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- PDB-6unx: Structure of E. coli FtsZ(L178E)-GTP complex -

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Basic information

Entry
Database: PDB / ID: 6unx
TitleStructure of E. coli FtsZ(L178E)-GTP complex
ComponentsCell division protein FtsZ
KeywordsCELL CYCLE / FtsZ / cell division / divisive
Function / homology
Function and homology information


divisome complex / chloroplast fission / FtsZ-dependent cytokinesis / division septum assembly / cell division site / protein polymerization / cell division / GTPase activity / GTP binding / identical protein binding ...divisome complex / chloroplast fission / FtsZ-dependent cytokinesis / division septum assembly / cell division site / protein polymerization / cell division / GTPase activity / GTP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Tubulin-like protein FtsZ/CetZ / 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/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal ...Tubulin-like protein FtsZ/CetZ / 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/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
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / : / Cell division protein FtsZ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsSchumacher, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: High-resolution crystal structures of Escherichia coli FtsZ bound to GDP and GTP.
Authors: Schumacher, M.A. / Ohashi, T. / Corbin, L. / Erickson, H.P.
History
DepositionOct 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell division protein FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4432
Polymers33,9201
Non-polymers5231
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.316, 85.142, 41.274
Angle α, β, γ (deg.)90.000, 107.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cell division protein FtsZ


Mass: 33920.301 Da / Num. of mol.: 1 / Mutation: L178E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ftsZ, FIS42_13605 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A501LCM6, UniProt: P0A9A6*PLUS
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 1.85 Å3/Da / Density % sol: 33.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Peg 8000, Cacodylate buffer, 0.15 M calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→42.571 Å / Num. obs: 41849 / % possible obs: 86.3 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rpim(I) all: 0.025 / Rsym value: 0.045 / Net I/σ(I): 15.1
Reflection shellResolution: 1.4→1.435 Å / Mean I/σ(I) obs: 4.1 / Num. unique obs: 1322 / CC1/2: 0.99 / Rpim(I) all: 0.105 / Rsym value: 0.125

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UMK

6umk


Resolution: 1.4→42.571 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 25.25
RfactorNum. reflection% reflection
Rfree0.2033 2000 4.78 %
Rwork0.183 --
obs0.184 41849 86.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 107.94 Å2 / Biso mean: 26.5633 Å2 / Biso min: 9.1 Å2
Refinement stepCycle: final / Resolution: 1.4→42.571 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2198 0 32 304 2534
Biso mean--24.75 35.75 -
Num. residues----306
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4-1.4350.3001660.2382132240
1.435-1.47380.2669840.2241167451
1.4738-1.51720.28731010.2174200161
1.5172-1.56610.2651260.2276251676
1.5661-1.62210.25111570.2095312994
1.6221-1.68710.24391590.2058317998
1.6871-1.76380.22811610.2135320098
1.7638-1.85680.22751640.2104326498
1.8568-1.97320.23741620.2026322698
1.9732-2.12550.20621610.1816321198
2.1255-2.33940.20531630.1799324598
2.3394-2.67790.20041630.183326299
2.6779-3.37360.20261660.1784329399
3.3736-42.5710.16731670.1614332799
Refinement TLS params.Method: refined / Origin x: 14.8742 Å / Origin y: -0.1179 Å / Origin z: 6.9942 Å
111213212223313233
T0.0748 Å2-0.005 Å20.0111 Å2-0.0713 Å2-0.0084 Å2--0.0693 Å2
L1.2016 °20.4948 °2-0.212 °2-0.9514 °2-0.2741 °2--0.6853 °2
S0.0055 Å °0.111 Å °0.0947 Å °0.0508 Å °0.0629 Å °0.0863 Å °0.0013 Å °0.0251 Å °0.1245 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA9 - 316
2X-RAY DIFFRACTION1allT500
3X-RAY DIFFRACTION1allS1 - 305

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