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- PDB-7ohn: SaFtsZ complexed with GDP, AlF4- and Mg2+ -

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Basic information

Entry
Database: PDB / ID: 7ohn
TitleSaFtsZ complexed with GDP, AlF4- and Mg2+
ComponentsCell division protein FtsZ
KeywordsCELL CYCLE / Cell division protein
Function / homology
Function and homology information


division septum assembly / FtsZ-dependent cytokinesis / cell division site / protein polymerization / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
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. / Tubulin-like protein FtsZ/CetZ / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; ...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. / Tubulin-like protein FtsZ/CetZ / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; / 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 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TETRAFLUOROALUMINATE ION / GUANOSINE-5'-DIPHOSPHATE / : / Cell division protein FtsZ
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsFernandez-Tornero, C. / Ruiz, F.M. / Andreu, J.M.
CitationJournal: Plos Biol. / Year: 2022
Title: FtsZ filament structures in different nucleotide states reveal the mechanism of assembly dynamics.
Authors: Ruiz, F.M. / Huecas, S. / Santos-Aledo, A. / Prim, E.A. / Andreu, J.M. / Fernandez-Tornero, C.
History
DepositionMay 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 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

Downloads & links

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Assembly

Deposited unit
A: Cell division protein FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4395
Polymers33,8291
Non-polymers6104
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-14 kcal/mol
Surface area13610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.141, 52.006, 87.492
Angle α, β, γ (deg.)90.000, 109.794, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cell division protein FtsZ


Mass: 33829.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: ftsZ / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0A031

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Non-polymers , 5 types, 249 molecules

#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.21 Å3/Da / Density % sol: 44.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris-HCl pH 8.6, 24% PEG 5000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9787 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.62→41.16 Å / Num. obs: 37431 / % possible obs: 99.24 % / Redundancy: 3.3 % / Biso Wilson estimate: 22.43 Å2 / CC1/2: 0.996 / Net I/σ(I): 11.9
Reflection shellResolution: 1.62→1.68 Å / Num. unique obs: 3590 / CC1/2: 0.797

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Processing

Software
NameVersionClassification
XDS1.18.2_3874data reduction
PHENIX1.18.2_3874refinement
MOLREPphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RVN

6rvn


Resolution: 1.62→41.16 Å / SU ML: 0.2219 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.4732
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2014 1795 4.8 %
Rwork0.1599 35619 -
obs0.1619 37414 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.09 Å2
Refinement stepCycle: LAST / Resolution: 1.62→41.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2217 0 35 245 2497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00962313
X-RAY DIFFRACTIONf_angle_d1.09923137
X-RAY DIFFRACTIONf_chiral_restr0.0591372
X-RAY DIFFRACTIONf_plane_restr0.0064415
X-RAY DIFFRACTIONf_dihedral_angle_d19.4013864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.670.38761410.32372560X-RAY DIFFRACTION94.44
1.67-1.710.33311550.26112692X-RAY DIFFRACTION99.58
1.71-1.770.25921180.23072771X-RAY DIFFRACTION99.83
1.77-1.830.24631180.21642757X-RAY DIFFRACTION99.76
1.83-1.910.24471340.18322754X-RAY DIFFRACTION99.72
1.91-1.990.18631430.16752758X-RAY DIFFRACTION99.79
1.99-2.10.19681520.15552702X-RAY DIFFRACTION99.79
2.1-2.230.18881390.15112756X-RAY DIFFRACTION99.83
2.23-2.40.1961720.1512727X-RAY DIFFRACTION99.86
2.4-2.640.20171220.14942749X-RAY DIFFRACTION99.55
2.64-3.030.2241250.15652788X-RAY DIFFRACTION99.56
3.03-3.810.18921400.14672759X-RAY DIFFRACTION99.45
3.81-41.160.16841360.14452846X-RAY DIFFRACTION99.04
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)
12.63064529322-1.82545059885-0.1607978689895.352160484660.1206565255742.51523537652-0.115375081480.2400446939420.522229939011-0.0812297222538-0.0483971856891-0.0808914836649-0.3539765248090.01737269529830.05922152246410.215921554326-0.0173478748451-0.05731071086730.158649016950.02277660068040.243362509524-0.5034597583374.9138576596725.7674355387
26.32047203142-2.24747411666-0.6986304487317.17287962307-0.08067591155855.41464123185-0.01503040712850.2009930673060.691780585844-0.15934582581-0.0385245969942-0.277620194905-0.4990804154520.17829966570.1203547075720.21480566303-0.0405207988615-0.03874986048030.169852244308-0.009304297864610.2513584437616.559083808332.9622618716229.6375872475
33.04665516987-3.32890745205-1.24735607787.608134150292.774995173932.52472295404-0.254362527457-0.384388774251-0.008806425447430.4821470444070.226644972334-0.1049907034840.1622335267060.1800281764030.04601219501150.225050834420.0210506109127-0.02213699667530.2148981689710.02282627815510.1361815049764.96942650549-9.04324620538.939419731
42.73023840256-1.82126808134-0.6589060629863.092112958571.340179295032.81078049349-0.116739207086-0.0731268871922-0.04002372218060.1515395269710.01939493829350.106568341838-0.0156325288298-0.04481314571320.1115256336770.114155731075-0.00760138759320.004192879197530.12392767945-0.0006159304172730.163094325895-4.64217983013-5.9596557163329.0438451819
53.0920730879-4.13041488201-4.675242357837.857060731014.533330520178.66793487435-0.1011877907980.0428313680735-0.602658560794-0.0598696282196-0.4132694588070.4716622597370.1416343490990.009043650970450.5662335835790.1708424063340.012146709920.001239442947080.201139814172-0.00253608821320.291804182321-4.658547981-17.899370904525.1071097588
62.27568188278-0.00347843991456-2.309256228540.758855870852-0.2490765266574.0342891871-0.02426244169140.2155814344490.0614323516887-0.07988166061940.03246058327050.02872727797820.116583083481-0.1531700943120.007410808015840.1679181095480.00429256301775-0.01684525989190.191189616160.0005292125905340.175900066826-4.21989640376-8.6011026607413.5833994937
77.87730159767-6.80196350235-4.745653009787.830544388865.058635226876.180253251570.2037678569180.007041140662130.480352238278-0.263687608646-0.0251252915027-0.286413281762-0.2300615863740.0149863705135-0.1861033058970.224839266769-0.00909544940964-0.01201784327980.1669574834010.01744391184590.208276965022-3.432263690253.6828959494616.353264405
83.69812766361-1.92927923493-0.01122870333495.14753968761-0.194170411583.09423386774-0.06968796902960.09915326187410.1865330064140.2648345584650.03664344989050.0482590547137-0.261016773657-0.05751227776330.03942335449420.1747826524210.0336791537741-0.007687681857390.205002994141-0.009349768072170.185886495725-19.8724055987.1687573294625.51080155
94.337808222160.318102188761-0.4702549150327.78769653755-2.846868248734.404396151510.2616189691840.7357700880750.115363550797-0.630594735796-0.240562695706-0.1018003670840.2463934345290.6765445111140.0177894684890.2204742319050.11064030280.04540810790980.4110874044270.008284747900550.213034774129-16.3020291466.211976111576.08785836588
102.58928448107-2.450551773511.154711702283.84400139435-0.9982356724472.424538845930.1527876053070.270385983234-0.138767677357-0.140263192816-0.09455949358960.1509009740870.03158145303920.180979831829-0.04893041438370.1397121010470.01468504219090.01002479055880.225313515514-0.01656886057370.185887968695-21.10263144196.0559212702512.3961356794
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 9 through 33 )9 - 331 - 25
22chain 'A' and (resid 34 through 60 )34 - 6026 - 54
33chain 'A' and (resid 61 through 93 )61 - 9355 - 87
44chain 'A' and (resid 94 through 140 )94 - 14088 - 134
55chain 'A' and (resid 141 through 155 )141 - 155135 - 149
66chain 'A' and (resid 156 through 178 )156 - 178150 - 174
77chain 'A' and (resid 179 through 202 )179 - 202175 - 202
88chain 'A' and (resid 203 through 224 )203 - 224203 - 224
99chain 'A' and (resid 225 through 245 )225 - 245225 - 245
1010chain 'A' and (resid 246 through 315 )246 - 315246 - 319

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