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- PDB-5iu0: Rubisco from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 5iu0
TitleRubisco from Arabidopsis thaliana
Components(Ribulose bisphosphate carboxylase ...RuBisCO) x 2
KeywordsLYASE / Ribulose-Bisphosphate-Carboxylase / Arabidopsis thaliana
Function / homology
Function and homology information


chloroplast membrane / plastoglobule / photorespiration / thylakoid / ribulose-bisphosphate carboxylase / response to abscisic acid / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / apoplast / chloroplast envelope ...chloroplast membrane / plastoglobule / photorespiration / thylakoid / ribulose-bisphosphate carboxylase / response to abscisic acid / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / apoplast / chloroplast envelope / cell wall / plastid / chloroplast stroma / chloroplast thylakoid membrane / response to cadmium ion / cytosolic ribosome / chloroplast / monooxygenase activity / protein domain specific binding / mRNA 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 1B, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.499 Å
AuthorsValegaard, K. / Hasse, D. / Gunn, L. / Andersson, I.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Structure of Rubisco from Arabidopsis thaliana in complex with 2-carboxyarabinitol-1,5-bisphosphate.
Authors: Valegard, K. / Hasse, D. / Andersson, I. / Gunn, L.H.
History
DepositionMar 17, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.2Feb 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns / reflns_shell / Item: _reflns.pdbx_CC_half / _reflns_shell.pdbx_CC_half
Revision 1.4Jan 10, 2024Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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
J: Ribulose bisphosphate carboxylase small chain 1B, chloroplastic
I: Ribulose bisphosphate carboxylase small chain 1B, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,31221
Polymers146,7444
Non-polymers1,56817
Water18,3211017
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21300 Å2
ΔGint-61 kcal/mol
Surface area37470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.860, 111.860, 197.710
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
11B-974-

HOH

21J-325-

HOH

31I-444-

HOH

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Components

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

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


Mass: 53063.883 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: O03042, ribulose-bisphosphate carboxylase
#2: Protein Ribulose bisphosphate carboxylase small chain 1B, chloroplastic / RuBisCO small subunit 1B


Mass: 20308.262 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: P10796, 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: isolated from a natural source / Formula: C6H14O13P2

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Non-polymers , 3 types, 1032 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1017 / 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: 2.31 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M HEPEs pH 8, 0.1M NaCl, 20% PEG4000, 0.01M NaHCO3, 0.01M MgCl2

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
Reflection twinOperator: -h,k,-l / Fraction: 0.48
ReflectionResolution: 1.499→49.43 Å / Num. obs: 192721 / % possible obs: 99.6 % / Observed criterion σ(I): 1.82 / Redundancy: 5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.101 / Net I/σ(I): 8.94
Reflection shellResolution: 1.499→1.54 Å / Redundancy: 5 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1.82 / CC1/2: 0.439 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8RUC

8ruc


Resolution: 1.499→49.428 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.01 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1524 9659 5.01 %
Rwork0.1358 --
obs0.1448 192721 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.499→49.428 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9294 0 96 1017 10407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069630
X-RAY DIFFRACTIONf_angle_d0.84213047
X-RAY DIFFRACTIONf_dihedral_angle_d15.7093505
X-RAY DIFFRACTIONf_chiral_restr0.0771382
X-RAY DIFFRACTIONf_plane_restr0.0061681
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4995-1.52530.30194820.28129146X-RAY DIFFRACTION94
1.5253-1.55310.29134780.26569076X-RAY DIFFRACTION95
1.5531-1.5830.25544850.24899225X-RAY DIFFRACTION95
1.583-1.61530.2414790.24099095X-RAY DIFFRACTION95
1.6153-1.65040.24564820.2289168X-RAY DIFFRACTION95
1.6504-1.68880.23854820.21899143X-RAY DIFFRACTION95
1.6888-1.7310.21934770.20999080X-RAY DIFFRACTION95
1.731-1.77780.21424810.20359128X-RAY DIFFRACTION94
1.7778-1.83010.19194810.18769141X-RAY DIFFRACTION95
1.8301-1.88920.18154810.17759147X-RAY DIFFRACTION95
1.8892-1.95670.18644810.17399138X-RAY DIFFRACTION95
1.9567-2.03510.17854810.16949143X-RAY DIFFRACTION95
2.0351-2.12770.17974820.16559141X-RAY DIFFRACTION95
2.1277-2.23990.17934820.16259174X-RAY DIFFRACTION95
2.2399-2.38020.16224850.14849201X-RAY DIFFRACTION95
2.3802-2.5640.15714810.14159144X-RAY DIFFRACTION95
2.564-2.8220.1554830.13219184X-RAY DIFFRACTION95
2.822-3.23030.13474830.11589164X-RAY DIFFRACTION95
3.2303-4.06950.12414840.09499202X-RAY DIFFRACTION95
4.0695-48.70450.11054860.09029225X-RAY DIFFRACTION94

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