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- PDB-5k58: Structure of the K. pneumonia SlmA-DNA complex bound to the C-ter... -

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Basic information

Entry
Database: PDB / ID: 5k58
TitleStructure of the K. pneumonia SlmA-DNA complex bound to the C-terminal of the cell division protein FtsZ
Components
  • DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*C)-3')
  • Nucleoid occlusion factor SlmA
  • Octapeptide
KeywordsDNA BINDING PROTEIN/DNA / SlmA / DNA / FtsZ / nucleoid occlusion / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


division septum site selection / negative regulation of protein polymerization / negative regulation of division septum assembly / bacterial nucleoid / divisome complex / chloroplast fission / FtsZ-dependent cytokinesis / division septum assembly / cell division site / protein polymerization ...division septum site selection / negative regulation of protein polymerization / negative regulation of division septum assembly / bacterial nucleoid / divisome complex / chloroplast fission / FtsZ-dependent cytokinesis / division septum assembly / cell division site / protein polymerization / sequence-specific DNA binding / transcription cis-regulatory region binding / cell cycle / DNA-binding transcription factor activity / cell division / GTPase activity / regulation of DNA-templated transcription / GTP binding / protein homodimerization activity / DNA binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Nucleoid occlusion factor SlmA / Tubulin-like protein FtsZ/CetZ / Cell division protein FtsZ / Cell division protein FtsZ, conserved site / Cell division protein FtsZ, C-terminal / FtsZ family, C-terminal domain / FtsZ protein signature 1. / FtsZ protein signature 2. / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. ...Nucleoid occlusion factor SlmA / Tubulin-like protein FtsZ/CetZ / Cell division protein FtsZ / Cell division protein FtsZ, conserved site / Cell division protein FtsZ, C-terminal / FtsZ family, C-terminal domain / FtsZ protein signature 1. / FtsZ protein signature 2. / 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. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Nucleoid occlusion factor SlmA / Cell division protein FtsZ / Nucleoid occlusion factor SlmA
Similarity search - Component
Biological speciesEscherichia coli O139:H28 (bacteria)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.772 Å
AuthorsSchumacher, M.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016
Title: Structures of the nucleoid occlusion protein SlmA bound to DNA and the C-terminal domain of the cytoskeletal protein FtsZ.
Authors: Schumacher, M.A. / Zeng, W.
History
DepositionMay 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Nucleoid occlusion factor SlmA
F: Nucleoid occlusion factor SlmA
A: Nucleoid occlusion factor SlmA
B: Nucleoid occlusion factor SlmA
R: DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*C)-3')
T: DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*C)-3')
L: Octapeptide
K: Octapeptide
N: Octapeptide
M: Octapeptide


Theoretical massNumber of molelcules
Total (without water)99,09110
Polymers99,09110
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15940 Å2
ΔGint-83 kcal/mol
Surface area36200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.800, 84.800, 161.600
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Nucleoid occlusion factor SlmA


Mass: 21996.338 Da / Num. of mol.: 4 / Fragment: UNP residues 9-198
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O139:H28 (strain E24377A / ETEC) (bacteria)
Strain: E24377A / ETEC / Gene: slmA, EcE24377A_4142 / Production host: Escherichia coli (E. coli) / References: UniProt: A7ZTJ2, UniProt: P0C093*PLUS
#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 / Source: (synth.) Synthetic construct (others)
#3: Protein/peptide
Octapeptide


Mass: 945.137 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: LEU-ASP-ILE-PRO-ALA-PHE-LEU-ARG / Source: (synth.) Synthetic construct (others) / References: UniProt: P0A9A6*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 3.39 Å3/Da / Density % sol: 63.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 29% PEG 3000, 0.1 M Tris HCl pH 7.0, 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.36
ReflectionResolution: 2.77→43.435 Å / Num. obs: 32384 / % possible obs: 98.15 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 7
Reflection shellHighest resolution: 2.77 Å / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 1.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.772→43.435 Å / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 39.75
RfactorNum. reflection% reflection
Rfree0.2675 2006 6.19 %
Rwork0.2466 --
obs0.2453 32384 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 112.88 Å2 / Biso mean: 57.21 Å2 / Biso min: 25.72 Å2
Refinement stepCycle: final / Resolution: 2.772→43.435 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6418 486 0 70 6974
Biso mean---47.88 -
Num. residues----814
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057046
X-RAY DIFFRACTIONf_angle_d0.9239574
X-RAY DIFFRACTIONf_chiral_restr0.0331090
X-RAY DIFFRACTIONf_plane_restr0.0041160
X-RAY DIFFRACTIONf_dihedral_angle_d21.1352762
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7794-2.84880.32831500.31182148229890
2.8488-2.92580.31261500.30082194234494
2.9258-3.01190.26011440.27012178232294
3.0119-3.1090.29151420.28072198234094
3.109-3.220.2781540.25842194234893
3.22-3.34890.2381460.21872200234694
3.3489-3.50110.21681400.20852188232894
3.5011-3.68550.40461360.35182078221488
3.6855-3.91610.49671390.45612033217289
3.9161-4.21790.25361270.24812128225590
4.2179-4.64130.18961400.17582198233894
4.6413-5.31070.18641450.17552214235994
5.3107-6.68210.21241430.20152175231894
6.6821-33.43180.1851480.1682192234094

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