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- PDB-1e0r: Beta-apical domain of thermosome -

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Basic information

Entry
Database: PDB / ID: 1e0r
TitleBeta-apical domain of thermosome
ComponentsTHERMOSOME
KeywordsCHAPERONIN / HSP60 / THERMOSOME / TCP1 / GROEL / THERMOPLASMA ACIDOPHILUM
Function / homology
Function and homology information


chaperonin-containing T-complex / ATP-dependent protein folding chaperone / unfolded protein binding / ATP hydrolysis activity / ATP binding
Similarity search - Function
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 / 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 / Alpha Beta
Similarity search - Domain/homology
Thermosome subunit beta
Similarity search - Component
Biological speciesTHERMOPLASMA ACIDOPHILUM (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBosch, G. / Baumeister, W. / Essen, L.-O.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Crystal Structure of the Beta-Apical Domain from Thermosome Reveals Structural Plasticity in Protrusion Region
Authors: Bosch, G. / Baumeister, W. / Essen, L.-O.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1998
Title: Crystal Structure of the Thermosome, the Archaeal Chaperonin and Homolog of Cct
Authors: Ditzel, L. / Lowe, J. / Stock, D. / Stetter, K.O. / Huber, H. / Huber, R. / Steinbacher, S.
#2: Journal: Cell(Cambridge,Mass.) / Year: 1997
Title: Structure of the Substrate-Binding Domain of the Thermosome, an Archaeal Group II Chaperonin
Authors: Klumpp, M. / Baumeister, W. / Essen, L.-O.
History
DepositionApr 6, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 6, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: THERMOSOME


Theoretical massNumber of molelcules
Total (without water)17,7631
Polymers17,7631
Non-polymers00
Water00
1
B: THERMOSOME

B: THERMOSOME


Theoretical massNumber of molelcules
Total (without water)35,5272
Polymers35,5272
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area2510 Å2
ΔGint-7.8 kcal/mol
Surface area18010 Å2
MethodPQS
Unit cell
Length a, b, c (Å)57.320, 57.320, 106.140
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein THERMOSOME / BETA-APICAL DOMAIN


Mass: 17763.393 Da / Num. of mol.: 1 / Fragment: SUBSTRATE-BINDING DOMAIN / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: LYS 364 IS FOLLOWED BY ASN 365 AND HEXAHISTIDINE TAIL
Source: (gene. exp.) THERMOPLASMA ACIDOPHILUM (acidophilic) / Cellular location: CYTOPLASM / Plasmid: PET22B / Cellular location (production host): CYTOPLASM / Gene (production host): THSB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P48425
Compound detailsCHAIN B ENGINEERED MUTATION CYS364SER
Sequence detailsHIS: HISTIDINE TAG FROM HIS 368 - HIS 372 NOT SEEN IN ELECTRON DENSITY

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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: 2.83 Å3/Da / Density % sol: 50 %
Crystal growpH: 9.1 / Details: pH 9.10
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / pH: 9.1
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 %(w/v)PEG200001reservoir
22 %(v/v)dioxane1reservoir
30.1 Mbicine1reservoirpH9.1
410 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.99
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1998 / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.8→25 Å / Num. obs: 5170 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 95 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 27
Reflection shellResolution: 2.8→2.87 Å / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 3.3 / % possible all: 96.8
Reflection
*PLUS
Num. measured all: 19163
Reflection shell
*PLUS
% possible obs: 96.8 %

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS0.9phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ASS WITHOUT I245-K274

1ass


Resolution: 2.8→15 Å / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.318 266 5.1 %RANDOM
Rwork0.261 ---
obs0.261 4984 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.8 Å2 / ksol: 0.293 e/Å3
Displacement parametersBiso mean: 76 Å2
Baniso -1Baniso -2Baniso -3
1--4.799 Å2-8.908 Å20 Å2
2---4.799 Å20 Å2
3---9.597 Å2
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1160 0 0 0 1160
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007567
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_deg1.33994
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.551.5
X-RAY DIFFRACTIONc_mcangle_it2.792
X-RAY DIFFRACTIONc_scbond_it1.582
X-RAY DIFFRACTIONc_scangle_it2.612.5
LS refinement shellResolution: 2.8→2.9 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.433 30
Rwork0.45 417
Xplor fileSerial no: 1 / Param file: PROTEIN.PARAM / Topol file: PROTEIN.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Num. reflection all: 5135
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007567
X-RAY DIFFRACTIONc_angle_deg1.33994

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