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- PDB-1q3s: Crystal structure of the chaperonin from Thermococcus strain KS-1... -

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Basic information

Entry
Database: PDB / ID: 1q3s
TitleCrystal structure of the chaperonin from Thermococcus strain KS-1 (FormIII crystal complexed with ADP)
ComponentsThermosome alpha subunit
KeywordsCHAPERONE / chaperonin / thermosome
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / ATP hydrolysis activity / ATP binding
Similarity search - Function
GROEL; domain 2 / TCP-1-like chaperonin intermediate domain / GROEL; domain 1 / GroEL-like equatorial domain / GroEL / GroEL / Thermosome, archaeal / Chaperonins TCP-1 signature 1. / : / Chaperonins TCP-1 signature 2. ...GROEL; domain 2 / TCP-1-like chaperonin intermediate domain / GROEL; domain 1 / GroEL-like equatorial domain / GroEL / GroEL / Thermosome, archaeal / Chaperonins TCP-1 signature 1. / : / Chaperonins TCP-1 signature 2. / 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 / 3-Layer(bba) Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Thermosome subunit alpha / Thermosome subunit alpha
Similarity search - Component
Biological speciesThermococcus sp. (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsShomura, Y. / Yoshida, T. / Iizuka, R. / Maruyama, T. / Yohda, M. / Miki, K.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Crystal Structures of the Group II Chaperonin from Thermococcus strain KS-1: Steric Hindrance by the Substituted Amino Acid, and Inter-subunit Rearrangement between Two Crystal Forms.
Authors: Shomura, Y. / Yoshida, T. / Iizuka, R. / Maruyama, T. / Yohda, M. / Miki, K.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Crystallization and preliminary X-ray characterization of archaeal group II chaperonin alpha-subunit from Thermococcus strain KS-1
Authors: Shomura, Y. / Yoshida, T. / Maruyama, T. / Yohda, M. / Miki, K.
History
DepositionJul 31, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 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: Thermosome alpha subunit
B: Thermosome alpha subunit
C: Thermosome alpha subunit
D: Thermosome alpha subunit
E: Thermosome alpha subunit
F: Thermosome alpha subunit
G: Thermosome alpha subunit
H: Thermosome alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)477,96023
Polymers474,3738
Non-polymers3,58815
Water00
1
A: Thermosome alpha subunit
B: Thermosome alpha subunit
C: Thermosome alpha subunit
D: Thermosome alpha subunit
E: Thermosome alpha subunit
F: Thermosome alpha subunit
G: Thermosome alpha subunit
H: Thermosome alpha subunit
hetero molecules

A: Thermosome alpha subunit
B: Thermosome alpha subunit
C: Thermosome alpha subunit
D: Thermosome alpha subunit
E: Thermosome alpha subunit
F: Thermosome alpha subunit
G: Thermosome alpha subunit
H: Thermosome alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)955,92146
Polymers948,74516
Non-polymers7,17530
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Unit cell
Length a, b, c (Å)207.425, 236.230, 234.106
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a hexadecamer generated from the octamer in the asymmetric unit by the operations: -x+1, y, -z+1/2

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Components

#1: Protein
Thermosome alpha subunit / Thermosome subunit 1 / Chaperonin alpha subunit


Mass: 59296.586 Da / Num. of mol.: 8 / Mutation: G65C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus sp. (archaea) / Strain: KS-1 / Gene: THSA OR CPKA / Plasmid details: derivative of pET9a / Plasmid: pK1E-alpha1-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O24729, UniProt: P61112*PLUS, EC: 3.6.4.9
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 8 / 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: 3.02 Å3/Da / Density % sol: 59.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: lithium sulfate, PEG 3350, ADA, magnesium chloride, ADP, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
14 mMADP1drop
25 mM1dropMgCl2
3100 mMADA1reservoirpH6.1
4100 mM1reservoirLi2SO4
514 %(w/v)PEG33501reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45PX / Wavelength: 1.14 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE
RadiationMonochromator: Diamond trichromater / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.14 Å / Relative weight: 1
ReflectionResolution: 3→100 Å / Num. all: 112368 / Num. obs: 112339 / % possible obs: 98 % / Redundancy: 5 % / Rsym value: 0.119 / Net I/σ(I): 13.4
Reflection shellHighest resolution: 3 Å / Mean I/σ(I) obs: 1.9 / Rsym value: 0.384 / % possible all: 93.7
Reflection
*PLUS
Num. measured all: 556555 / Rmerge(I) obs: 0.119
Reflection shell
*PLUS
% possible obs: 93.7 % / Rmerge(I) obs: 0.384

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q2V

1q2v


Resolution: 3→73.62 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 16921226.3 / Data cutoff high rms absF: 16921226.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.288 5646 5 %RANDOM
Rwork0.251 ---
obs0.251 112339 98 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.6014 Å2 / ksol: 0.391713 e/Å3
Displacement parametersBiso mean: 38 Å2
Baniso -1Baniso -2Baniso -3
1--5.05 Å20 Å20 Å2
2--9.38 Å20 Å2
3----4.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.85 Å0.75 Å
Refinement stepCycle: LAST / Resolution: 3→73.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31528 0 223 0 31751
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it2.412
X-RAY DIFFRACTIONc_scbond_it2.312
X-RAY DIFFRACTIONc_scangle_it3.542.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.397 849 4.7 %
Rwork0.366 17048 -
obs--94.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3ADP.PARADP.TOP
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 73.6 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89

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