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- PDB-3m8e: Protein structure of Type III plasmid segregation TubR -

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Basic information

Entry
Database: PDB / ID: 3m8e
TitleProtein structure of Type III plasmid segregation TubR
ComponentsPutative DNA-binding protein
KeywordsDNA BINDING PROTEIN / winged helix-turn-helix / ArsR family
Function / homology
Function and homology information


plasmid partitioning / DNA-templated transcription / DNA binding / identical protein binding
Similarity search - Function
Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA-binding transcriptional repressor TubR
Similarity search - Component
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsNi, L. / Schumacher, M.A.
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 17, 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 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative DNA-binding protein
B: Putative DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)28,0202
Polymers28,0202
Non-polymers00
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-19 kcal/mol
Surface area10780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.499, 61.556, 51.249
Angle α, β, γ (deg.)90.00, 112.00, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-118-

HOH

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Components

#1: Protein Putative DNA-binding protein


Mass: 14009.907 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Strain: serovar israelensis / Gene: pBt157 / Plasmid: pET15b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: Q8KNP2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.34 Å3/Da / Density % sol: 47.44 %
Crystal growTemperature: 293 K / pH: 6.2
Details: 40 mM Na/K phosphate, 2.5 M NaCl, pH 6.2, 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: 0.95704,0.97966
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 30, 2008 / Details: MIRROR
RadiationMonochromator: KHOZU DOUBLE FLAT CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.957041
20.979661
ReflectionResolution: 2→49.81 Å / Num. obs: 17963 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 7.5 % / Biso Wilson estimate: 20.24 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 21.9
Reflection shellResolution: 2→2.11 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 6.2 / % 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→49.81 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.872 / SU B: 7.445 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27 917 5.1 %RANDOM
Rwork0.238 ---
obs0.24 17045 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.99 Å20 Å20.81 Å2
2---1.35 Å20 Å2
3----1.04 Å2
Refinement stepCycle: LAST / Resolution: 2→49.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1524 0 0 159 1683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221551
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0081.9442095
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2315191
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.93725.13276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.52815268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.989156
X-RAY DIFFRACTIONr_chiral_restr0.0740.2238
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021174
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.2684
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.21072
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2115
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.260
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.441.51004
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.67421546
X-RAY DIFFRACTIONr_scbond_it1.2313631
X-RAY DIFFRACTIONr_scangle_it1.7534.5549
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 73 -
Rwork0.243 1272 -
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)
12.4659-0.0712-1.06352.7377-0.31262.9130.0241-0.10010.04720.12-0.0129-0.0841-0.08550.032-0.0112-0.0783-0.0059-0.005-0.1648-0.0188-0.119917.598622.069511.3272
21.9203-0.0302-0.84213.8296-0.42822.4568-0.0044-0.0111-0.0965-0.0488-0.05010.21560.0731-0.17820.0545-0.104-0.00470.0074-0.1152-0.0027-0.111815.24714.334910.9767
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 102
2X-RAY DIFFRACTION2B4 - 100

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