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- PDB-7q6i: Vibrio maritimus FtsA 1-396 ATP and FtsN 1-29, bent tetramers in ... -

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Basic information

Entry
Database: PDB / ID: 7q6i
TitleVibrio maritimus FtsA 1-396 ATP and FtsN 1-29, bent tetramers in double filament arrangement
Components
  • Cell division protein FtsA
  • Cell division protein FtsN (polyAla model)
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 / ATP 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'-TRIPHOSPHATE / Cell division protein FtsA
Similarity search - Component
Biological speciesVibrio maritimus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 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
C: Cell division protein FtsA
D: Cell division protein FtsA
E: Cell division protein FtsA
F: Cell division protein FtsA
G: Cell division protein FtsA
H: Cell division protein FtsA
I: Cell division protein FtsA
J: Cell division protein FtsA
K: Cell division protein FtsA
L: Cell division protein FtsA
M: Cell division protein FtsA
N: Cell division protein FtsA
O: Cell division protein FtsA
P: Cell division protein FtsA
X: Cell division protein FtsN (polyAla model)
Y: Cell division protein FtsN (polyAla model)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)697,23350
Polymers688,72918
Non-polymers8,50432
Water00
1
A: Cell division protein FtsA
X: Cell division protein FtsN (polyAla model)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1734
Polymers46,6422
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
3
C: Cell division protein FtsA
Y: Cell division protein FtsN (polyAla model)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1734
Polymers46,6422
Non-polymers5312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 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
5
E: 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
6
F: 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
7
G: 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
8
H: 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
9
I: 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
10
J: 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
11
K: 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
12
L: 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
13
M: 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
14
N: 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
15
O: 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
16
P: 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)98.692, 119.993, 329.788
Angle α, β, γ (deg.)90.000, 93.760, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
31chain E
41chain G
51chain I
61chain K
71chain M
81chain O
12(chain B and (resid 8 through 269 or resid 290 through 389 or resid 501 through 502))
22chain D
32(chain F and (resid 8 through 269 or resid 290 through 389 or resid 501 through 502))
42(chain H and (resid 8 through 269 or resid 290 through 389 or resid 501 through 502))
52(chain J and (resid 8 through 269 or resid 290 through 389 or resid 501 through 502))
62(chain L and (resid 8 through 269 or resid 290 through 389 or resid 501 through 502))
72(chain N and (resid 8 through 269 or resid 290 through 389 or resid 501 through 502))
82(chain P and (resid 8 through 269 or resid 290 through 389 or resid 501 through 502))
13chain Y
23chain X

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASNASNSERSERchain AAA8 - 3898 - 389
211ASNASNSERSERchain CCC8 - 3898 - 389
311ASNASNSERSERchain EEE8 - 3898 - 389
411ASNASNSERSERchain GGG8 - 3898 - 389
511ASNASNSERSERchain III8 - 3898 - 389
611ASNASNSERSERchain KKK8 - 3898 - 389
711ASNASNSERSERchain MMM8 - 3898 - 389
811ASNASNSERSERchain OOO8 - 3898 - 389
112ASNASNVALVAL(chain B and (resid 8 through 269 or resid 290 through 389 or resid 501 through 502))BB8 - 2698 - 269
122ARGARGSERSER(chain B and (resid 8 through 269 or resid 290 through 389 or resid 501 through 502))BB290 - 389290 - 389
132ATPATPMGMG(chain B and (resid 8 through 269 or resid 290 through 389 or resid 501 through 502))BU - V501 - 502
212ASNASNSERSERchain DDD8 - 3898 - 389
312ASNASNVALVAL(chain F and (resid 8 through 269 or resid 290 through 389 or resid 501 through 502))FF8 - 2698 - 269
322ARGARGSERSER(chain F and (resid 8 through 269 or resid 290 through 389 or resid 501 through 502))FF290 - 389290 - 389
332ATPATPMGMG(chain F and (resid 8 through 269 or resid 290 through 389 or resid 501 through 502))FCA - DA501 - 502
412ASNASNVALVAL(chain H and (resid 8 through 269 or resid 290 through 389 or resid 501 through 502))HH8 - 2698 - 269
422ARGARGSERSER(chain H and (resid 8 through 269 or resid 290 through 389 or resid 501 through 502))HH290 - 389290 - 389
432ATPATPMGMG(chain H and (resid 8 through 269 or resid 290 through 389 or resid 501 through 502))HGA - HA501 - 502
512ASNASNVALVAL(chain J and (resid 8 through 269 or resid 290 through 389 or resid 501 through 502))JJ8 - 2698 - 269
522ARGARGSERSER(chain J and (resid 8 through 269 or resid 290 through 389 or resid 501 through 502))JJ290 - 389290 - 389
532ATPATPMGMG(chain J and (resid 8 through 269 or resid 290 through 389 or resid 501 through 502))JKA - LA501 - 502
612ASNASNVALVAL(chain L and (resid 8 through 269 or resid 290 through 389 or resid 501 through 502))LL8 - 2698 - 269
622ARGARGSERSER(chain L and (resid 8 through 269 or resid 290 through 389 or resid 501 through 502))LL290 - 389290 - 389
632ATPATPMGMG(chain L and (resid 8 through 269 or resid 290 through 389 or resid 501 through 502))LOA - PA501 - 502
712ASNASNVALVAL(chain N and (resid 8 through 269 or resid 290 through 389 or resid 501 through 502))NN8 - 2698 - 269
722ARGARGSERSER(chain N and (resid 8 through 269 or resid 290 through 389 or resid 501 through 502))NN290 - 389290 - 389
732ATPATPMGMG(chain N and (resid 8 through 269 or resid 290 through 389 or resid 501 through 502))NSA - TA501 - 502
812ASNASNVALVAL(chain P and (resid 8 through 269 or resid 290 through 389 or resid 501 through 502))PP8 - 2698 - 269
822ARGARGSERSER(chain P and (resid 8 through 269 or resid 290 through 389 or resid 501 through 502))PP290 - 389290 - 389
832ATPATPMGMG(chain P and (resid 8 through 269 or resid 290 through 389 or resid 501 through 502))PWA - XA501 - 502
113UNKUNKUNKUNKchain YYR1 - 830 - 37
213UNKUNKUNKUNKchain XXQ1 - 830 - 37

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Cell division protein FtsA


Mass: 42531.809 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Details: chain D: amino acids 270-289 are disordered / Source: (gene. exp.) Vibrio maritimus (bacteria) / Gene: ftsA, JCM19240_1885 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A0A090T942
#2: Protein/peptide Cell division protein FtsN (polyAla model)


Mass: 4109.900 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Vibrio maritimus FtsN 1-29 polyAla model for 8 amino acids,Vibrio maritimus FtsN 1-29 polyAla model for 8 amino acids
Source: (synth.) Vibrio maritimus (bacteria)
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / 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: 56.61 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop
Details: 21.645 % v/v PEG 600, 0.125 M MgCl2, 0.1 M Tris/HCl pH 8.5

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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 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00915 Å / Relative weight: 1
ReflectionResolution: 3.6→75.98 Å / Num. obs: 89730 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 111.78 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.067 / Rrim(I) all: 0.177 / Net I/σ(I): 8.6 / Num. measured all: 620636 / Scaling rejects: 1876
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
3.6-3.697.11.1974675065790.9830.4891.2941.8100
16.1-75.986.50.049700610720.9970.020.0532398.9

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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: 7Q6F

7q6f


Resolution: 3.6→49.88 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.287 4323 4.85 %
Rwork0.2406 84808 -
obs0.2428 89131 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 791.37 Å2 / Biso mean: 115.6282 Å2 / Biso min: 36.34 Å2
Refinement stepCycle: final / Resolution: 3.6→49.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms45750 0 512 0 46262
Biso mean--97.2 --
Num. residues----6109
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A9320X-RAY DIFFRACTION8.987TORSIONAL
12C9320X-RAY DIFFRACTION8.987TORSIONAL
13E9320X-RAY DIFFRACTION8.987TORSIONAL
14G9320X-RAY DIFFRACTION8.987TORSIONAL
15I9320X-RAY DIFFRACTION8.987TORSIONAL
16K9320X-RAY DIFFRACTION8.987TORSIONAL
17M9320X-RAY DIFFRACTION8.987TORSIONAL
18O9320X-RAY DIFFRACTION8.987TORSIONAL
21B8784X-RAY DIFFRACTION8.987TORSIONAL
22D8784X-RAY DIFFRACTION8.987TORSIONAL
23F8784X-RAY DIFFRACTION8.987TORSIONAL
24H8784X-RAY DIFFRACTION8.987TORSIONAL
25J8784X-RAY DIFFRACTION8.987TORSIONAL
26L8784X-RAY DIFFRACTION8.987TORSIONAL
27N8784X-RAY DIFFRACTION8.987TORSIONAL
28P8784X-RAY DIFFRACTION8.987TORSIONAL
31Y46X-RAY DIFFRACTION8.987TORSIONAL
32X46X-RAY DIFFRACTION8.987TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.6-3.640.41251370.36852827296499
3.64-3.680.41381250.35822782290799
3.68-3.730.37221450.34172802294799
3.73-3.780.38071210.33742822294399
3.78-3.830.4191260.318328122938100
3.83-3.880.39551510.309828162967100
3.88-3.930.33721400.31812787292799
3.93-3.990.35261400.299128582998100
3.99-4.050.32411560.294827432899100
4.05-4.120.39721660.291228633029100
4.12-4.190.32781520.282527352887100
4.19-4.270.32281370.256728342971100
4.27-4.350.27141260.2528092935100
4.35-4.440.29141530.239228773030100
4.44-4.540.28861730.224427352908100
4.54-4.640.25741290.219528242953100
4.64-4.760.28471420.215428222964100
4.76-4.890.2661590.223428242983100
4.89-5.030.25241590.223828312990100
5.03-5.190.29721400.234828663006100
5.19-5.380.30131320.24428092941100
5.38-5.590.34621350.255228222957100
5.59-5.850.3211450.258828442989100
5.85-6.150.33851420.257428583000100
6.15-6.540.28151450.24728452990100
6.54-7.040.28781530.236128733026100
7.04-7.750.261580.207528062964100
7.75-8.860.20241430.178728693012100
8.86-11.150.17821400.16528923032100
11.15-49.880.24871530.2212921307499

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