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- PDB-4gr6: Crystal structure of AtRbcX2 from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 4gr6
TitleCrystal structure of AtRbcX2 from Arabidopsis thaliana
ComponentsAtRbcX2
KeywordsCHAPERONE / Rubisco / RbcX
Function / homology
Function and homology information


chloroplast stroma / chaperone-mediated protein folding / protein folding chaperone
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 2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGrudnik, P. / Golik, 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 ...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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AtRbcX2
B: AtRbcX2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1403
Polymers30,0782
Non-polymers621
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-28 kcal/mol
Surface area11830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.770, 63.300, 57.320
Angle α, β, γ (deg.)90.00, 96.57, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-332-

HOH

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Components

#1: Protein AtRbcX2 / Chaperonin-like RbcX protein / Putative uncharacterized protein At5g19855


Mass: 15039.025 Da / Num. of mol.: 2 / Fragment: UNP residues 79-203 / Mutation: C91A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g19855 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8L9X2
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.75 Å3/Da / Density % sol: 55.26 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 15% PEG 400, 100 mM sodium citrate , pH 5.6, VAPOR DIFFUSION, SITTING 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
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→33.75 Å / Num. all: 21808 / Num. obs: 21808 / % possible obs: 100 %

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Processing

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

2z44


Resolution: 2→21.167 Å / SU ML: 0.16 / σ(F): 1.35 / Phase error: 21.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1964 1112 5.1 %RANDOM
Rwork0.1737 ---
all0.175 ---
obs0.175 21785 98.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→21.167 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1700 0 4 91 1795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121780
X-RAY DIFFRACTIONf_angle_d1.2062413
X-RAY DIFFRACTIONf_dihedral_angle_d14.301653
X-RAY DIFFRACTIONf_chiral_restr0.077258
X-RAY DIFFRACTIONf_plane_restr0.006308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.0910.22511240.19642523X-RAY DIFFRACTION97
2.091-2.20110.19581160.17872581X-RAY DIFFRACTION97
2.2011-2.33890.19321280.16692535X-RAY DIFFRACTION98
2.3389-2.51920.21491610.16222565X-RAY DIFFRACTION98
2.5192-2.77220.1961410.16152595X-RAY DIFFRACTION99
2.7722-3.17220.18921440.17552596X-RAY DIFFRACTION99
3.1722-3.99230.17751440.16932618X-RAY DIFFRACTION100
3.9923-21.16850.2051540.1812660X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -12.1395 Å / Origin y: 19.2645 Å / Origin z: -14.6886 Å
111213212223313233
T0.2837 Å2-0.0224 Å20.0261 Å2-0.3016 Å2-0.0064 Å2--0.2259 Å2
L1.899 °21.4364 °20.0103 °2-1.0191 °20.0042 °2---0.0588 °2
S-0.0012 Å °-0.0564 Å °-0.1154 Å °-0.0111 Å °-0.0414 Å °-0.0353 Å °0.0737 Å °-0.0628 Å °0.0523 Å °
Refinement TLS groupSelection details: all

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