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- PDB-4gct: structure of No factor protein-DNA complex -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4gct
Titlestructure of No factor protein-DNA complex
Components
  • DNA (5'-D(*TP*TP*AP*CP*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*CP*GP*TP*AP*A)-3')
  • Nucleoid occlusion factor SlmA
Keywordsdna binding protein/DNA / dna binding protein / dna binding protein-DNA complex / Nucleoid occlusion / ftsz and slma
Function / homology
Function and homology information


negative regulation of division septum assembly / bacterial nucleoid / transcription cis-regulatory region binding / DNA-binding transcription factor activity / cell division / regulation of DNA-templated transcription / cytoplasm
Similarity search - Function
Nucleoid occlusion factor SlmA / : / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Nucleoid occlusion factor SlmA
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsSchumacher, M.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: SlmA forms a higher-order structure on DNA that inhibits cytokinetic Z-ring formation over the nucleoid.
Authors: Tonthat, N.K. / Milam, S.L. / Chinnam, N. / Whitfill, T. / Margolin, W. / Schumacher, M.A.
History
DepositionJul 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Feb 28, 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:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoid occlusion factor SlmA
B: Nucleoid occlusion factor SlmA
C: Nucleoid occlusion factor SlmA
D: Nucleoid occlusion factor SlmA
W: DNA (5'-D(*TP*TP*AP*CP*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*CP*GP*TP*AP*A)-3')
Z: DNA (5'-D(*TP*TP*AP*CP*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*CP*GP*TP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)103,4916
Polymers103,4916
Non-polymers00
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12340 Å2
ΔGint-62 kcal/mol
Surface area36530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.100, 61.360, 121.080
Angle α, β, γ (deg.)90.00, 99.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Nucleoid occlusion factor SlmA


Mass: 22806.291 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: slmA, VC_0214 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KVD2
#2: DNA chain DNA (5'-D(*TP*TP*AP*CP*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*CP*GP*TP*AP*A)-3')


Mass: 6132.991 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: peg 8000, calcium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.03 Å
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.45→119.32 Å / Num. obs: 33622 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 44.7 Å2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→63.75 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1192049.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.276 2678 7.9 %RANDOM
Rwork0.225 ---
obs0.225 33622 90.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.7726 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 48.8 Å2
Baniso -1Baniso -2Baniso -3
1--4.07 Å20 Å2-3.34 Å2
2--10.37 Å20 Å2
3----6.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.45→63.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6154 814 0 228 7196
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d19.3
X-RAY DIFFRACTIONc_improper_angle_d0.99
X-RAY DIFFRACTIONc_mcbond_it2.581.5
X-RAY DIFFRACTIONc_mcangle_it3.952
X-RAY DIFFRACTIONc_scbond_it4.032
X-RAY DIFFRACTIONc_scangle_it5.732.5
LS refinement shellResolution: 2.45→2.6 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.414 335 8 %
Rwork0.384 3857 -
obs--68.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4dna-rna_rep.paramdna-rna.top

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