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- PDB-4gck: structure of no-dna complex -

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Basic information

Entry
Database: PDB / ID: 4gck
Titlestructure of no-dna complex
Components
  • DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*C)-3')
  • Nucleoid occlusion factor SlmA
Keywordsdna binding protein/DNA / no / dna binding / dna binding protein-DNA complex
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 / cytoplasm
Similarity search - Function
Tetracyclin repressor-like, C-terminal domain / Nucleoid occlusion factor SlmA / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / : / 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 ...Tetracyclin repressor-like, C-terminal domain / Nucleoid occlusion factor SlmA / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / : / 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 speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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(*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*C)-3')
Z: DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)104,8506
Polymers104,8506
Non-polymers00
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10760 Å2
ΔGint-51 kcal/mol
Surface area33700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.490, 80.750, 201.300
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
Nucleoid occlusion factor SlmA


Mass: 24381.303 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Strain: 342 / Gene: slmA, KPK_0113 / Production host: Escherichia coli (E. coli) / References: UniProt: B5XTG2
#2: DNA chain DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*C)-3')


Mass: 3662.404 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 2.77 Å3/Da / Density % sol: 55.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 200 mM phosphate, 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
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 12, 2011 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.05→74 Å / Num. all: 70495 / Num. obs: 70400 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 23.2 Å2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→74 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2784819.54 / 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
Rfree0.243 7056 10 %RANDOM
Rwork0.218 ---
obs0.218 70239 94.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.2251 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 37.3 Å2
Baniso -1Baniso -2Baniso -3
1--6.49 Å20 Å20 Å2
2--18.51 Å20 Å2
3----12.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.05→74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6154 486 0 448 7088
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d19.9
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_mcbond_it3.071.5
X-RAY DIFFRACTIONc_mcangle_it4.042
X-RAY DIFFRACTIONc_scbond_it5.332
X-RAY DIFFRACTIONc_scangle_it7.052.5
LS refinement shellResolution: 2.05→2.18 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.371 1189 10.4 %
Rwork0.349 10228 -
obs--93.8 %
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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