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- PDB-8ada: Crystal structure of ClpC2 N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 8ada
TitleCrystal structure of ClpC2 N-terminal domain
ComponentsUncharacterized protein Rv2667
KeywordsDNA BINDING PROTEIN / ClpC2 / CymA / N-terminal domain / Transcription factor
Function / homologyClp amino terminal domain, pathogenicity island component / Clp repeat (R) domain profile. / Clp, repeat (R) domain / Clp, N-terminal domain superfamily / cytosol / Uncharacterized protein Rv2667
Function and homology information
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / molecular replacement / Resolution: 1.996 Å
AuthorsTaylor, G. / Cui, H.J. / Leodolter, J. / Giese, C. / Weber-Ban, E.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: Commun Biol / Year: 2023
Title: ClpC2 protects mycobacteria against a natural antibiotic targeting ClpC1-dependent protein degradation.
Authors: Taylor, G. / Cui, H. / Leodolter, J. / Giese, C. / Weber-Ban, E.
History
DepositionJul 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 5, 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein Rv2667
B: Uncharacterized protein Rv2667


Theoretical massNumber of molelcules
Total (without water)15,6582
Polymers15,6582
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.140, 48.140, 110.018
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11A-129-

HOH

21A-132-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 7 or resid 11 through 21 or resid 23 through 72))
21(chain B and (resid 10 through 21 or resid 23 through 72))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 7 or resid 11 through 21 or resid 23 through 72))A7
121(chain A and (resid 7 or resid 11 through 21 or resid 23 through 72))A11 - 21
131(chain A and (resid 7 or resid 11 through 21 or resid 23 through 72))A23 - 72
211(chain B and (resid 10 through 21 or resid 23 through 72))B10 - 21
221(chain B and (resid 10 through 21 or resid 23 through 72))B23 - 72

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Components

#1: Protein Uncharacterized protein Rv2667


Mass: 7828.809 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv2667, MTCY441.36 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P9WPC7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.35 Å3/Da / Density % sol: 47.67 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 25 % w/v PEG 3350, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.996→41.69 Å / Num. obs: 10183 / % possible obs: 99.6 % / Redundancy: 9.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.034 / Rrim(I) all: 0.106 / Net I/σ(I): 14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.058.91.18960226790.6950.4081.262.194.1
8.93-41.697.90.0511181410.9940.020.05434.399.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.7data scaling
Arcimboldophasing
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.996→41.69 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2095 525 5.17 %
Rwork0.1798 9622 -
obs0.1814 10147 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.59 Å2 / Biso mean: 38.9323 Å2 / Biso min: 23.62 Å2
Refinement stepCycle: final / Resolution: 1.996→41.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1005 0 0 52 1057
Biso mean---44.62 -
Num. residues----132
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A547X-RAY DIFFRACTION14.077TORSIONAL
12B547X-RAY DIFFRACTION14.077TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9961-2.19690.29961300.2307235099
2.1969-2.51480.22591010.19822408100
2.5148-3.16820.2191600.20222376100
3.1682-41.690.18521340.15792488100

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