 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17745 0 4 1732 19481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01218299
X-RAY DIFFRACTIONf_angle_d1.33324822
X-RAY DIFFRACTIONf_dihedral_angle_d13.2236640
X-RAY DIFFRACTIONf_chiral_restr0.0542625
X-RAY DIFFRACTIONf_plane_restr0.0083225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7809-1.80110.25463330.22596597X-RAY DIFFRACTION92
1.8011-1.82230.27673780.22117111X-RAY DIFFRACTION97
1.8223-1.84450.25033880.20957089X-RAY DIFFRACTION97
1.8445-1.86790.25183810.20266998X-RAY DIFFRACTION98
1.8679-1.89250.2433160.19637135X-RAY DIFFRACTION98
1.8925-1.91840.24553880.18967117X-RAY DIFFRACTION98
1.9184-1.94580.22143760.18287125X-RAY DIFFRACTION98
1.9458-1.97480.23194000.17237107X-RAY DIFFRACTION98
1.9748-2.00570.21433570.16947134X-RAY DIFFRACTION98
2.0057-2.03860.2193910.17137085X-RAY DIFFRACTION98
2.0386-2.07370.20493970.16167124X-RAY DIFFRACTION98
2.0737-2.11140.20683580.16737199X-RAY DIFFRACTION98
2.1114-2.1520.19213950.15887116X-RAY DIFFRACTION99
2.152-2.1960.19753690.15467210X-RAY DIFFRACTION99
2.196-2.24370.1973940.15097161X-RAY DIFFRACTION99
2.2437-2.29590.18023880.14657210X-RAY DIFFRACTION99
2.2959-2.35330.17193680.14397171X-RAY DIFFRACTION99
2.3533-2.41690.183470.14127255X-RAY DIFFRACTION99
2.4169-2.48810.17673620.13987203X-RAY DIFFRACTION99
2.4881-2.56840.18953680.13987246X-RAY DIFFRACTION99
2.5684-2.66010.17544010.13877204X-RAY DIFFRACTION99
2.6601-2.76660.17463880.14017219X-RAY DIFFRACTION99
2.7666-2.89250.1743710.14527198X-RAY DIFFRACTION99
2.8925-3.0450.183840.14757240X-RAY DIFFRACTION99
3.045-3.23570.19473640.15767285X-RAY DIFFRACTION99
3.2357-3.48550.18993930.1547248X-RAY DIFFRACTION99
3.4855-3.8360.15334170.14117218X-RAY DIFFRACTION100
3.836-4.39070.15743700.13257282X-RAY DIFFRACTION100
4.3907-5.53020.16443800.13967283X-RAY DIFFRACTION99
5.5302-44.4290.19064060.17637287X-RAY DIFFRACTION99

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