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- PDB-3m8k: Protein structure of type III plasmid segregation TubZ -

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Basic information

Entry
Database: PDB / ID: 3m8k
TitleProtein structure of type III plasmid segregation TubZ
ComponentsFtsZ/tubulin-related protein
KeywordsSTRUCTURAL PROTEIN / tubulin-like protein / plasmid segregation / GTP-binding / Nucleotide-binding
Function / homology
Function and homology information


plasmid partitioning / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / GTPase activity / GTP binding / metal ion binding / identical protein binding / cytoplasm
Similarity search - Function
: / Tubulin/FtsZ-like protein TubZ-like, C-terminal domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Tubulin-like protein TubZ
Similarity search - Component
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsSchumacher, M.A. / Ni, L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: From the Cover: Plasmid protein TubR uses a distinct mode of HTH-DNA binding and recruits the prokaryotic tubulin homolog TubZ to effect DNA partition.
Authors: Ni, L. / Xu, W. / Kumaraswami, M. / Schumacher, M.A.
History
DepositionMar 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FtsZ/tubulin-related protein


Theoretical massNumber of molelcules
Total (without water)48,6091
Polymers48,6091
Non-polymers00
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)131.601, 131.601, 76.116
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein FtsZ/tubulin-related protein


Mass: 48609.066 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-428
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Strain: serovar israelensis / Gene: pBt156 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-GOLD(DE3) / References: UniProt: Q8KNP3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.61 Å3/Da / Density % sol: 52.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 4 M NaFormate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.97963,1.01995,0.97974
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2009 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: KHOZU Double flat crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979631
21.019951
30.979741
ReflectionResolution: 2.3→65.79 Å / Num. all: 21805 / Num. obs: 21740 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 6.1 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 19.4
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 4.6 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SOLVEphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→65.79 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.921 / SU B: 13.341 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.32 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25077 1111 5.1 %RANDOM
Rwork0.21363 ---
obs0.21542 20625 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.279 Å2
Baniso -1Baniso -2Baniso -3
1--2.51 Å2-1.25 Å20 Å2
2---2.51 Å20 Å2
3---3.76 Å2
Refinement stepCycle: LAST / Resolution: 2.3→65.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3116 0 0 87 3203
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223175
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2641.9534292
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9565391
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.24925.092163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.45515554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2681518
X-RAY DIFFRACTIONr_chiral_restr0.0960.2470
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022437
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.21458
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22172
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2116
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2250.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5681.52008
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.94623138
X-RAY DIFFRACTIONr_scbond_it1.17631314
X-RAY DIFFRACTIONr_scangle_it1.8254.51154
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 93 -
Rwork0.249 1491 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.17446.76073.44915.73030.083715.0905-0.21690.66820.4015-1.10850.06130.8002-0.17350.0260.1556-0.13480.07220.0426-0.15150.05990.068432.162764.654337.2051
23.154-0.80370.03133.0365-0.31111.1552-0.066-0.73520.04390.53840.06980.3446-0.1399-0.2245-0.0037-0.10750.04020.0866-0.0265-0.0491-0.091442.905850.580358.5937
33.2156-0.68330.67064.30732.53484.0313-0.1231-0.29730.25680.22920.02460.3370.1399-0.08860.0985-0.22010.04670.0515-0.21710.0150.00140.077960.360844.9391
41.5336-0.33520.54122.4739-0.96692.5532-0.05690.33190.2246-0.5438-0.0179-0.0610.0507-0.02480.0747-0.1437-0.0120.009-0.19450.0053-0.07549.468956.656632.5441
54.75912.85145.735112.35738.437313.3446-0.1525-0.41110.90530.4776-0.01310.0456-0.64410.30330.1655-0.08260.0140.0442-0.0821-0.14610.006465.635561.78958.2392
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 13
2X-RAY DIFFRACTION2A25 - 222
3X-RAY DIFFRACTION3A236 - 257
4X-RAY DIFFRACTION4A267 - 377
5X-RAY DIFFRACTION5A381 - 400

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