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- PDB-1srv: THERMUS THERMOPHILUS GROEL (HSP60 CLASS) FRAGMENT (APICAL DOMAIN)... -

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Basic information

Entry
Database: PDB / ID: 1srv
TitleTHERMUS THERMOPHILUS GROEL (HSP60 CLASS) FRAGMENT (APICAL DOMAIN) COMPRISING RESIDUES 192-336
ComponentsPROTEIN (GROEL (HSP60 CLASS))
KeywordsCHAPERONE / HSP60 / GROEL / CELL DIVISION / ATP-BINDING / PHOSPHORYLATION
Function / homology
Function and homology information


ATP binding / cytoplasm
Similarity search - Function
GroEL / GroEL / 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
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MAD / Resolution: 1.7 Å
AuthorsWalsh, M.A. / Dementieva, I. / Evans, G. / Sanishvili, R. / Joachimiak, A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Taking MAD to the extreme: ultrafast protein structure determination.
Authors: Walsh, M.A. / Dementieva, I. / Evans, G. / Sanishvili, R. / Joachimiak, A.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: A structural model for GroEL-polypeptide recognition.
Authors: Buckle, A.M. / Zahn, R. / Fersht, A.R.
History
DepositionMar 2, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Mar 12, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (GROEL (HSP60 CLASS))


Theoretical massNumber of molelcules
Total (without water)15,7541
Polymers15,7541
Non-polymers00
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.470, 65.960, 75.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221

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Components

#1: Protein PROTEIN (GROEL (HSP60 CLASS)) / 60 KD CHAPERONIN / PROTEIN CPN60


Mass: 15754.218 Da / Num. of mol.: 1 / Fragment: APICAL DOMAIN, RESIDUES 191 - 376
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Cellular location: CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: P61491
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.4 Å3/Da / Density % sol: 48 %
Description: MAD DATA WERE COLLECTED AT THE STRUCTURAL BIOLOGY CENTER'S UNDULATOR BEAMLINE 19ID AT THE APS
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5 / Details: pH 7.5, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Temperature: 293 K
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
121 mg/mlprotein1drop
24.5 %PEG60001drop
350 mMHEPES1drop
42.5 %MPD1drop
59 %PEG60001reservoir
6100 mMHEPES1reservoir
75 %MPD1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Nov 15, 1997 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 15546 / % possible obs: 88 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 30.7 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 17.2
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.2 / % possible all: 46

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Processing

Software
NameClassification
MLPHAREphasing
CCP4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.7→10 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.257 791 5 %RANDOM
Rwork0.199 ---
all0.193 17661 --
obs0.193 17661 89.32 %-
Displacement parametersBiso mean: 41.7 Å2
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1143 0 0 80 1223
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.02
X-RAY DIFFRACTIONp_angle_d0.0380.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.040.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.9033
X-RAY DIFFRACTIONp_mcangle_it3.9055
X-RAY DIFFRACTIONp_scbond_it7.0156
X-RAY DIFFRACTIONp_scangle_it9.9058
X-RAY DIFFRACTIONp_plane_restr0.0290.03
X-RAY DIFFRACTIONp_chiral_restr0.190.15
X-RAY DIFFRACTIONp_singtor_nbd0.2360.3
X-RAY DIFFRACTIONp_multtor_nbd0.3310.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.3050.3
X-RAY DIFFRACTIONp_planar_tor4.87
X-RAY DIFFRACTIONp_staggered_tor18.515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor21.720
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: CCP4 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 10 Å / Num. reflection obs: 15676 / σ(F): 0 / % reflection Rfree: 5 % / Rfactor all: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 41.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_plane_restr0.03
X-RAY DIFFRACTIONp_chiral_restr0.19

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