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- PDB-3nxc: Molecular mechanism by which the Escherichia coli nucleoid occlus... -

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Basic information

Entry
Database: PDB / ID: 3nxc
TitleMolecular mechanism by which the Escherichia coli nucleoid occlusion factor, SlmA, keeps cytokinesis in check
ComponentsHTH-type protein slmA
KeywordsDNA BINDING PROTEIN / nucleoid occlusion / cell division / TetR family member
Function / homology
Function and homology information


division septum site selection / negative regulation of protein polymerization / negative regulation of division septum assembly / bacterial nucleoid / sequence-specific DNA binding / transcription cis-regulatory region binding / cell cycle / DNA-binding transcription factor activity / cell division / regulation of DNA-templated transcription ...division septum site selection / negative regulation of protein polymerization / negative regulation of division septum assembly / bacterial nucleoid / sequence-specific DNA binding / transcription cis-regulatory region binding / cell cycle / DNA-binding transcription factor activity / cell division / regulation of DNA-templated transcription / protein homodimerization activity / DNA binding / identical protein binding / 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
Nucleoid occlusion factor SlmA / Nucleoid occlusion factor SlmA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsTonthat, N.K. / Schumacher, M.A.
CitationJournal: Embo J. / Year: 2011
Title: Molecular mechanism by which the nucleoid occlusion factor, SlmA, keeps cytokinesis in check.
Authors: Tonthat, N.K. / Arold, S.T. / Pickering, B.F. / Van Dyke, M.W. / Liang, S. / Lu, Y. / Beuria, T.K. / Margolin, W. / Schumacher, M.A.
History
DepositionJul 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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

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Assembly

Deposited unit
A: HTH-type protein slmA


Theoretical massNumber of molelcules
Total (without water)24,3211
Polymers24,3211
Non-polymers00
Water23413
1
A: HTH-type protein slmA

A: HTH-type protein slmA


Theoretical massNumber of molelcules
Total (without water)48,6422
Polymers48,6422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+2/31
Buried area2910 Å2
ΔGint-5 kcal/mol
Surface area17240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.380, 50.380, 121.320
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein HTH-type protein slmA


Mass: 24321.148 Da / Num. of mol.: 1 / Fragment: unp residues 1-198
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ttk, APECO1_2820, Ecok1_36180 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: A1AHH2, UniProt: P0C093*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 1.83 Å3/Da / Density % sol: 32.69 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris pH 8.5, 10% PEG 400, 58 mM LiSO4, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9795, 0.97953, 0.95372
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 12, 2008 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: KHOZU Double flat crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.979531
30.953721
ReflectionResolution: 2.5→43.727 Å / Num. obs: 6647 / % possible obs: 99.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 6.6 % / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 18.8
Reflection shellResolution: 2.5→2.5 Å / Redundancy: 7 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 4.1 / % possible all: 99.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→43.727 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.265 892 -random
Rwork0.224 ---
obs0.224 6647 71.6 %-
all-6647 --
Displacement parametersBiso mean: 31.078 Å2
Baniso -1Baniso -2Baniso -3
1-2.554 Å20 Å20 Å2
2--2.554 Å20 Å2
3----5.108 Å2
Refinement stepCycle: LAST / Resolution: 2.5→43.727 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1406 0 0 13 1419
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.47
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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