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- PDB-4w5w: Rubisco activase from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 4w5w
TitleRubisco activase from Arabidopsis thaliana
ComponentsRibulose bisphosphate carboxylase/oxygenase activase, chloroplastic
KeywordsCHAPERONE / Rubisco activase / Photosynthetic carbon fixation
Function / homology
Function and homology information


ribulose-1,5-bisphosphate carboxylase/oxygenase activator activity / stromule / leaf senescence / response to jasmonic acid / plastoglobule / apoplast / thylakoid / cell wall / chloroplast envelope / chloroplast stroma ...ribulose-1,5-bisphosphate carboxylase/oxygenase activator activity / stromule / leaf senescence / response to jasmonic acid / plastoglobule / apoplast / thylakoid / cell wall / chloroplast envelope / chloroplast stroma / chloroplast thylakoid membrane / response to light stimulus / enzyme regulator activity / response to cold / chloroplast / ADP binding / defense response to bacterium / Golgi apparatus / ATP binding / nucleus
Similarity search - Function
Helicase, Ruva Protein; domain 3 - #1070 / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ribulose bisphosphate carboxylase/oxygenase activase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsHasse, D. / Larsson, A.M. / Andersson, I.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council Sweden
FORMAS Sweden
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structure of Arabidopsis thaliana Rubisco activase
Authors: Hasse, D. / Larsson, A.M. / Andersson, I.
History
DepositionAug 19, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribulose bisphosphate carboxylase/oxygenase activase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9503
Polymers43,7581
Non-polymers1922
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-25 kcal/mol
Surface area16250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.850, 83.850, 105.820
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Ribulose bisphosphate carboxylase/oxygenase activase, chloroplastic / RuBisCO activase


Mass: 43757.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Cell line: Col-0 / Gene: RCA, At2g39730, T5I7.3 / Plasmid: pASG-IBA3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P10896
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.45 Å3/Da / Density % sol: 49.88 % / Description: Small hexagonal crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Protein:Reservoir 1:1 Protein sample:8 mg ml-1 protein, 20 mM Bis-Tris propane pH 8, 50 mM KCl, 10% glycerol, 5 mM TCEP Reservoir solution: 100 mM Tris pH 7, 0.15 M AmSO4, 13% PEG 3350, 5 mM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.9→41.93 Å / Num. all: 9423 / Num. obs: 9423 / % possible obs: 99.9 % / Redundancy: 4.4 % / Biso Wilson estimate: 87.67 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.031 / Net I/σ(I): 19.5 / Num. measured all: 41585
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.9-3.084.50.5083.1676515090.8530.27599.9
8.7-41.934.10.01470.7150537010.00899.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSMarch 30, 2013data reduction
Aimless0.1.29data scaling
PHASER2.5.2phasing
BUSTER2.10.0refinement
O15.0.0model building
PDB_EXTRACT3.14data extraction
XSCALEdata scaling
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T15

3t15


Resolution: 2.9→41.93 Å / Cor.coef. Fo:Fc: 0.9287 / Cor.coef. Fo:Fc free: 0.9127 / SU R Cruickshank DPI: 0.983 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.781 / SU Rfree Blow DPI: 0.334 / SU Rfree Cruickshank DPI: 0.346
RfactorNum. reflection% reflectionSelection details
Rfree0.2495 441 4.69 %RANDOM
Rwork0.1957 ---
obs0.1983 9393 99.84 %-
Displacement parametersBiso max: 160.07 Å2 / Biso mean: 82.79 Å2 / Biso min: 32.44 Å2
Baniso -1Baniso -2Baniso -3
1--10.224 Å20 Å20 Å2
2---10.224 Å20 Å2
3---20.4481 Å2
Refine analyzeLuzzati coordinate error obs: 0.395 Å
Refinement stepCycle: final / Resolution: 2.9→41.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2143 0 10 5 2158
Biso mean--122.36 59.97 -
Num. residues----269
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d801SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes61HARMONIC2
X-RAY DIFFRACTIONt_gen_planes308HARMONIC5
X-RAY DIFFRACTIONt_it2198HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion284SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2436SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2198HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2956HARMONIC21.19
X-RAY DIFFRACTIONt_omega_torsion2.43
X-RAY DIFFRACTIONt_other_torsion21.53
LS refinement shellResolution: 2.9→3.24 Å
RfactorNum. reflection% reflection
Rfree0.3025 121 4.58 %
Rwork0.231 2520 -
obs--99.84 %

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