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- PDB-7q6f: Vibrio maritimus FtsA 1-396 ATP, double filament -

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Basic information

Entry
Database: PDB / ID: 7q6f
TitleVibrio maritimus FtsA 1-396 ATP, double filament
ComponentsCell division protein FtsA
KeywordsCELL CYCLE / Bacterial cell division / Divisome / Actin homologue
Function / homology
Function and homology information


FtsZ-dependent cytokinesis / cell division site / cytoplasmic side of plasma membrane
Similarity search - Function
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 / Cell division protein FtsA
Similarity search - Component
Biological speciesVibrio maritimus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.31 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 7, 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division protein FtsA
B: Cell division protein FtsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,1276
Polymers85,0642
Non-polymers1,0634
Water00
1
A: Cell division protein FtsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0633
Polymers42,5321
Non-polymers5312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cell division protein FtsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0633
Polymers42,5321
Non-polymers5312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.503, 109.628, 92.490
Angle α, β, γ (deg.)90.000, 102.140, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: SER / End label comp-ID: SER / Auth seq-ID: 8 - 389 / Label seq-ID: 8 - 389

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein Cell division protein FtsA


Mass: 42531.809 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio maritimus (bacteria) / Gene: ftsA, JCM19240_1885 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: A0A090T942
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestY

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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: 2.83 Å3/Da / Density % sol: 56.48 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop
Details: 25.236 % v/v PEG 400, 2 % v/v 2 propanol, 0.17 M MgCl2, 0.04 M CaAc2, 0.08 M Tris/HCl pH 8.5, 0.02 M MES/NaOH pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.31→109.76 Å / Num. obs: 14187 / % possible obs: 99.4 % / Redundancy: 6.9 % / Biso Wilson estimate: 59.64 Å2 / CC1/2: 0.978 / Rmerge(I) obs: 0.297 / Rpim(I) all: 0.12 / Rrim(I) all: 0.321 / Net I/σ(I): 5.9 / Num. measured all: 98562 / Scaling rejects: 182
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.31-3.46.41.309668610380.9540.5441.4192.299
14.8-109.766.60.08611721770.9950.0340.0929.799.7

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Processing

Software
NameVersionClassification
PHENIX1.20rc1_4392refinement
REFMAC5.8.0230refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7Q6D

7q6d


Resolution: 3.31→47.42 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2686 701 4.99 %
Rwork0.2303 13357 -
obs0.2322 14058 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.44 Å2 / Biso mean: 57.1669 Å2 / Biso min: 14.99 Å2
Refinement stepCycle: final / Resolution: 3.31→47.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5726 0 64 0 5790
Biso mean--42.13 --
Num. residues----764
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2330X-RAY DIFFRACTION1.41TORSIONAL
12B2330X-RAY DIFFRACTION1.41TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.31-3.570.36451340.31742627276198
3.57-3.920.3051220.268126812803100
3.92-4.490.25121660.217826672833100
4.49-5.660.26261310.20962667279899
5.66-47.420.22731480.19432715286399

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