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- PDB-5x9u: Crystal structure of group III chaperonin in the open state -

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Basic information

Entry
Database: PDB / ID: 5x9u
TitleCrystal structure of group III chaperonin in the open state
ComponentsThermosome, alpha subunit
KeywordsCHAPERONE / group III / Archaeal-like bacterial chaperonin / closed states / pivot joints / ancestral CPN60
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / unfolded protein binding / ATP hydrolysis activity / ATP binding / metal ion binding / identical protein binding
Similarity search - Function
GROEL; domain 1 / GroEL-like equatorial domain / Chaperonin TCP-1, conserved site / Chaperonins TCP-1 signature 3. / Chaperone tailless complex polypeptide 1 (TCP-1) / 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 ...GROEL; domain 1 / GroEL-like equatorial domain / Chaperonin TCP-1, conserved site / Chaperonins TCP-1 signature 3. / Chaperone tailless complex polypeptide 1 (TCP-1) / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Thermosome, alpha subunit
Similarity search - Component
Biological speciesCarboxydothermus hydrogenoformans Z-2901 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.001 Å
AuthorsAn, Y.J. / Cha, S.S.
CitationJournal: Nat Commun / Year: 2017
Title: Structural and mechanistic characterization of an archaeal-like chaperonin from a thermophilic bacterium
Authors: An, Y.J. / Rowland, S.E. / Na, J.H. / Spigolon, D. / Hong, S.K. / Yoon, Y.J. / Lee, J.H. / Robb, F.T. / Cha, S.S.
History
DepositionMar 9, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thermosome, alpha subunit
B: Thermosome, alpha subunit
C: Thermosome, alpha subunit
D: Thermosome, alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,4698
Polymers226,7604
Non-polymers1,7094
Water00
1
A: Thermosome, alpha subunit
B: Thermosome, alpha subunit
C: Thermosome, alpha subunit
D: Thermosome, alpha subunit
hetero molecules

A: Thermosome, alpha subunit
B: Thermosome, alpha subunit
C: Thermosome, alpha subunit
D: Thermosome, alpha subunit
hetero molecules

A: Thermosome, alpha subunit
B: Thermosome, alpha subunit
C: Thermosome, alpha subunit
D: Thermosome, alpha subunit
hetero molecules

A: Thermosome, alpha subunit
B: Thermosome, alpha subunit
C: Thermosome, alpha subunit
D: Thermosome, alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)913,87532
Polymers907,04016
Non-polymers6,83516
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area54030 Å2
ΔGint-336 kcal/mol
Surface area345320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)209.780, 209.780, 169.813
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein
Thermosome, alpha subunit / chaperonin


Mass: 56689.996 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carboxydothermus hydrogenoformans Z-2901 (bacteria)
Strain: Z-2901 / Gene: CHY_0413 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3AF10
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: 4.12 Å3/Da / Density % sol: 70.14 %
Crystal growTemperature: 295 K / Method: microbatch
Details: 3 mM ADP, 200 mM NH4Cl, 10mM MgCl2, 50mM HEPES sodium (pH 7.0), 5% w/v Polyethylene glycol PEG 8000, 3% 1,8-Diaminooctane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 4→50 Å / Num. obs: 32570 / % possible obs: 99.7 % / Redundancy: 20.3 % / Net I/σ(I): 8.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata processing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X9V,3KFE

5x9v

3kfe


Resolution: 4.001→49.446 Å / SU ML: 0.72 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.321 1647 5.07 %
Rwork0.2529 --
obs0.2563 32468 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.001→49.446 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14665 0 108 0 14773
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00514953
X-RAY DIFFRACTIONf_angle_d1.02920262
X-RAY DIFFRACTIONf_dihedral_angle_d15.1155448
X-RAY DIFFRACTIONf_chiral_restr0.0382437
X-RAY DIFFRACTIONf_plane_restr0.0042604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.0008-4.11840.44691370.3672483X-RAY DIFFRACTION98
4.1184-4.25130.41411240.34242522X-RAY DIFFRACTION100
4.2513-4.40320.40541180.31022523X-RAY DIFFRACTION100
4.4032-4.57930.34051530.30682539X-RAY DIFFRACTION100
4.5793-4.78760.36511260.29442550X-RAY DIFFRACTION100
4.7876-5.03980.33571410.28342542X-RAY DIFFRACTION100
5.0398-5.35520.37981530.28852532X-RAY DIFFRACTION100
5.3552-5.76810.40261320.30812568X-RAY DIFFRACTION100
5.7681-6.34750.391470.29032567X-RAY DIFFRACTION100
6.3475-7.26350.31561340.24152599X-RAY DIFFRACTION100
7.2635-9.14180.23251400.18782612X-RAY DIFFRACTION100
9.1418-49.44940.23481420.1742784X-RAY DIFFRACTION100

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