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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 / homologyChaperonin TCP-1, conserved site / Chaperonin Cpn60/TCP-1 family / Thermosome, archaeal / Chaperone tailless complex polypeptide 1 (TCP-1) / GroEL-like apical domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like equatorial domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonins TCP-1 signature 1. / Chaperonins TCP-1 signature 2. ...Chaperonin TCP-1, conserved site / Chaperonin Cpn60/TCP-1 family / Thermosome, archaeal / Chaperone tailless complex polypeptide 1 (TCP-1) / GroEL-like apical domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like equatorial domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonins TCP-1 signature 1. / Chaperonins TCP-1 signature 2. / Chaperonins TCP-1 signature 3. / protein folding / unfolded protein binding / ATP binding / Thermosome subunit alpha / Thermosome subunit beta
Function and homology information
Specimen sourceThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER SYNTHESIS / 3.2 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 24, 1998 / Release: Mar 23, 1999
RevisionDateData content typeGroupProviderType
1.0Mar 23, 1999Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelDerived calculations / Version format compliance

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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
Polyers116,8762
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
Polyers935,01216
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
Polyers467,5068
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 area (Å2)47480
ΔGint (kcal/M)-359
Surface area (Å2)138280
MethodPISA
Unit cell
γ
α
β
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-MI 4 2 2

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Components

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Protein/peptide , 2 types, 2 molecules AB

#1: Protein/peptide THERMOSOME (ALPHA SUBUNIT)


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


Mass: 58552.629 Da / Num. of mol.: 1 / Source: (natural) Thermoplasma acidophilum (acidophilic) / Genus: Thermoplasma / 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 / Formula: Mg / Magnesium
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#5: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE


Mass: 83.977 Da / Num. of mol.: 2 / Formula: AlF3 / Aluminium fluoride
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Formula: H2O / Water

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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 / Density percent sol: 63 %
Crystal growpH: 5.6 / Details: pH 5.6
Crystal grow
*PLUS
Temp: 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

Crystal ID: 1

IDConcCommon nameSol IDChemical formulaDetails
13.3 mg/mlproteindrop
220 mMTris-HCldrop
30.02 %dropNaN3
42 Mammonium sulfatereservoirprecipitant
50.1 Msodium acetatereservoirprecipitant

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Data collection

DiffractionMean temperature: 295 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Details: MIRRORS / Detector: IMAGE PLATE / Collection date: Dec 15, 1997
RadiationMonochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionD resolution high: 3.2 Å / D resolution low: 15 Å / Number obs: 22043 / Observed criterion sigma I: 0 / Rsym value: 0.113 / NetI over sigmaI: 6.2 / Redundancy: 3.5 % / Percent possible obs: 92
Reflection shellHighest resolution: 3.2 Å / Lowest resolution: 3.28 Å / MeanI over sigI obs: 1.6 / Rsym value: 0.458 / Redundancy: 1.7 % / Percent possible all: 61.4
Reflection
*PLUS
Rmerge I obs: 0.113
Reflection shell
*PLUS
Percent 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
RefineMethod to determine structure: DIFFERENCE FOURIER SYNTHESIS / R Free selection details: RANDOM / Data cutoff high absF: 1 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 0
Displacement parametersB iso mean: 38.4 Å2
Least-squares processR factor R free: 0.285 / R factor R work: 0.181 / R factor obs: 0.181 / Highest resolution: 3.2 Å / Lowest resolution: 8 Å / Number reflection R free: 1044 / Number reflection obs: 20792 / Percent reflection R free: 5 / Percent reflection obs: 92.5
Refine hist #LASTHighest resolution: 3.2 Å / Lowest resolution: 8 Å
Number of atoms included #LASTProtein: 7582 / Nucleic acid: 0 / Ligand: 64 / Solvent: 2 / Total: 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
Refine LS shellHighest resolution: 3.2 Å / R factor R free: 0.305 / R factor R work: 0.262 / Lowest resolution: 3.34 Å / Number reflection R free: 99 / Number reflection R work: 1937 / Total number of bins used: 8 / Percent reflection R free: 3.56 / Percent reflection 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
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
Refine LS shell
*PLUS
R factor obs: 0.262

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