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- PDB-6mj1: Crystal structure of RefZ (regulator of FtsZ) from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 6mj1
TitleCrystal structure of RefZ (regulator of FtsZ) from Bacillus subtilis
ComponentsProbable HTH-type transcriptional regulator YttP
KeywordsDNA BINDING PROTEIN / TetR family / cell division / FtsZ regulator
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function
DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Probable HTH-type transcriptional regulator YttP
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsKrieger, I.V. / Brown, E.E. / Herman, J.K. / Sacchettini, J.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1514629 United States
CitationJournal: J.Bacteriol. / Year: 2019
Title: A DNA-Binding Protein Tunes Septum Placement during Bacillus subtilis Sporulation.
Authors: Brown, E.E. / Miller, A.K. / Krieger, I.V. / Otto, R.M. / Sacchettini, J.C. / Herman, J.K.
History
DepositionSep 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 30, 2020Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.5Mar 13, 2024Group: 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:
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Assembly

Deposited unit
A: Probable HTH-type transcriptional regulator YttP


Theoretical massNumber of molelcules
Total (without water)24,4161
Polymers24,4161
Non-polymers00
Water45025
1
A: Probable HTH-type transcriptional regulator YttP

A: Probable HTH-type transcriptional regulator YttP


Theoretical massNumber of molelcules
Total (without water)48,8322
Polymers48,8322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3450 Å2
ΔGint-21 kcal/mol
Surface area19310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.021, 100.021, 100.177
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-319-

HOH

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Components

#1: Protein Probable HTH-type transcriptional regulator YttP / Stress response protein YttP


Mass: 24416.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: yttP, BSU29630 / Production host: Escherichia coli (E. coli) / References: UniProt: O34970
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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

Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8
Details: 10% ethanol (v/v), 0.1 M imidazole [pH 8.0], and 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 16237 / % possible obs: 100 % / Redundancy: 17.59 % / Rmerge(I) obs: 0.1127 / Net I/σ(I): 11.59
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 14.05 % / Rmerge(I) obs: 0.7929 / Num. unique obs: 714 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
SAINTdata reduction
SADABSdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→44.745 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.81
RfactorNum. reflection% reflection
Rfree0.2536 734 4.58 %
Rwork0.222 --
obs0.2236 16039 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→44.745 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1671 0 0 25 1696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091730
X-RAY DIFFRACTIONf_angle_d1.0822335
X-RAY DIFFRACTIONf_dihedral_angle_d7.4261469
X-RAY DIFFRACTIONf_chiral_restr0.056257
X-RAY DIFFRACTIONf_plane_restr0.007290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.80070.36321400.3393013X-RAY DIFFRACTION100
2.8007-3.08250.39551320.30563026X-RAY DIFFRACTION99
3.0825-3.52840.33081520.27682964X-RAY DIFFRACTION97
3.5284-4.44480.24291260.2213077X-RAY DIFFRACTION99
4.4448-44.75130.20861840.17823225X-RAY DIFFRACTION100

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