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- PDB-3nx6: Crystal Structure of co-chaperonin, GroES (Xoo4289) from Xanthomo... -

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Basic information

Entry
Database: PDB / ID: 3nx6
TitleCrystal Structure of co-chaperonin, GroES (Xoo4289) from Xanthomonas oryzae pv. oryzae KACC10331
Components10kDa chaperonin
KeywordsCHAPERONE / Bacterial blight / Xoo4289 / GroES / Xanthomonas oryzae pv. oryzae KACC10331
Function / homology
Function and homology information


protein folding chaperone / unfolded protein binding / protein-folding chaperone binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
10 Kd Chaperonin, Protein Cpn10; Chain O / GroES chaperonin / Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / GroES-like superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesXanthomonas oryzae pv. oryzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsNatarajan, S. / Doan, T.T.N. / Kang, L.-W.
CitationJournal: to be published
Title: Crystal Structure of co-chaperonin, GroES (Xoo4289) from Xanthomonas oryzae pv. oryzae KACC10331
Authors: Natarajan, S. / Doan, T.T.N. / Kang, L.-W.
History
DepositionJul 13, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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

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Assembly

Deposited unit
A: 10kDa chaperonin


Theoretical massNumber of molelcules
Total (without water)9,9741
Polymers9,9741
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.410, 64.410, 36.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
DetailsIN SOLUTION IT COULD FORM HEPTAMER.

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Components

#1: Protein 10kDa chaperonin / co-chaperonin / GroES


Mass: 9974.401 Da / Num. of mol.: 1 / Fragment: UNP residues 40-134 / Mutation: R55H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas oryzae pv. oryzae (bacteria)
Strain: KACC10331 / Gene: Xoo4289 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q5GUT0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.19 Å3/Da / Density % sol: 43.87 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 4.1
Details: 0.2M Sodium citrate pH 4.1, 16% PEG 400, 0.2M Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→55.78 Å / Num. all: 6225 / Num. obs: 5590 / % possible obs: 94.52 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.97→2.08 Å / % possible all: 98.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WNR

1wnr


Resolution: 1.97→32.21 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.912 / SU B: 6.215 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29163 271 4.6 %RANDOM
Rwork0.21394 ---
all0.21722 6225 --
obs0.21722 5590 94.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.821 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.01 Å20 Å2
2---0.03 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.97→32.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms559 0 0 37 596
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.022567
X-RAY DIFFRACTIONr_bond_other_d0.0010.02386
X-RAY DIFFRACTIONr_angle_refined_deg2.171.996765
X-RAY DIFFRACTIONr_angle_other_deg1.0493955
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.399573
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.3424.73719
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.90615101
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.39152
X-RAY DIFFRACTIONr_chiral_restr0.1120.290
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021613
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0297
X-RAY DIFFRACTIONr_mcbond_it1.3571.5368
X-RAY DIFFRACTIONr_mcbond_other0.231.5154
X-RAY DIFFRACTIONr_mcangle_it2.5192593
X-RAY DIFFRACTIONr_scbond_it3.3233199
X-RAY DIFFRACTIONr_scangle_it6.0994.5172
LS refinement shellResolution: 1.974→2.025 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.497 17 -
Rwork0.397 376 -
obs--83.44 %

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