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- PDB-4gcl: structure of no-dna factor -

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Basic information

Entry
Database: PDB / ID: 4gcl
Titlestructure of no-dna factor
Components
  • DNA (5'-D(*AP*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*CP*T)-3')
  • Nucleoid occlusion factor SlmA
Keywordsdna binding protein/DNA / dna binding protein / dna binding protein-DNA complex
Function / homology
Function and homology information


negative regulation of division septum assembly / bacterial nucleoid / cell cycle / sequence-specific DNA binding / cell division / cytoplasm
Similarity search - Function
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 ...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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
E: Nucleoid occlusion factor SlmA
F: Nucleoid occlusion factor SlmA
G: Nucleoid occlusion factor SlmA
H: Nucleoid occlusion factor SlmA
W: DNA (5'-D(*AP*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*CP*T)-3')
Z: DNA (5'-D(*AP*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*CP*T)-3')
R: DNA (5'-D(*AP*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*CP*T)-3')
T: DNA (5'-D(*AP*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,46916
Polymers211,68812
Non-polymers7814
Water7,062392
1
A: Nucleoid occlusion factor SlmA
B: Nucleoid occlusion factor SlmA
C: Nucleoid occlusion factor SlmA
D: Nucleoid occlusion factor SlmA
W: DNA (5'-D(*AP*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*CP*T)-3')
Z: DNA (5'-D(*AP*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,2358
Polymers105,8446
Non-polymers3902
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12920 Å2
ΔGint-50 kcal/mol
Surface area34260 Å2
MethodPISA
2
E: Nucleoid occlusion factor SlmA
F: Nucleoid occlusion factor SlmA
G: Nucleoid occlusion factor SlmA
H: Nucleoid occlusion factor SlmA
R: DNA (5'-D(*AP*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*CP*T)-3')
T: DNA (5'-D(*AP*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,2358
Polymers105,8446
Non-polymers3902
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12950 Å2
ΔGint-46 kcal/mol
Surface area33530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.290, 160.520, 201.100
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: 24321.148 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: UTI89 / UPEC / Gene: ttk, slmA, UTI89_C4185 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1R4V1
#2: DNA chain
DNA (5'-D(*AP*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*CP*T)-3')


Mass: 4279.803 Da / Num. of mol.: 4 / Source method: obtained synthetically
#3: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.68 Å3/Da / Density % sol: 54.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: sodium/potassium phosphate, pH 7.5, 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 23, 2011
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.65→125 Å / Num. all: 3494 / Num. obs: 61320 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 57.5 Å2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→64.39 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3029863.65 / 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 6993 11.4 %RANDOM
Rwork0.23 ---
obs0.23 61320 91.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.9868 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 50.5 Å2
Baniso -1Baniso -2Baniso -3
1--12.43 Å20 Å20 Å2
2--36.12 Å20 Å2
3----23.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 2.65→64.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12346 1136 48 392 13922
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d19.2
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it4.071.5
X-RAY DIFFRACTIONc_mcangle_it5.952
X-RAY DIFFRACTIONc_scbond_it6.812
X-RAY DIFFRACTIONc_scangle_it9.112.5
LS refinement shellResolution: 2.65→2.82 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.392 1120 11.1 %
Rwork0.352 8966 -
obs--91.3 %
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
X-RAY DIFFRACTION5mes.param.txtmes.top

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