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- PDB-5haw: structures of the NO factor SlmA bound to DNA and the cytoskeleta... -

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Basic information

Entry
Database: PDB / ID: 5haw
Titlestructures of the NO factor SlmA bound to DNA and the cytoskeletal cell division protein FtsZ
Components
  • DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*C)-3')
  • FtsZ CTT
  • Nucleoid occlusion factor SlmA
KeywordsCELL CYCLE/DNA / SlmA / nucleoid occlusion / FTsZ / cytokinesis / CELL CYCLE-DNA complex
Function / homology
Function and homology information


negative regulation of division septum assembly / bacterial nucleoid / divisome complex / FtsZ-dependent cytokinesis / division septum assembly / cell division site / protein polymerization / transcription cis-regulatory region binding / cell cycle / DNA-binding transcription factor activity ...negative regulation of division septum assembly / bacterial nucleoid / divisome complex / FtsZ-dependent cytokinesis / division septum assembly / cell division site / protein polymerization / transcription cis-regulatory region binding / cell cycle / DNA-binding transcription factor activity / cell division / GTPase activity / GTP binding / regulation of DNA-templated transcription / 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. / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily ...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. / 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) / Cell division protein FtsZ / Nucleoid occlusion factor SlmA
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 Å
AuthorsSchumacher, M.A. / Zeng, W.
CitationJournal: Proc.Natl.Acad.Sci.USA / 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
DepositionDec 31, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2May 17, 2023Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _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
A: Nucleoid occlusion factor SlmA
B: Nucleoid occlusion factor SlmA
Z: DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*C)-3')
L: FtsZ CTT
K: FtsZ CTT


Theoretical massNumber of molelcules
Total (without water)51,7745
Polymers51,7745
Non-polymers00
Water4,792266
1
A: Nucleoid occlusion factor SlmA
B: Nucleoid occlusion factor SlmA
Z: DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*C)-3')
L: FtsZ CTT
K: FtsZ CTT

A: Nucleoid occlusion factor SlmA
B: Nucleoid occlusion factor SlmA
Z: DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*C)-3')
L: FtsZ CTT
K: FtsZ CTT


Theoretical massNumber of molelcules
Total (without water)103,54710
Polymers103,54710
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area16460 Å2
ΔGint-78 kcal/mol
Surface area34830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.585, 69.585, 249.795
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Nucleoid occlusion factor SlmA


Mass: 22832.260 Da / Num. of mol.: 2 / Fragment: UNP residues 6-196
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (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(*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*C)-3')


Mass: 3662.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein/peptide FtsZ CTT


Mass: 1223.398 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P0A9A6*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 3.52 Å3/Da / Density % sol: 65.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 8000, 0.1 M Imidazole, 0.1 M CaCl2

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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: Oct 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→34.253 Å / Num. obs: 88652 / % possible obs: 82 % / Redundancy: 3 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 10

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALAdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→34.253 Å / FOM work R set: 0.8282 / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0.94 / Phase error: 24.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2198 1994 3.71 %
Rwork0.1922 85366 -
obs0.1932 88652 81.83 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.491 Å2 / ksol: 0.393 e/Å3
Displacement parametersBiso max: 140.12 Å2 / Biso mean: 49.35 Å2 / Biso min: 23.21 Å2
Baniso -1Baniso -2Baniso -3
1-7.3555 Å2-0 Å20 Å2
2--7.3555 Å20 Å2
3----14.711 Å2
Refinement stepCycle: final / Resolution: 1.89→34.253 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3232 243 0 266 3741
Biso mean---55.25 -
Num. residues----405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063548
X-RAY DIFFRACTIONf_angle_d0.9554815
X-RAY DIFFRACTIONf_chiral_restr0.06537
X-RAY DIFFRACTIONf_plane_restr0.003588
X-RAY DIFFRACTIONf_dihedral_angle_d16.8161397
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.89-1.95760.29162030.28855307551051
1.9576-2.03590.25952370.24836513675062
2.0359-2.12860.24893350.23138367870281
2.1286-2.24080.20823360.20899179951587
2.2408-2.38120.24863420.20339191953388
2.3812-2.5650.24023580.19659346970489
2.565-2.8230.21383580.19219297965590
2.823-3.23120.22223850.1939463984891
3.2312-4.06990.19813850.167896671005293
4.0699-34.25880.21933470.19169036938387
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4821-0.41310.20450.1936-0.18010.3187-0.1586-0.5759-0.2587-0.2718-0.2407-0.21550.330.4157-0.00020.3253-0.08920.06820.51310.11040.340430.9145-19.467128.5731
21.1616-0.45030.01640.0214-0.42591.14050.0181-0.59530.026-0.0347-0.13430.0462-0.22120.317-0.00080.3487-0.16210.05010.3933-0.02710.237328.4061-10.613628.9268
30.27690.32150.46990.6525-0.05471.7589-0.0572-0.17780.08250.0433-0.05240.0532-0.24260.0335-00.3626-0.10250.02540.1976-0.02950.308823.2498-4.566115.7115
40.83410.58620.40530.37480.21041.0637-0.18990.09650.0894-0.19620.05040.0717-0.1935-0.029700.4856-0.1306-0.00670.2203-0.01570.337523.0841-5.00113.1856
50.7995-0.5439-0.1390.7748-0.57180.8896-0.110.1291-0.16540.02520.08460.3080.2277-0.4704-00.442-0.26940.08070.5083-0.04050.40880.5961-29.79119.4625
60.5365-0.1999-0.23910.96590.17590.538-0.10660.04420.1995-0.29170.07340.29670.1944-0.495100.4483-0.1672-0.05720.35640.00160.38136.5912-18.625-2.8063
70.8955-0.0295-0.07910.4720.68690.8387-0.08670.0858-0.0399-0.1964-0.0822-0.01750.06370.07630.00020.4793-0.18740.02370.2558-0.0070.293318.2724-20.4278-1.4385
80.57560.14450.30550.53570.07520.288-0.085-0.09370.16-0.0342-0.16280.0499-0.3091-0.149-0.00010.4219-0.0645-0.01930.2923-0.03260.413611.7786-6.75713.3173
90.0624-0.04170.00370.0466-0.02710.00250.2775-0.2301-0.06790.1478-0.2926-0.2946-0.35720.0546-0.00010.5802-0.27360.05480.51530.01730.341137.8793-2.032612.2397
10-0.00380.00250.00060.0161-0.00840.0155-0.0076-0.0172-0.2461-0.32530.0562-0.3751-0.38270.51180.00030.4719-0.21210.10750.4872-0.00120.476337.3805-11.89923.0594
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 7:30)A7 - 30
2X-RAY DIFFRACTION2(chain A and resid 31:79)A31 - 79
3X-RAY DIFFRACTION3(chain A and resid 80:140)A80 - 140
4X-RAY DIFFRACTION4(chain A and resid 141:196)A141 - 196
5X-RAY DIFFRACTION5(chain B and resid 8:61)B8 - 61
6X-RAY DIFFRACTION6(chain B and resid 62:106)B62 - 106
7X-RAY DIFFRACTION7(chain B and resid 107:161)B107 - 161
8X-RAY DIFFRACTION8(chain B and resid 162:196)B162 - 196
9X-RAY DIFFRACTION9(chain L and resid 370:374)L370 - 374
10X-RAY DIFFRACTION10(chain L and resid 375:379)L375 - 379

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