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- PDB-7yop: Spiroplasma melliferum FtsZ bound to GMPPNP -

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Basic information

Entry
Database: PDB / ID: 7yop
TitleSpiroplasma melliferum FtsZ bound to GMPPNP
ComponentsCell division protein FtsZ
KeywordsCELL CYCLE / FtsZ / GTP binding / GTPase / cytoskeletal / tubulin homolog
Function / homologyGUANOSINE-5'-DIPHOSPHATE / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / :
Function and homology information
Biological speciesSpiroplasma melliferum KC3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.20003123654 Å
AuthorsChakraborty, J. / Pananghat, G.
Funding support India, 1items
OrganizationGrant numberCountry
Not fundedNot funded India
CitationJournal: To Be Published
Title: Structural basis of kinetic polarity of FtsZ from a cell wall-less bacterium Spiroplasma
Authors: Chakraborty, J. / Pananghat, G.
History
DepositionAug 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release

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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)68,3485
Polymers67,2602
Non-polymers1,0883
Water6,161342
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 area8820 Å2
ΔGint-65 kcal/mol
Surface area23410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.593, 106.593, 128.609
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-694-

HOH

21B-702-

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-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.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 2.96 Å3/Da / Density % sol: 58.45 % / Description: Needle shape crystals
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
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: Diamond / Beamline: I04 / Wavelength: 0.97623 Å
DetectorType: DECTRIS PILATUS 6M-F / 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: 2.2→49.2361734647 Å / Num. obs: 38294 / % possible obs: 99.5 % / Redundancy: 5.8 % / Biso Wilson estimate: 33.3678269305 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.031 / Rrim(I) all: 0.075 / Net I/σ(I): 17
Reflection shellResolution: 2.2→2.2 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 17906 / CC1/2: 0.894 / Rpim(I) all: 0.28 / Rrim(I) all: 0.485 / % possible all: 98.9

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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: 2.20003123654→49.2361734647 Å / SU ML: 0.223321967793 / Cross valid method: FREE R-VALUE / σ(F): 1.37111906751 / Phase error: 22.6612563806
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.220382125568 1915 5.00954822508 %
Rwork0.174612619998 36312 -
obs0.176964298638 38227 99.9372565423 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.6665595695 Å2
Refinement stepCycle: LAST / Resolution: 2.20003123654→49.2361734647 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4196 0 68 342 4606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009784789298734296
X-RAY DIFFRACTIONf_angle_d1.014618787675831
X-RAY DIFFRACTIONf_chiral_restr0.0622762461201721
X-RAY DIFFRACTIONf_plane_restr0.00576558943591754
X-RAY DIFFRACTIONf_dihedral_angle_d15.4759178922562
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.20003123654-2.2550.2653622384341340.2142663186562533X-RAY DIFFRACTION99.2556754745
2.255-2.30030.206312015031500.187281176862807X-RAY DIFFRACTION99.9324095978
2.3003-2.3160.2605857832591340.2038679543572543X-RAY DIFFRACTION100
2.316-2.38420.2754644107511310.2001274392582556X-RAY DIFFRACTION100
2.3842-2.46110.2726782617531130.1902987594152570X-RAY DIFFRACTION100
2.4611-2.54910.2039129500531210.1803073033252559X-RAY DIFFRACTION100
2.5491-2.65110.2193494210741340.1824642186172584X-RAY DIFFRACTION100
2.6511-2.77180.2611216087721300.1791897002622547X-RAY DIFFRACTION100
2.7718-2.91790.237846330161570.1861851258922559X-RAY DIFFRACTION100
2.9179-3.10070.2648262016761330.1907367454422591X-RAY DIFFRACTION100
3.1007-3.340.2639557895241320.1807549219922616X-RAY DIFFRACTION100
3.34-3.67610.2127365093711550.1666710904142578X-RAY DIFFRACTION100
3.6761-4.20780.1969932079741530.1473354665432603X-RAY DIFFRACTION100
4.2078-5.30030.1693655760081380.1477257119162666X-RAY DIFFRACTION100

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