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- PDB-6ll6: Crsyal structure of EcFtsZ (residues 11-316) -

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Basic information

Entry
Database: PDB / ID: 6ll6
TitleCrsyal structure of EcFtsZ (residues 11-316)
ComponentsCell division protein FtsZ
KeywordsCELL CYCLE / cell division / Escherichia coli
Function / homology
Function and homology information


divisome complex / division septum assembly / FtsZ-dependent cytokinesis / cell division site / protein polymerization / cell division / GTPase activity / GTP binding / identical protein binding / plasma membrane / 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 family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal ...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 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'-DIPHOSPHATE / Cell division protein FtsZ / Cell division protein FtsZ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsYoshizawa, T. / Fujita, J. / Terakada, H. / Ozawa, M. / Kuroda, N. / Tanaka, S. / Uehara, R. / Matsumura, H.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)15J00589 Japan
Japan Agency for Medical Research and Development (AMED)19am0101070 Japan
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Crystal structures of the cell-division protein FtsZ from Klebsiella pneumoniae and Escherichia coli.
Authors: Yoshizawa, T. / Fujita, J. / Terakado, H. / Ozawa, M. / Kuroda, N. / Tanaka, S.I. / Uehara, R. / Matsumura, H.
History
DepositionDec 21, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Refinement description / Category: 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 FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2562
Polymers31,8131
Non-polymers4431
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-5 kcal/mol
Surface area12890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.280, 41.670, 45.030
Angle α, β, γ (deg.)88.789, 72.057, 72.445
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Cell division protein FtsZ


Mass: 31813.107 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ftsZ, DNQ45_06620 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A2W6PFK5, UniProt: P0A9A6*PLUS
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.04 Å3/Da / Density % sol: 39.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PCB buffer, PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 8681 / % possible obs: 99.6 % / Redundancy: 6.3 % / Biso Wilson estimate: 41.33 Å2 / CC1/2: 0.975 / Net I/σ(I): 5.64
Reflection shellResolution: 2.5→2.56 Å / Num. unique obs: 869 / CC1/2: 0.856

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: unreleased

Resolution: 2.5→42.71 Å / SU ML: 0.3197 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 27.3589
RfactorNum. reflection% reflection
Rfree0.2415 433 4.99 %
Rwork0.1836 --
obs0.1865 8678 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 44.22 Å2
Refinement stepCycle: LAST / Resolution: 2.5→42.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2167 0 28 10 2205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00782216
X-RAY DIFFRACTIONf_angle_d1.00813003
X-RAY DIFFRACTIONf_chiral_restr0.0568359
X-RAY DIFFRACTIONf_plane_restr0.0045396
X-RAY DIFFRACTIONf_dihedral_angle_d20.783797
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.860.29831430.21322737X-RAY DIFFRACTION99.76
2.86-3.610.27071450.20592756X-RAY DIFFRACTION99.79
3.61-42.710.2111450.16382752X-RAY DIFFRACTION99.72

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