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- PDB-7ojz: SaFtsZ complexed with GMPCP -

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Basic information

Entry
Database: PDB / ID: 7ojz
TitleSaFtsZ complexed with GMPCP
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, GTPase domain / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain ...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, GTPase domain / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANOSYL ESTER / : / Cell division protein FtsZ
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 17, 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)32,4824
Polymers31,9401
Non-polymers5423
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-0 kcal/mol
Surface area13330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.777, 52.180, 85.978
Angle α, β, γ (deg.)90.000, 109.246, 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

#1: Protein Cell division protein FtsZ


Mass: 31940.100 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(DE3) (bacteria) / References: UniProt: P0A031
#2: Chemical ChemComp-GP2 / PHOSPHOMETHYLPHOSPHONIC ACID GUANOSYL ESTER


Mass: 441.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17N5O10P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O
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: 2.34 Å3/Da / Density % sol: 47.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M lithium sulphate , 10% (v/v) ethylene glycol, 0.1 M Tris-HCl pH 8.6, and 26% polyethylene glycol 5000 monomethyl ether

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.65→41.13 Å / Num. obs: 34420 / % possible obs: 96.17 % / Redundancy: 3.4 % / Biso Wilson estimate: 20.35 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.44
Reflection shellResolution: 1.65→1.71 Å / Mean I/σ(I) obs: 2.15 / Num. unique obs: 3365 / CC1/2: 0.777

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Processing

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

6rvn


Resolution: 1.65→41.13 Å / SU ML: 0.1505 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.4332
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1754 1734 5.04 %
Rwork0.1488 32680 -
obs0.1501 34414 96.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.91 Å2
Refinement stepCycle: LAST / Resolution: 1.65→41.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2218 0 33 236 2487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00962330
X-RAY DIFFRACTIONf_angle_d1.12633163
X-RAY DIFFRACTIONf_chiral_restr0.0605378
X-RAY DIFFRACTIONf_plane_restr0.0062418
X-RAY DIFFRACTIONf_dihedral_angle_d21.3036869
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.70.25031320.23062675X-RAY DIFFRACTION94.58
1.7-1.750.28491290.20632704X-RAY DIFFRACTION95.29
1.75-1.820.24641350.19432656X-RAY DIFFRACTION95.06
1.82-1.890.19311510.17572678X-RAY DIFFRACTION95.83
1.89-1.970.21531530.16082709X-RAY DIFFRACTION96.01
1.97-2.080.20671400.14922736X-RAY DIFFRACTION96.32
2.08-2.210.15351520.14612712X-RAY DIFFRACTION96.2
2.21-2.380.15791440.1372713X-RAY DIFFRACTION96.55
2.38-2.620.19421610.1412750X-RAY DIFFRACTION97.29
2.62-30.16941650.14612720X-RAY DIFFRACTION97.53
3-3.780.1661510.14212771X-RAY DIFFRACTION96.63
3.78-41.130.14061210.13692856X-RAY DIFFRACTION96.78
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)
12.92372408014-0.874981371415-2.259365380431.031679646051.095216701472.97579987878-0.0163835585330.1698802773980.635846901785-0.0973722667045-0.0208827811798-0.108249938693-0.3520798738-0.185377267663-0.01639476853470.1775580608220.0261661488176-0.06575375858770.183603309076-0.004775556361130.258029609421-0.6362580744155.0043510113225.6584331896
25.68389473349-2.44857436240.1091926050736.78027432525-0.8058743088214.87402004148-0.02858124407670.1369778333330.627393412176-0.0497013938057-0.0541878565735-0.323975119383-0.3781864723620.09843228887070.1240060824130.176149647564-0.000305044701991-0.0259792260860.15180423499-0.009603967758750.2368202757526.774832234562.8482917429629.8042577702
32.80939672616-2.26380228694-0.938168002875.520246010711.629092980731.83015018496-0.142734455793-0.420990546397-0.02026754154590.5185649920840.0353553544195-0.09673163838120.155326010114-0.03253655591640.08014490599580.2575382461560.0251429357695-0.03379268026680.2692421298880.007966125154180.1376951500774.76771967993-9.1733414993838.9821382016
42.27786944927-1.60223907992-0.4229636316262.516787872261.014315739841.6378570425-0.100429496737-0.1850474261850.02577518661660.1582475955840.03754977441760.0215034505562-0.00285742169839-0.1043917577170.07107964628450.1144853249140.02017859150610.01203494387490.142076542104-0.01462272602490.132941983714-4.82046995621-5.9414038879729.0234311953
54.00113452075-3.77128707677-5.563228833543.56306015085.261968452237.8442774955-0.003657889742920.0557512065686-0.295821300807-0.063104387914-0.3069946059450.3049274492520.0578459930103-0.2767745918630.4078372907650.1971085529870.0121573118038-0.005015019138720.1874950596710.006100788308960.258708285334-4.77618594351-17.702491255825.3855474539
61.795429729680.100463260435-1.621799687750.7988213322620.1919070016853.00186034816-0.07667245332850.120912005312-0.004970910862270.01786890214690.004990394983890.01725505493760.125187819731-0.09866618040460.08396095846690.1486625546910.0240091719832-0.00738346203230.169612877577-0.006431146321020.155147542704-4.35648082795-8.3797475375713.54109766
77.30530345777-6.68556326592-4.273552590057.620909617715.254944959095.900296195760.176217661254-0.07089590792450.470433246269-0.358143048075-0.00742847191763-0.316128782893-0.3182649204780.0419722778742-0.1461975009790.1885509705350.0064237243213-0.01326960830040.1648531879520.009060560304070.194874743591-3.704493997773.9583312290816.5646010975
81.47398436835-0.661790749438-0.03608561275132.652632272090.3791401247091.60305904642-0.155981216857-0.08615510670760.06144394916990.2619864560510.207497930740.11074065379-0.0247151150549-0.00101846416905-0.03988684357180.1671658888530.0511838697370.009889039376030.198793350796-0.01466566530520.184624576636-20.10396512337.2579265450225.6603933426
94.294034992080.275026560002-0.1450905172978.01846588995-3.004360427654.96802454180.1613536255510.5957538299660.0822461898557-0.5415333670930.04306417136460.006020635743380.2048154833810.491015574083-0.1451994174710.1619341403090.05890739656830.05398284451790.270718999739-0.02525831468210.175976227719-16.28194796356.921257545496.33399225756
101.35687533763-2.145459621210.6528662082444.24797514128-0.9695867081231.936023527420.1160661531870.155159726631-0.0443816792188-0.0869856894372-0.05691794554920.09776519991010.02083802749970.0792408174379-0.05490974036260.1183456663560.01302255044710.01643028707690.194519054917-0.01270133159370.143439445285-21.34268947126.391908548312.3174122207
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 - 136
55chain 'A' and (resid 141 through 155 )141 - 155137 - 151
66chain 'A' and (resid 156 through 178 )156 - 178152 - 176
77chain 'A' and (resid 179 through 202 )179 - 202177 - 206
88chain 'A' and (resid 203 through 224 )203 - 224207 - 232
99chain 'A' and (resid 225 through 245 )225 - 245233 - 257
1010chain 'A' and (resid 246 through 315 )246 - 315258 - 327

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