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- PDB-8ibp: Crystal structure of Mycobacterium tuberculosis R21K ClpC1 N-term... -

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Basic information

Entry
Database: PDB / ID: 8ibp
TitleCrystal structure of Mycobacterium tuberculosis R21K ClpC1 N-terminal domain in complex with Lassomycin
Components
  • Lassomycin
  • Negative regulator of genetic competence ClpC/mecB
KeywordsCHAPERONE
Function / homologyClp amino terminal domain, pathogenicity island component / Clp repeat (R) domain profile. / Clp, repeat (R) domain / Clp, N-terminal domain superfamily / P-loop containing nucleoside triphosphate hydrolase / ATP binding / ACETATE ION / Negative regulator of genetic competence ClpC/mecB
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
Lentzea kentuckyensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsJagdev, M.K. / Vasudevan, D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: Crystal structure of the N-terminal domain of MtClpC1 in complex with the anti-mycobacterial natural peptide Lassomycin.
Authors: Jagdev, M.K. / Tompa, D.R. / Ling, L.L. / Peoples, A.J. / Dandapat, J. / Mohapatra, C. / Lewis, K. / Vasudevan, D.
History
DepositionFeb 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1May 8, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Negative regulator of genetic competence ClpC/mecB
C: Lassomycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7324
Polymers17,6142
Non-polymers1182
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-9 kcal/mol
Surface area7820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.537, 58.483, 64.754
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Negative regulator of genetic competence ClpC/mecB


Mass: 15754.162 Da / Num. of mol.: 1 / Mutation: R21K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: clpC_1 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A655JDN0
#2: Protein/peptide Lassomycin


Mass: 1860.173 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Lentzea kentuckyensis (bacteria)
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.57 Å3/Da / Density % sol: 52.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.4 M sodium acetate, 0.1 M sodium cacodylate (pH 6.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 1.0723 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 1.45→38.35 Å / Num. obs: 29919 / % possible obs: 91.9 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 17.4
Reflection shellResolution: 1.45→1.48 Å / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2992

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Processing

Software
NameVersionClassification
REFMAC5refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→38.35 Å / SU B: 5.342 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.071 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20893 1481 5 %RANDOM
Rwork0.17578 ---
obs0.17741 28400 91.42 %-
Displacement parametersBiso mean: 31.554 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å2-0 Å2-0 Å2
2---3.32 Å20 Å2
3---4.14 Å2
Refinement stepCycle: LAST / Resolution: 1.45→38.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1238 0 8 55 1301

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