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- PDB-7tfm: Atomic Structure of the Leishmania spp. Hsp100 N-Domain -

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Basic information

Entry
Database: PDB / ID: 7tfm
TitleAtomic Structure of the Leishmania spp. Hsp100 N-Domain
ComponentsATP-dependent Clp protease subunit, heat shock protein 100 (HSP100)
KeywordsCHAPERONE / Molecular chaperone / Protein unfoldase
Function / homology
Function and homology information


peptidase activity / ATP hydrolysis activity / proteolysis / ATP binding
Similarity search - Function
ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / : / Clp, repeat (R) domain / Clp repeat (R) domain profile. ...ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / : / Clp, repeat (R) domain / Clp repeat (R) domain profile. / Clp, N-terminal domain superfamily / ClpA/B family / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Putative ATP-dependent Clp protease subunit, heat shock protein 100 (HSP100)
Similarity search - Component
Biological speciesLeishmania mexicana MHOM/GT/2001/U1103 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.055 Å
AuthorsMercado, J.M. / Lee, S. / Chang, C. / Sung, N. / Soong, L. / Catic, A. / Tsai, F.T.F.
Funding support United States, 8items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM104980 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM142143 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01-DK115454 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR140038 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10-OD030246 United States
Welch FoundationQ-1530-20190330 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32-GM008289 United States
CitationJournal: Proteins / Year: 2022
Title: Atomic structure of the Leishmania spp. Hsp100 N-domain.
Authors: Mercado, J.M. / Lee, S. / Chang, C. / Sung, N. / Soong, L. / Catic, A. / Tsai, F.T.F.
History
DepositionJan 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent Clp protease subunit, heat shock protein 100 (HSP100)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5182
Polymers17,4261
Non-polymers921
Water3,567198
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.971, 60.971, 71.807
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-385-

HOH

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Components

#1: Protein ATP-dependent Clp protease subunit, heat shock protein 100 (HSP100)


Mass: 17425.877 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania mexicana MHOM/GT/2001/U1103 (eukaryote)
Strain: MHOM/GT/2001/U1103 / Gene: LMXM_08_29_1270 / Plasmid: pProEX-HTb
Details (production host): Tobacco Etch Virus (TEV) protease cleavable N-terminal His6-tag
Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Variant (production host): CodonPlus (DE3)-RIL / References: UniProt: E9ALU6
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.92 Å3/Da / Density % sol: 35.76 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 5% PEG 2000, 5% PEG 3350, 5% PEG 4000, 5% PEGME 5000, 0.1 M KCl, 0.1 M MgCl2, 0.1 M PIPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.05→50 Å / Num. obs: 61983 / % possible obs: 97.1 % / Redundancy: 9.1 % / Rpim(I) all: 0.023 / Rsym value: 0.071 / Net I/σ(I): 10.9
Reflection shellResolution: 1.05→1.07 Å / Num. unique obs: 2900 / CC1/2: 0.838 / CC star: 0.955 / Rpim(I) all: 0.259 / Rrim(I) all: 0.591 / Rsym value: 0.528

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WBW

5wbw


Resolution: 1.055→36.963 Å / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1528 2515 3.47 %
Rwork0.1339 70028 -
obs0.1345 41615 60.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.54 Å2 / Biso mean: 21.5248 Å2 / Biso min: 9.77 Å2
Refinement stepCycle: final / Resolution: 1.055→36.963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1082 0 6 198 1286
Biso mean--19.35 30.44 -
Num. residues----142
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.055-1.07520.116220.2718441
1.0752-1.09720.021410.2048972
1.0972-1.1210.10840.1622134
1.121-1.14710.1629140.1426355
1.1471-1.17580.1168270.124826
1.1758-1.20760.1435690.1187170727
1.2076-1.24310.14321050.1138276743
1.2431-1.28320.14291550.1223437069
1.2832-1.32910.13351850.1288552986
1.3291-1.38230.16232140.1265588292
1.3823-1.44520.15572230.1232618697
1.4452-1.52140.14072260.1181619397
1.5214-1.61680.13842220.1181611396
1.6168-1.74160.13432130.1238605594
1.7416-1.91680.18152210.1293609596
1.9168-2.19420.13662230.128604795
2.1942-2.76430.14662050.1415585992
2.7643-36.9630.1642060.1419576990

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