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- PDB-1q3q: Crystal structure of the chaperonin from Thermococcus strain KS-1... -

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Basic information

Entry
Database: PDB / ID: 1q3q
TitleCrystal structure of the chaperonin from Thermococcus strain KS-1 (two-point mutant complexed with AMP-PNP)
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Thermosome subunit alpha / Thermosome subunit alpha
Similarity search - Component
Biological speciesThermococcus sp. (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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: Derived calculations / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,26012
Polymers237,1384
Non-polymers2,1228
Water12,502694
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)957,04148
Polymers948,55216
Non-polymers8,48832
Water28816
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
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)478,52024
Polymers474,2768
Non-polymers4,24416
Water1448
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 area55220 Å2
ΔGint-361 kcal/mol
Surface area142750 Å2
MethodPISA, PQS
3
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)478,52024
Polymers474,2768
Non-polymers4,24416
Water1448
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 area56020 Å2
ΔGint-350 kcal/mol
Surface area141180 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)210.829, 210.829, 156.421
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: 59284.531 Da / Num. of mol.: 4 / Mutation: G65C, 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-alpha / 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 694 / 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: 3.66 Å3/Da / Density % sol: 66.43 %
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: BL45XU / Wavelength: 1 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 Å / Relative weight: 1
ReflectionResolution: 2.3→100 Å / Num. all: 148110 / Num. obs: 148110 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 13.6 Å2 / Rsym value: 0.117 / Net I/σ(I): 12.4
Reflection shellHighest resolution: 2.3 Å / Mean I/σ(I) obs: 2.6 / Rsym value: 0.304 / % possible all: 89.7
Reflection
*PLUS
Lowest resolution: 40 Å / Num. measured all: 590450 / Rmerge(I) obs: 0.117
Reflection shell
*PLUS
% possible obs: 89.7 % / Rmerge(I) obs: 0.304

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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: 2.3→41.97 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 6506997.13 / Data cutoff high rms absF: 6506997.13 / 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
Rfree0.25 7449 5 %RANDOM
Rwork0.213 ---
obs0.213 148077 96.1 %-
all-148077 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.9202 Å2 / ksol: 0.378076 e/Å3
Displacement parametersBiso mean: 25.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.45 Å20 Å20 Å2
2---2.45 Å20 Å2
3---4.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.3→41.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15788 0 128 694 16610
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.282
X-RAY DIFFRACTIONc_scbond_it2.542
X-RAY DIFFRACTIONc_scangle_it3.792.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.303 1181 5.2 %
Rwork0.259 21734 -
obs--90.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
X-RAY DIFFRACTION4ANP.PARANP.TOP
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 41.9 Å / Rfactor Rfree: 0.25
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_deg0.77

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