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- PDB-4gr2: Structure of AtRbcX1 from Arabidopsis thaliana. -

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Basic information

Entry
Database: PDB / ID: 4gr2
TitleStructure of AtRbcX1 from Arabidopsis thaliana.
ComponentsAtRbcX1
KeywordsCHAPERONE / Rubisco / RbcX
Function / homology
Function and homology information


ribulose bisphosphate carboxylase complex assembly / chloroplast thylakoid / response to water deprivation / carbon fixation / : / response to salt stress / photosynthesis / protein folding chaperone / response to cold
Similarity search - Function
Chaperonin-like RbcX / Chaperonin-like RbcX superfamily / RbcX protein / Chaperonin-like RbcX / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chaperonin-like RBCX protein 1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGolik, P. / Grudnik, P. / Kolesinski, P. / Dubin, G. / Szczepaniak, A.
CitationJournal: Biochim.Biophys.Acta / Year: 2013
Title: Insights into eukaryotic Rubisco assembly - Crystal structures of RbcX chaperones from Arabidopsis thaliana.
Authors: Kolesinski, P. / Golik, P. / Grudnik, P. / Piechota, J. / Markiewicz, M. / Tarnawski, M. / Dubin, G. / Szczepaniak, A.
History
DepositionAug 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AtRbcX1
B: AtRbcX1


Theoretical massNumber of molelcules
Total (without water)29,7672
Polymers29,7672
Non-polymers00
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-34 kcal/mol
Surface area12210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.270, 47.640, 140.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11A-227-

HOH

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Components

#1: Protein AtRbcX1 / Chaperonin-like RbcX protein / Putative uncharacterized protein At4g04330


Mass: 14883.720 Da / Num. of mol.: 2 / Fragment: UNP residues 47-174 / Mutation: C62L, C87A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli) / References: UniProt: Q94AU9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.55 Å3/Da / Density % sol: 51.81 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 32% isopropanol, 100 mM MES , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→19.73 Å / Num. all: 20075 / Num. obs: 20075 / % possible obs: 100 %

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1062)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Z44

2z44


Resolution: 2→19.73 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 27.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2583 1035 5.16 %RANDOM
Rwork0.209 ---
all0.2115 ---
obs0.2115 20069 93.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1824 0 0 104 1928
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091901
X-RAY DIFFRACTIONf_angle_d1.0912571
X-RAY DIFFRACTIONf_dihedral_angle_d13.706710
X-RAY DIFFRACTIONf_chiral_restr0.075279
X-RAY DIFFRACTIONf_plane_restr0.004336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.10510.32311280.262597X-RAY DIFFRACTION92
2.1051-2.23680.2791430.22392640X-RAY DIFFRACTION93
2.2368-2.40920.28911470.2142658X-RAY DIFFRACTION93
2.4092-2.65120.2581540.22042701X-RAY DIFFRACTION94
2.6512-3.03360.28791750.21762706X-RAY DIFFRACTION95
3.0336-3.81750.28851480.20692789X-RAY DIFFRACTION95
3.8175-19.73340.20831400.19512943X-RAY DIFFRACTION95

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