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- PDB-1a6e: THERMOSOME-MG-ADP-ALF3 COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1a6e
TitleTHERMOSOME-MG-ADP-ALF3 COMPLEX
Components
  • THERMOSOME (ALPHA SUBUNIT)
  • THERMOSOME (BETA SUBUNIT)
KeywordsCHAPERONIN / THERMOPLASMA ACIDOPHILUM / GROUP II CHAPERONIN / CCT / TRIC / PROTEIN FOLDING / ATPASE / TRANSITION STATE COMPLEX / ATP HYDROLYSIS
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / unfolded protein binding / 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
ADENOSINE-5'-DIPHOSPHATE / ALUMINUM FLUORIDE / Thermosome subunit alpha / Thermosome subunit beta
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER SYNTHESIS / Resolution: 3.2 Å
AuthorsDitzel, L. / Loewe, J. / Stock, D. / Stetter, K.-O. / Huber, H. / Huber, R. / Steinbacher, S.
CitationJournal: 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.
History
DepositionFeb 24, 1998Processing site: BNL
Revision 1.0Mar 23, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 (BETA SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,9478
Polymers116,8762
Non-polymers1,0716
Water362
1
A: THERMOSOME (ALPHA SUBUNIT)
B: THERMOSOME (BETA SUBUNIT)
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)943,57964
Polymers935,01216
Non-polymers8,56848
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
MethodPQS
2
A: THERMOSOME (ALPHA SUBUNIT)
B: THERMOSOME (BETA SUBUNIT)
hetero molecules

A: THERMOSOME (ALPHA SUBUNIT)
B: THERMOSOME (BETA SUBUNIT)
hetero molecules

A: THERMOSOME (ALPHA SUBUNIT)
B: THERMOSOME (BETA SUBUNIT)
hetero molecules

A: THERMOSOME (ALPHA SUBUNIT)
B: THERMOSOME (BETA SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)471,79032
Polymers467,5068
Non-polymers4,28424
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area47480 Å2
ΔGint-359 kcal/mol
Surface area138280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.800, 167.800, 202.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein THERMOSOME (ALPHA SUBUNIT)


Mass: 58323.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermoplasma acidophilum (acidophilic) / Cellular location: CYTOPLASM / References: UniProt: P48424
#2: Protein THERMOSOME (BETA SUBUNIT)


Mass: 58552.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermoplasma acidophilum (acidophilic) / Cellular location: CYTOPLASM / References: UniProt: P48425

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Non-polymers , 4 types, 8 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE


Mass: 83.977 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.3 Å3/Da / Density % sol: 63 %
Crystal growpH: 5.6 / Details: pH 5.6
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Details: 0.005ml of drop solution was mixed with 0.0025 ml of precipitant
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
13.3 mg/mlprotein1drop
220 mMTris-HCl1drop
30.02 %1dropNaN3
42 Mammonium sulfate1reservoirprecipitant
50.1 Msodium acetate1reservoirprecipitant

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 1997 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→15 Å / Num. obs: 22043 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rsym value: 0.113 / Net I/σ(I): 6.2
Reflection shellResolution: 3.2→3.28 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.458 / % possible all: 61.4
Reflection
*PLUS
Rmerge(I) obs: 0.113
Reflection shell
*PLUS
% possible obs: 61.4 % / Rmerge(I) obs: 0.458

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
MOSFLMdata reduction
CCP4data scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER SYNTHESIS / Resolution: 3.2→8 Å / Data cutoff high absF: 100000000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1044 5 %RANDOM
Rwork0.181 ---
obs0.181 20792 92.5 %-
Displacement parametersBiso mean: 38.4 Å2
Refinement stepCycle: LAST / Resolution: 3.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7582 0 64 2 7648
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
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: 3.2→3.34 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.305 99 3.56 %
Rwork0.262 1937 -
obs--73.7 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PARHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOL
X-RAY DIFFRACTION3PAR_HBOND.DNA
X-RAY DIFFRACTION4PAR_WAT_19.PRO
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_deg21.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4
LS refinement shell
*PLUS
Rfactor obs: 0.262

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