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- PDB-8grw: Spiroplasma melliferum FtsZ F224M bound to GDP -

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Basic information

Entry
Database: PDB / ID: 8grw
TitleSpiroplasma melliferum FtsZ F224M bound to GDP
ComponentsCell division protein FtsZ
KeywordsCELL CYCLE / FtsZ / GTPase / cytoskeletal / Tubulin homolog
Function / homologyGUANOSINE-5'-DIPHOSPHATE / :
Function and homology information
Biological speciesSpiroplasma melliferum KC3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.40005414899 Å
AuthorsChakraborty, J. / Pananghat, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Dynamics of interdomain rotation facilitates FtsZ filament assembly.
Authors: Chakraborty, J. / Poddar, S. / Dutta, S. / Bahulekar, V. / Harne, S. / Srinivasan, R. / Gayathri, P.
History
DepositionSep 2, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: Database references / Category: citation / citation_author
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell division protein FtsZ
B: Cell division protein FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2375
Polymers67,2282
Non-polymers1,0093
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8880 Å2
ΔGint-63 kcal/mol
Surface area23140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.669, 106.669, 128.781
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11B-570-

HOH

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Components

#1: Protein Cell division protein FtsZ


Mass: 33614.074 Da / Num. of mol.: 2 / Mutation: F224M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spiroplasma melliferum KC3 (bacteria) / Gene: ftsZ, SPM_000165 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 AI / References: UniProt: A0A037UPJ1
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.72 Å3/Da / Density % sol: 59.28 % / Description: Needle shape crystal
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.3M sodium acetate, 0.1M Tris pH 8.5, 15% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→106.67 Å / Num. obs: 29504 / % possible obs: 99.5 % / Redundancy: 7 % / Biso Wilson estimate: 38.6527126985 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.096 / Net I/σ(I): 15.1
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.684 / Num. unique obs: 3038 / CC1/2: 0.785

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YSZ

7ysz


Resolution: 2.40005414899→49.2757806587 Å / SU ML: 0.270757548432 / Cross valid method: FREE R-VALUE / σ(F): 1.34748269832 / Phase error: 24.4056862686
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.237706230635 1503 5.09889066051 %
Rwork0.193474856323 27974 -
obs0.195785312543 29477 99.215752272 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.2142735292 Å2
Refinement stepCycle: LAST / Resolution: 2.40005414899→49.2757806587 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4148 0 64 122 4334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006668705205634238
X-RAY DIFFRACTIONf_angle_d0.8322690153015742
X-RAY DIFFRACTIONf_chiral_restr0.0538132201063710
X-RAY DIFFRACTIONf_plane_restr0.00414079178607743
X-RAY DIFFRACTIONf_dihedral_angle_d16.7766119342541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.47750.2807407873761300.2256778677682476X-RAY DIFFRACTION98.6000756716
2.4775-2.56610.2686914538591200.2245219853072516X-RAY DIFFRACTION99.5092487731
2.5661-2.66880.2804039025021270.2214036062812513X-RAY DIFFRACTION99.4724943482
2.6688-2.79020.2817481811331440.2145322565082496X-RAY DIFFRACTION99.3227990971
2.7902-2.93730.2788874353771390.2213640732592508X-RAY DIFFRACTION99.4365138993
2.9373-3.12130.3068082226171330.2205754630872535X-RAY DIFFRACTION99.7010463378
3.1213-3.36230.3212298598641280.2269292509012537X-RAY DIFFRACTION99.2551210428
3.3623-3.70060.2513903456311550.1945335020922533X-RAY DIFFRACTION99.5924416451
3.7006-4.23580.2050330086111520.1775117765482551X-RAY DIFFRACTION99.375
4.2358-5.33560.1869688303631320.1596780363022606X-RAY DIFFRACTION99.3108451215

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