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- PDB-6rvn: aFtsz-GDP-Wat -

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Basic information

Entry
Database: PDB / ID: 6rvn
TitleaFtsz-GDP-Wat
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
GUANOSINE-5'-DIPHOSPHATE / Cell division protein FtsZ
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.242 Å
AuthorsFernandez-Tornero, C. / Andreu, J.M.
CitationJournal: Febs J. / Year: 2020
Title: Nucleotide-induced folding of cell division protein FtsZ from Staphylococcus aureus.
Authors: Huecas, S. / Canosa-Valls, A.J. / Araujo-Bazan, L. / Ruiz, F.M. / Laurents, D.V. / Fernandez-Tornero, C. / Andreu, J.M.
History
DepositionMay 31, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: 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)32,3083
Polymers31,8251
Non-polymers4832
Water3,423190
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-16 kcal/mol
Surface area13680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.670, 51.324, 88.171
Angle α, β, γ (deg.)90.00, 110.88, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cell division protein FtsZ


Mass: 31825.014 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 (E. coli) / References: UniProt: P0A031
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

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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: 2.38 Å3/Da / Density % sol: 48.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25% PEG5K MME, 10% EthGly, 0.2 M Li2SO4, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 273 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.24→41.19 Å / Num. obs: 84186 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.993 / Net I/σ(I): 8.2
Reflection shellResolution: 1.24→1.31 Å / Num. unique obs: 12233 / CC1/2: 0.71

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MN4

5mn4


Resolution: 1.242→41.19 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 24.72
RfactorNum. reflection% reflection
Rfree0.2098 3983 4.75 %
Rwork0.1949 --
obs0.1957 83877 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.242→41.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2221 0 29 190 2440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192268
X-RAY DIFFRACTIONf_angle_d1.6823067
X-RAY DIFFRACTIONf_dihedral_angle_d18.145832
X-RAY DIFFRACTIONf_chiral_restr0.114366
X-RAY DIFFRACTIONf_plane_restr0.012404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2416-1.25670.35811340.33182809X-RAY DIFFRACTION97
1.2567-1.27270.30731470.30632752X-RAY DIFFRACTION98
1.2727-1.28940.30621200.29632851X-RAY DIFFRACTION98
1.2894-1.30710.31420.28572779X-RAY DIFFRACTION98
1.3071-1.32570.28351370.27992822X-RAY DIFFRACTION99
1.3257-1.34550.33581330.27222825X-RAY DIFFRACTION99
1.3455-1.36660.28131310.25412854X-RAY DIFFRACTION100
1.3666-1.3890.25631330.24532869X-RAY DIFFRACTION100
1.389-1.41290.22451340.24862859X-RAY DIFFRACTION100
1.4129-1.43860.27151430.23162858X-RAY DIFFRACTION100
1.4386-1.46630.26441350.22922890X-RAY DIFFRACTION100
1.4663-1.49620.24831260.2292819X-RAY DIFFRACTION99
1.4962-1.52870.22671460.21812864X-RAY DIFFRACTION100
1.5287-1.56430.25271550.20622841X-RAY DIFFRACTION100
1.5643-1.60340.22851650.19822830X-RAY DIFFRACTION100
1.6034-1.64680.24031510.20022842X-RAY DIFFRACTION100
1.6468-1.69520.20291520.18752887X-RAY DIFFRACTION100
1.6952-1.750.23771340.19612831X-RAY DIFFRACTION100
1.75-1.81250.21561270.19832880X-RAY DIFFRACTION100
1.8125-1.88510.21911520.19822878X-RAY DIFFRACTION100
1.8851-1.97090.26091360.20272875X-RAY DIFFRACTION100
1.9709-2.07480.19931360.18672847X-RAY DIFFRACTION100
2.0748-2.20480.20821680.18332880X-RAY DIFFRACTION100
2.2048-2.3750.19381220.18272863X-RAY DIFFRACTION100
2.375-2.61390.19651240.18632916X-RAY DIFFRACTION99
2.6139-2.99210.20161530.19412873X-RAY DIFFRACTION99
2.9921-3.76930.21041740.18422862X-RAY DIFFRACTION100
3.7693-41.21220.17331730.17542938X-RAY DIFFRACTION99

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