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- PDB-7q6d: E. coli FtsA 1-405 ATP 3 Ni -

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Basic information

Entry
Database: PDB / ID: 7q6d
TitleE. coli FtsA 1-405 ATP 3 Ni
ComponentsCell division protein FtsA
KeywordsCELL CYCLE / Bacterial cell division / Divisome / Actin homologue
Function / homology
Function and homology information


divisome complex / division septum assembly / FtsZ-dependent cytokinesis / cell division site / cytoplasmic side of plasma membrane / cell division / ATP binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Cell division protein FtsA / SHS2 domain inserted in FTSA / Cell division protein FtsA / SHS2 domain inserted in FtsA / Cell division protein FtsA / : / ATPase, nucleotide binding domain
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / NICKEL (II) ION / Cell division protein FtsA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsNierhaus, T. / Kureisaite-Ciziene, D. / Lowe, J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust202754/Z/16/Z United Kingdom
Medical Research Council (MRC, United Kingdom)U105184326 United Kingdom
CitationJournal: Nat Microbiol / Year: 2022
Title: Bacterial divisome protein FtsA forms curved antiparallel double filaments when binding to FtsN.
Authors: Nierhaus, T. / McLaughlin, S.H. / Burmann, F. / Kureisaite-Ciziene, D. / Maslen, S.L. / Skehel, J.M. / Yu, C.W.H. / Freund, S.M.V. / Funke, L.F.H. / Chin, J.W. / Lowe, J.
History
DepositionNov 6, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.2Oct 5, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Oct 12, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell division protein FtsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1866
Polymers43,4791
Non-polymers7085
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-35 kcal/mol
Surface area17810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.102, 64.177, 65.285
Angle α, β, γ (deg.)90.000, 96.070, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cell division protein FtsA


Mass: 43478.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ftsA, divA, b0094, JW0092 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P0ABH0
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationY

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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: 2.45 Å3/Da / Density % sol: 49.76 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop
Details: 20 % w/v PEG 4K, 0.175 M (NH4)2SO4, 5 mM Ni(II)Cl2, 0.1 M Tris/HAc pH 7.5, 0.017 M MES/NaOH pH 5.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97948 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 2.7→45.64 Å / Num. all: 11651 / Num. obs: 11651 / % possible obs: 99.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 48.03 Å2 / Rpim(I) all: 0.091 / Rrim(I) all: 0.169 / Rsym value: 0.142 / Net I/av σ(I): 5.3 / Net I/σ(I): 6.8 / Num. measured all: 39110
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.7-2.853.40.8630.9567316830.5521.0270.8631.499.9
2.85-3.023.40.5431.4551316200.3450.6450.5432.199.9
3.02-3.233.40.3662.1506214770.2310.4340.3663.299.9
3.23-3.493.30.2173.6469914030.1390.2590.2175.199.9
3.49-3.823.40.1525436512970.0970.1810.1527.199.9
3.82-4.273.40.0977.7405211810.0620.1150.09710.399.7
4.27-4.933.30.089.1335610240.0520.0960.0812.599.6
4.93-6.043.20.0848.728948920.0540.10.0841199.9
6.04-8.543.30.06511.322856860.0410.0770.06513.699.2
8.54-45.643.10.0415.512113880.0260.0470.0421.298.4

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Processing

Software
NameVersionClassification
PHENIX1.20rc1_4392refinement
REFMAC5.8.230refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WQT (without IC domain)

3wqt


Resolution: 2.8→45.64 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.12 / Phase error: 31.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2691 963 4.93 %
Rwork0.2167 18568 -
obs0.2194 10448 96.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.59 Å2 / Biso mean: 50.9265 Å2 / Biso min: 10.16 Å2
Refinement stepCycle: final / Resolution: 2.8→45.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2877 0 35 0 2912
Biso mean--36.89 --
Num. residues----383
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.950.42351420.32462636277896
2.95-3.130.36961350.28662667280297
3.13-3.370.31221210.24882710283197
3.37-3.710.27181170.22252650276796
3.71-4.250.24821930.19212586277996
4.25-5.350.26471080.17922695280396
5.36-45.640.20361470.1942624277195

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