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- PDB-5hsz: Structure of the K. pneumonia SlmA protein bound to the C-termina... -

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Basic information

Entry
Database: PDB / ID: 5hsz
TitleStructure of the K. pneumonia SlmA protein bound to the C-terminal tail of the cytoskeletal cell division protein FtsZ
Components
  • C-terminal Tail of FtsZ
  • Nucleoid occlusion factor SlmA
KeywordsCELL CYCLE / SlmA / nucleoid occlusion / FtsZ / Z-ring / cell division / cytokinesis
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 / sequence-specific DNA binding / cell cycle / cell division ...negative regulation of division septum assembly / bacterial nucleoid / divisome complex / FtsZ-dependent cytokinesis / division septum assembly / cell division site / protein polymerization / sequence-specific DNA binding / cell cycle / cell division / GTPase activity / GTP 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
Nucleoid occlusion factor SlmA / Cell division protein FtsZ
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsZeng, W. / Schumacher, M.A.
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
DepositionJan 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / 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
K: C-terminal Tail of FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8706
Polymers46,5823
Non-polymers2883
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-53 kcal/mol
Surface area17830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.261, 69.261, 325.613
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Nucleoid occlusion factor SlmA


Mass: 22654.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578) (bacteria)
Strain: ATCC 700721 / MGH 78578 / Gene: slmA, KPN78578_39420, KPN_03981 / Production host: Escherichia coli (E. coli) / References: UniProt: A6TFN2
#2: Protein/peptide C-terminal Tail of FtsZ


Mass: 1273.523 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P0A9A6*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.42 Å3/Da / Density % sol: 49.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 600 mM Sodium phosphate, 1200 mM potassium phosphate, 0.1 M imidazole pH 8.0, 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: Dec 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→59.982 Å / Num. obs: 34960 / % possible obs: 90 % / Redundancy: 4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→59.982 Å / FOM work R set: 0.7878 / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.08 / Phase error: 27.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2674 3497 10 %
Rwork0.2156 31463 -
obs0.2207 34960 90.04 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.151 Å2 / ksol: 0.334 e/Å3
Displacement parametersBiso max: 173.82 Å2 / Biso mean: 50.71 Å2 / Biso min: 10.42 Å2
Baniso -1Baniso -2Baniso -3
1-5.8222 Å2-0 Å2-0 Å2
2--5.8222 Å20 Å2
3----11.6445 Å2
Refinement stepCycle: final / Resolution: 2.3→59.982 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3219 0 15 108 3342
Biso mean--105.4 41.34 -
Num. residues----397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023272
X-RAY DIFFRACTIONf_angle_d0.5344393
X-RAY DIFFRACTIONf_chiral_restr0.039497
X-RAY DIFFRACTIONf_plane_restr0.001567
X-RAY DIFFRACTIONf_dihedral_angle_d15.6361274
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 (%)
2.3-2.38220.31852370.24382085232260
2.3822-2.47760.32242760.25272446272270
2.4776-2.59040.31823130.24412785309881
2.5904-2.72690.31343560.23253225358192
2.7269-2.89780.29653860.25733471385799
2.8978-3.12150.34813830.251734793862100
3.1215-3.43560.28533960.232635013897100
3.4356-3.93270.23043900.191634663856100
3.9327-4.95440.20153840.168135333917100
4.9544-60.00220.26293760.21963472384899
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)
10.04670.07650.00190.1305-0.08310.1891-0.39990.0013-0.03910.14090.2162-0.0069-0.30640.004-0.00110.3888-0.06140.05810.25140.10530.258324.265-8.0717-32.6046
20.33780.1787-0.35090.30250.22131.3097-0.0465-0.13490.13530.023-0.071-0.0877-0.63450.1335-0.0230.0768-0.02110.02050.16320.0280.157323.3073-17.2898-11.8388
30.7818-0.1345-0.25971.6906-0.00060.661-0.0936-0.3249-0.1388-0.6463-0.1634-0.01490.1292-0.15860.0455-0.32930.05720.07240.15910.03010.181219.4653-27.5058-9.2473
40.7989-0.1775-0.03470.24270.36161.35540.017-0.1926-0.0758-0.03110.1067-0.0365-0.4695-0.4110.12730.11850.07390.03560.1790.02510.118511.5307-16.2987-3.8383
50.2415-0.09890.06040.0569-0.00710.032-0.1856-0.0755-0.0523-0.2508-0.0913-0.07020.14050.08310.00240.4512-0.1385-0.10851.15090.40150.4501-18.4942-19.6988-34.0256
60.20510.49860.03351.1929-0.0210.0814-0.42250.3457-0.0846-0.53960.74060.3310.4202-0.55120.01220.3046-0.0483-0.06770.85970.17850.1945-6.1388-17.4851-30.7993
70.879-0.0258-0.24580.46360.14470.83830.10780.02530.04280.0050.1612-0.104-0.5229-0.86520.31660.17610.23150.07040.40640.12210.1502-3.3781-13.9702-7.5967
80.75630.0629-0.14010.5789-0.06470.0449-0.2754-0.2486-0.16880.14340.4344-0.24960.1305-0.0822-0.1448-0.28210.16040.05060.25190.05490.18373.2685-25.8035-6.3898
90.0426-0.00050.0350.0038-0.01270.07110.0479-0.108-0.0109-0.1277-0.0149-0.1631-0.04090.0450.02150.3986-0.14560.09770.38420.04560.065128.5502-10.4015-11.1181
100.00820.0062-0.00490.0037-0.00190.00280.00270.0511-0.03370.0249-0.0497-0.06140.0430.0492-00.922-0.15430.17740.48340.06740.719230.6426-1.084-19.5303
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 11:55)A11 - 55
2X-RAY DIFFRACTION2(chain A and resid 56:115)A56 - 115
3X-RAY DIFFRACTION3(chain A and resid 116:150)A116 - 150
4X-RAY DIFFRACTION4(chain A and resid 151:198)A151 - 198
5X-RAY DIFFRACTION5(chain B and resid 3:17)B3 - 17
6X-RAY DIFFRACTION6(chain B and resid 18:74)B18 - 74
7X-RAY DIFFRACTION7(chain B and resid 75:172)B75 - 172
8X-RAY DIFFRACTION8(chain B and resid 173:198)B173 - 198
9X-RAY DIFFRACTION9(chain K and resid 372:377)K372 - 377
10X-RAY DIFFRACTION10(chain K and resid 378:382)K378 - 382

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