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- PDB-6kfv: GroEL from Xanthomonas oryzae pv. oryzae -

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Basic information

Entry
Database: PDB / ID: 6kfv
TitleGroEL from Xanthomonas oryzae pv. oryzae
Components60 kDa chaperonin
KeywordsCHAPERONE / GroEL / large double-ring complexes
Function / homology
Function and homology information


unfolded protein binding / protein refolding / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
GROEL; domain 2 / TCP-1-like chaperonin intermediate domain / GROEL; domain 1 / GroEL-like equatorial domain / Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily ...GROEL; domain 2 / TCP-1-like chaperonin intermediate domain / GROEL; domain 1 / GroEL-like equatorial domain / Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
60 kDa chaperonin / 60 kDa chaperonin
Similarity search - Component
Biological speciesXanthomonas oryzae pv. oryzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.22 Å
AuthorsTran, H.T. / Lee, J.H. / Kang, L.W.
CitationJournal: Crystals / Year: 2019
Title: Crystal Structure of Chaperonin GroEL from Xanthomonas oryzae pv. oryzae
Authors: Tran, H.T. / Lee, J. / Park, H. / Kim, J.G. / Kim, S. / Ahn, Y.J. / Kang, L.W.
History
DepositionJul 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 19, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 60 kDa chaperonin
B: 60 kDa chaperonin
C: 60 kDa chaperonin
D: 60 kDa chaperonin
E: 60 kDa chaperonin
F: 60 kDa chaperonin
G: 60 kDa chaperonin
H: 60 kDa chaperonin
I: 60 kDa chaperonin
J: 60 kDa chaperonin
K: 60 kDa chaperonin
L: 60 kDa chaperonin
M: 60 kDa chaperonin
N: 60 kDa chaperonin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)773,20919
Polymers772,74114
Non-polymers4685
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area52140 Å2
ΔGint-264 kcal/mol
Surface area295140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.092, 239.500, 278.253
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
60 kDa chaperonin / GroEL protein / Protein Cpn60


Mass: 55195.754 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas oryzae pv. oryzae (bacteria)
Gene: groL, groEL, BCR61_23115, EYR02_02960, EYR03_02675 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0U2JHN9, UniProt: Q5GUT1*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.96 Å3/Da / Density % sol: 58.42 % / Mosaicity: 0.585 °
Crystal growTemperature: 287 K / Method: evaporation / pH: 4.5
Details: 0.1M sodium chloride dihydrate, 0.1M sodium citrate, pH 4.0-4.5, 25-30% (v/v) (+/-)-2-methyl-2,4 pentadiol)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 145687 / % possible obs: 99.1 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.189 / Χ2: 1.844 / Net I/σ(I): 6.8 / Num. measured all: 683467
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
3.2-3.263.80.5971031.096197.6
3.26-3.313.90.55171571.094198
3.31-3.383.90.52570851.123198.2
3.38-3.454.10.47571511.18198.3
3.45-3.524.10.43172301.208198.9
3.52-3.64.20.38871971.296199
3.6-3.694.30.35372351.321199.2
3.69-3.794.40.33172541.422199.2
3.79-3.914.60.2872431.538199.4
3.91-4.034.70.23572101.742199.4
4.03-4.184.80.21573141.902199.4
4.18-4.344.90.272912.124199.7
4.34-4.5450.17973152.313199.5
4.54-4.7850.17272952.426199.6
4.78-5.085.10.17173302.317199.7
5.08-5.475.20.16873532.077199.5
5.47-6.025.20.15773571.871199.7
6.02-6.895.30.11974141.955199.7
6.89-8.675.80.07174942.26199.8
8.67-505.40.05976593.032198.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PKN

4pkn


Resolution: 3.22→47.36 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.834 / SU B: 36.895 / SU ML: 0.601 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.662
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3041 6843 5 %RANDOM
Rwork0.2188 ---
obs0.2231 129341 91.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 265.71 Å2 / Biso mean: 75.323 Å2 / Biso min: 15.28 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.02 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 3.22→47.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms53872 0 28 33 53933
Biso mean--99.31 36.85 -
Num. residues----7342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01354313
X-RAY DIFFRACTIONr_bond_other_d0.0020.01753443
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.63673322
X-RAY DIFFRACTIONr_angle_other_deg1.1991.582123932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.25957326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.1524.082436
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.125159939
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9815301
X-RAY DIFFRACTIONr_chiral_restr0.0560.27537
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0261474
X-RAY DIFFRACTIONr_gen_planes_other0.0020.029629
LS refinement shellResolution: 3.22→3.303 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 401 -
Rwork0.344 7110 -
all-7511 -
obs--69.51 %

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