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- PDB-6ll5: Crystal structure of KpFtsZ (residues 11-316) -

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Basic information

Entry
Database: PDB / ID: 6ll5
TitleCrystal structure of KpFtsZ (residues 11-316)
ComponentsCell division protein FtsZ
KeywordsCELL CYCLE / cell dividsion / Klebsiella pneumonie
Function / homology
Function and homology information


chloroplast fission / FtsZ-dependent cytokinesis / division septum assembly / cell division site / protein polymerization / GTPase activity / GTP binding / 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'-DIPHOSPHATE / Cell division protein FtsZ / Cell division protein FtsZ
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsYoshizawa, T. / Fujita, J. / Terakado, 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)JP19am0101070 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 1.1Nov 22, 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)32,3483
Polymers31,8131
Non-polymers5352
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-6 kcal/mol
Surface area13170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.120, 40.930, 44.200
Angle α, β, γ (deg.)89.215, 72.865, 73.443
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 / Filamenting temperature-sensitive mutant Z


Mass: 31813.107 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: ftsZ / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: W9BCK7, UniProt: A0A0H3GRR0*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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 1.93 Å3/Da / Density % sol: 36.2 %
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 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→42.11 Å / Num. obs: 22348 / % possible obs: 93.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 14.37 Å2 / CC1/2: 0.941 / Net I/σ(I): 5.41
Reflection shellResolution: 1.75→1.81 Å / Num. unique obs: 1826 / CC1/2: 0.632

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H5G

5h5g


Resolution: 1.75→42.11 Å / SU ML: 0.1661 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 21.1775
RfactorNum. reflection% reflection
Rfree0.2217 1117 5 %
Rwork0.1793 --
obs0.1814 22343 93.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 18.02 Å2
Refinement stepCycle: LAST / Resolution: 1.75→42.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2203 0 34 147 2384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00662298
X-RAY DIFFRACTIONf_angle_d0.94493125
X-RAY DIFFRACTIONf_chiral_restr0.0579375
X-RAY DIFFRACTIONf_plane_restr0.0045411
X-RAY DIFFRACTIONf_dihedral_angle_d19.0095843
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.830.2511400.21432664X-RAY DIFFRACTION93.69
1.83-1.930.24111420.2012695X-RAY DIFFRACTION94.32
1.93-2.050.2391420.18462698X-RAY DIFFRACTION94.57
2.05-2.210.2421400.1822664X-RAY DIFFRACTION93.75
2.21-2.430.24061400.18262651X-RAY DIFFRACTION93
2.43-2.780.22331370.1892598X-RAY DIFFRACTION91.75
2.78-3.50.21911350.17862589X-RAY DIFFRACTION91.07
3.5-42.110.19111410.15822667X-RAY DIFFRACTION93.54

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