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- PDB-7u4c: Borrelia burgdorferi HtpG N-terminal domain (1-228) in complex wi... -

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Basic information

Entry
Database: PDB / ID: 7u4c
TitleBorrelia burgdorferi HtpG N-terminal domain (1-228) in complex with BX-2819
ComponentsChaperone protein HtpG
KeywordsCHAPERONE/INHIBITOR / inhibitor / CHAPERONE-INHIBITOR complex
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / unfolded protein binding / ATP hydrolysis activity / ATP binding / membrane / cytosol
Similarity search - Function
Histidine kinase/HSP90-like ATPase / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Chem-819 / Chaperone protein HtpG
Similarity search - Component
Biological speciesBorreliella burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsKowalewski, M.E. / Lietzan, A. / Haystead, T. / Redinbo, M.R.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private5120725 United States
CitationJournal: Cell Chem Biol / Year: 2023
Title: Targeting Borrelia burgdorferi HtpG with a berserker molecule, a strategy for anti-microbial development.
Authors: Carlson, D.L. / Kowalewski, M. / Bodoor, K. / Lietzan, A.D. / Hughes, P.F. / Gooden, D. / Loiselle, D.L. / Alcorta, D. / Dingman, Z. / Mueller, E.A. / Irnov, I. / Modla, S. / Chaya, T. / ...Authors: Carlson, D.L. / Kowalewski, M. / Bodoor, K. / Lietzan, A.D. / Hughes, P.F. / Gooden, D. / Loiselle, D.L. / Alcorta, D. / Dingman, Z. / Mueller, E.A. / Irnov, I. / Modla, S. / Chaya, T. / Caplan, J. / Embers, M. / Miller, J.C. / Jacobs-Wagner, C. / Redinbo, M.R. / Spector, N. / Haystead, T.A.J.
History
DepositionFeb 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Nov 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chaperone protein HtpG
B: Chaperone protein HtpG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0634
Polymers54,2062
Non-polymers8572
Water2,162120
1
A: Chaperone protein HtpG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5312
Polymers27,1031
Non-polymers4291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chaperone protein HtpG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5312
Polymers27,1031
Non-polymers4291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.385, 52.428, 159.039
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Chaperone protein HtpG / Heat shock protein HtpG / High temperature protein G


Mass: 27102.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borreliella burgdorferi (Lyme disease spirochete)
Gene: htpG, BB_0560
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P42555
#2: Chemical ChemComp-819 / ethyl (4-{3-[2,4-dihydroxy-5-(1-methylethyl)phenyl]-5-sulfanyl-4H-1,2,4-triazol-4-yl}benzyl)carbamate


Mass: 428.505 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H24N4O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.94 Å3/Da / Density % sol: 36.52 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M magnesium chloride, 0.1 M Bis-Tris HCl, pH 5.5, 22.5% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.28→48.03 Å / Num. obs: 19889 / % possible obs: 99.7 % / Redundancy: 2 % / Biso Wilson estimate: 35.26 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.0497 / Rpim(I) all: 0.0497 / Rrim(I) all: 0.07028 / Net I/σ(I): 7.8
Reflection shellResolution: 2.28→2.34 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2739 / Mean I/σ(I) obs: 2.46 / Num. unique obs: 1938 / CC1/2: 0.697 / CC star: 0.906 / Rpim(I) all: 0.2739 / Rrim(I) all: 0.3874 / % possible all: 99.85

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
PHENIX1.20_4459phasing
Aimlessdata scaling
AutoProcessdata processing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3HHU

3hhu


Resolution: 2.28→48.03 Å / SU ML: 0.257 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.3586
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2322 1998 10.05 %
Rwork0.2059 17890 -
obs0.2086 19888 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.97 Å2
Refinement stepCycle: LAST / Resolution: 2.28→48.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3083 0 60 120 3263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00153200
X-RAY DIFFRACTIONf_angle_d0.4014333
X-RAY DIFFRACTIONf_chiral_restr0.0406491
X-RAY DIFFRACTIONf_plane_restr0.0018543
X-RAY DIFFRACTIONf_dihedral_angle_d10.4622453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.340.30231330.26141238X-RAY DIFFRACTION99.85
2.34-2.40.31251510.25751260X-RAY DIFFRACTION99.86
2.4-2.470.30481350.24111246X-RAY DIFFRACTION99.93
2.47-2.550.29981380.2411253X-RAY DIFFRACTION99.86
2.55-2.640.25341460.21831282X-RAY DIFFRACTION100
2.64-2.750.27481390.2291247X-RAY DIFFRACTION99.93
2.75-2.870.26211450.23911260X-RAY DIFFRACTION99.72
2.87-3.020.26881460.23021262X-RAY DIFFRACTION99.93
3.02-3.210.24291370.21541274X-RAY DIFFRACTION99.86
3.21-3.460.27881380.21302X-RAY DIFFRACTION99.86
3.46-3.810.19771480.1841279X-RAY DIFFRACTION99.44
3.81-4.360.19121410.18111287X-RAY DIFFRACTION99.3
4.36-5.490.18421440.17361309X-RAY DIFFRACTION99.05
5.49-48.030.2121570.2071391X-RAY DIFFRACTION99.1

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