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- PDB-7q6g: Xenorhabdus poinarii FtsA 1-396 ADP -

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Basic information

Entry
Database: PDB / ID: 7q6g
TitleXenorhabdus poinarii FtsA 1-396 ADP
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 / nucleotide binding / metal ion binding
Similarity search - Function
Dna Ligase; domain 1 - #110 / Cell division protein FtsA / SHS2 domain inserted in FTSA / Cell division protein FtsA / SHS2 domain inserted in FtsA / Cell division protein FtsA / : / Dna Ligase; domain 1 / ATPase, nucleotide binding domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Cell division protein FtsA
Similarity search - Component
Biological speciesXenorhabdus poinarii G6 (bacteria)
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 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 / pdbx_initial_refinement_model

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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)42,9613
Polymers42,5091
Non-polymers4522
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-18 kcal/mol
Surface area17510 Å2
Unit cell
Length a, b, c (Å)142.276, 70.715, 50.719
Angle α, β, γ (deg.)90.000, 100.980, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cell division protein FtsA


Mass: 42509.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenorhabdus poinarii G6 (bacteria) / Gene: ftsA, XPG1_0684 / Production host: Escherichia coli (E. coli) / Strain (production host): CD41(DE3) / References: UniProt: A0A068QZX9
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / 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: 2.95 Å3/Da / Density % sol: 58.25 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop
Details: 1 M sodium succinate pH 7.0, 0.1 M bis-tris-propane pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.00915 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00915 Å / Relative weight: 1
ReflectionResolution: 2.8→40.85 Å / Num. obs: 12283 / % possible obs: 99.9 % / Redundancy: 3.4 % / CC1/2: 0.796 / Rmerge(I) obs: 0.257 / Rpim(I) all: 0.165 / Rrim(I) all: 0.306 / Net I/σ(I): 4.4 / Num. measured all: 41563 / Scaling rejects: 82
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
2.8-2.8730.85726528950.6360.5841.0411.199.9
12.52-40.853.30.1194631410.9520.0770.142997.6

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.17.1_3660refinement
REFMAC5.8.0230refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7Q6D

7q6d


Resolution: 2.8→40.83 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 0.06 / Phase error: 28.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2603 1142 5.03 %
Rwork0.2181 21573 -
obs0.2201 12241 95.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.86 Å2 / Biso mean: 41.7795 Å2 / Biso min: 13.17 Å2
Refinement stepCycle: final / Resolution: 2.8→40.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2914 0 28 0 2942
Biso mean--36.78 --
Num. residues----388
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.930.3841480.31412521266991
2.93-3.080.30881510.27292704285595
3.08-3.270.32651430.26822689283296
3.27-3.530.36791450.26212664280994
3.53-3.880.29091510.24042719287095
3.88-4.440.25151070.19152761286896
4.44-5.60.18611340.17022751288596
5.6-40.830.18191630.17162764292798

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