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- PDB-1q3r: Crystal structure of the chaperonin from Thermococcus strain KS-1... -

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Basic information

Entry
Database: PDB / ID: 1q3r
TitleCrystal structure of the chaperonin from Thermococcus strain KS-1 (nucleotide-free form of single mutant)
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 1 / GroEL-like equatorial domain / GROEL; domain 2 / TCP-1-like chaperonin intermediate domain / Thermosome, archaeal / GroEL / GroEL / : / Chaperonins TCP-1 signature 1. / : ...GROEL; domain 1 / GroEL-like equatorial domain / GROEL; domain 2 / TCP-1-like chaperonin intermediate domain / Thermosome, archaeal / GroEL / GroEL / : / 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
Thermosome subunit alpha / Thermosome subunit alpha
Similarity search - Component
Biological speciesThermococcus sp. (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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
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

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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)237,3388
Polymers236,9544
Non-polymers3844
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)949,35232
Polymers947,81516
Non-polymers1,53716
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
2
C: Thermosome alpha subunit
D: Thermosome alpha subunit
hetero molecules

C: Thermosome alpha subunit
D: Thermosome alpha subunit
hetero molecules

C: Thermosome alpha subunit
D: Thermosome alpha subunit
hetero molecules

C: Thermosome alpha subunit
D: Thermosome alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)474,67616
Polymers473,9088
Non-polymers7698
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area49310 Å2
ΔGint-374 kcal/mol
Surface area144340 Å2
MethodPISA, PQS
3
A: Thermosome alpha subunit
B: Thermosome alpha subunit
hetero molecules

A: Thermosome alpha subunit
B: Thermosome alpha subunit
hetero molecules

A: Thermosome alpha subunit
B: Thermosome alpha subunit
hetero molecules

A: Thermosome alpha subunit
B: Thermosome alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)474,67616
Polymers473,9088
Non-polymers7698
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area50340 Å2
ΔGint-372 kcal/mol
Surface area142490 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)210.058, 210.058, 157.173
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
DetailsThe biological assembly is a hexadecamer generated from the tetramer in the asymmetric unit by the operations: (-x+1, -y, z), (y+1/2, -x+1/2, z), and (-y+1/2, x-1/2, z).

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Components

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


Mass: 59238.445 Da / Num. of mol.: 4 / Mutation: I125T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus sp. (archaea) / Strain: KS-1 / Gene: THSA OR CPKA / Plasmid details: pK1E-alpha1-2 / Plasmid: pET9a derivative / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4

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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: 3.66 Å3/Da / Density % sol: 66.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: ammonium sulfate, potassium chloride, Tris , pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115-20 mg/mlprotein1drop
2100 mMTris1reservoirpH8.0
32.1 Mammonium sulfate1reservoir
450 mM1reservoirKCl

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.9 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationMonochromator: fix-exit double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.9→100 Å / Num. all: 76135 / Num. obs: 76135 / % possible obs: 95 % / Redundancy: 5.7 % / Biso Wilson estimate: 59.4 Å2 / Rsym value: 0.095 / Net I/σ(I): 12.8
Reflection shellHighest resolution: 2.9 Å / Mean I/σ(I) obs: 3.5 / Rsym value: 0.178 / % possible all: 92
Reflection
*PLUS
Lowest resolution: 40 Å / Num. obs: 74163 / Num. measured all: 425665 / Rmerge(I) obs: 0.095
Reflection shell
*PLUS
% possible obs: 92 % / Rmerge(I) obs: 0.178

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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: 2.9→93.94 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 4573193.32 / Data cutoff high rms absF: 4573193.32 / 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
Rfree0.257 3835 5 %RANDOM
Rwork0.212 ---
obs0.212 76135 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 19.0717 Å2 / ksol: 0.374038 e/Å3
Displacement parametersBiso mean: 22.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å20 Å20 Å2
2---0.9 Å20 Å2
3---1.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.9→93.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15780 0 20 0 15800
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_d21.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it2.092
X-RAY DIFFRACTIONc_scbond_it2.182
X-RAY DIFFRACTIONc_scangle_it3.442.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.345 621 5 %
Rwork0.283 11864 -
obs--97.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 93.9 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_deg21.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8

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