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- PDB-7ysz: Spiroplasma melliferum FtsZ bound to GDP -

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Basic information

Entry
Database: PDB / ID: 7ysz
TitleSpiroplasma melliferum FtsZ bound to GDP
ComponentsCell division protein FtsZ
KeywordsCELL CYCLE / FtsZ / GTP binding / GTPase / cytoskeletal / tubulin homolog
Function / homologyGUANOSINE-5'-DIPHOSPHATE / :
Function and homology information
Biological speciesSpiroplasma melliferum KC3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.30004123971 Å
AuthorsChakraborty, J. / Pananghat, G.
Funding support India, 1items
OrganizationGrant numberCountry
Not funded India
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
DepositionAug 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 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

Downloads & links

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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)68,2695
Polymers67,2602
Non-polymers1,0093
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The protein is majorly monomer but gives a minor peak at dimer at high protein concentration. The crystal structure shows domain swap dimer of the protein.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8680 Å2
ΔGint-65 kcal/mol
Surface area23010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.546, 106.546, 127.603
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-624-

HOH

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Components

#1: Protein Cell division protein FtsZ


Mass: 33630.055 Da / Num. of mol.: 2
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-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
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.69 Å3/Da / Density % sol: 58.87 % / Description: Needle-like crystals
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 1.5M ammonium sulphate, 0.1M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97623 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2.3→49.1606915571 Å / Num. obs: 33121 / % possible obs: 99.7 % / Redundancy: 8.7 % / Biso Wilson estimate: 41.7708032157 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Net I/σ(I): 14.9
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 3217 / CC1/2: 0.808

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VXY

2vxy


Resolution: 2.30004123971→49.1606915571 Å / SU ML: 0.242383543955 / Cross valid method: FREE R-VALUE / σ(F): 1.36521938216 / Phase error: 23.7456102644
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.237164252973 1657 5.00755515261 %
Rwork0.177612682536 31433 -
obs0.180674101114 33090 99.4081773665 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.9619401453 Å2
Refinement stepCycle: LAST / Resolution: 2.30004123971→49.1606915571 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4130 0 64 207 4401
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009683173330294223
X-RAY DIFFRACTIONf_angle_d1.078814783875727
X-RAY DIFFRACTIONf_chiral_restr0.0657432593515709
X-RAY DIFFRACTIONf_plane_restr0.00624637563746741
X-RAY DIFFRACTIONf_dihedral_angle_d16.6886205512522
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.30004123971-2.36770.2967204784591370.2183246738912591X-RAY DIFFRACTION100
2.3677-2.44410.2877763265481160.201021561242600X-RAY DIFFRACTION99.9264164827
2.4441-2.53150.2487913653841240.1921219761262596X-RAY DIFFRACTION99.6702088677
2.5315-2.63280.2653903546091200.1922523241772596X-RAY DIFFRACTION99.7429305913
2.6328-2.75270.2599063418621390.1901790790652580X-RAY DIFFRACTION99.6700879765
2.7527-2.89780.2390337042591630.1819487615412581X-RAY DIFFRACTION99.7818181818
2.8978-3.07930.2778408047681310.1865556179312608X-RAY DIFFRACTION99.7087732071
3.0793-3.3170.2852825390511310.1928169256142618X-RAY DIFFRACTION99.6736765772
3.317-3.65070.25676172621540.1802653793172615X-RAY DIFFRACTION99.5685005394
3.6507-4.17870.2138697077751590.1597347811322619X-RAY DIFFRACTION99.3917710197
4.1787-5.26380.1876698090751390.1517414904092654X-RAY DIFFRACTION98.7274655355

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