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- PDB-1asx: APICAL DOMAIN OF THE CHAPERONIN FROM THERMOPLASMA ACIDOPHILUM -

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Basic information

Entry
Database: PDB / ID: 1asx
TitleAPICAL DOMAIN OF THE CHAPERONIN FROM THERMOPLASMA ACIDOPHILUM
ComponentsTHERMOSOME
KeywordsCHAPERONIN / HSP60 / THERMOSOME / TCP1 / GROEL / THERMOPLASMA ACIDOPHILUM / ATP-BINDING
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / unfolded protein binding / ATP hydrolysis activity / ATP binding
Similarity search - Function
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) ...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 / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Thermosome subunit alpha
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKlumpp, M. / Baumeister, W. / Essen, L.-O.
CitationJournal: 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
DepositionAug 11, 1997Processing site: BNL
Revision 1.0Dec 3, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THERMOSOME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9182
Polymers17,8231
Non-polymers951
Water1086
1
A: THERMOSOME
hetero molecules

A: THERMOSOME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8354
Polymers35,6452
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area2610 Å2
ΔGint-27 kcal/mol
Surface area15140 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)79.910, 79.910, 70.250
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein THERMOSOME


Mass: 17822.625 Da / Num. of mol.: 1
Fragment: ALPHA SUBUNIT, APICAL DOMAIN, SUBSTRATE-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Cell line: BL21 / Cellular location: CYTOPLASM / Gene: THSA / Plasmid: PRSET6A / Species (production host): Escherichia coli / Gene (production host): THSA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P48424
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.63 Å3/Da / Density % sol: 70 %
Crystal growpH: 3.5 / Details: pH 3.5
Crystal grow
*PLUS
Temperature: 30 ℃ / pH: 3.8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
127 mg/mlprotein1drop
23.0 Mammonium sulfate1drop
30.1 Msodium citrate1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1997
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→19 Å / Num. obs: 6335 / % possible obs: 94.8 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Biso Wilson estimate: 39.9 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 20.6
Reflection shellHighest resolution: 2.8 Å / Rmerge(I) obs: 0.145 / Mean I/σ(I) obs: 6.9 / % possible all: 71.8
Reflection
*PLUS
Num. measured all: 17354
Reflection shell
*PLUS
% possible obs: 71.8 %

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Processing

Software
NameVersionClassification
SOLOMONphasing
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: GLOBULAR DOMAIN PORTION OF CRYSTAL FORM A (PDB ENTRY 1ASS)

1ass


Resolution: 2.8→10 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: RFREE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.272 390 6.3 %CONCENTRIC SHELLS
Rwork0.222 ---
obs0.222 6205 94.8 %-
Displacement parametersBiso mean: 36 Å2
Baniso -1Baniso -2Baniso -3
1-20.55 Å214.18 Å20 Å2
2--20.55 Å20 Å2
3---34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1175 0 5 6 1186
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.575
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.93
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.351
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.8→2.9 Å / % reflection obs: 71.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.93
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.351

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