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- PDB-3m9a: Protein structure of type III plasmid segregation TubR -

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Basic information

Entry
Database: PDB / ID: 3m9a
TitleProtein structure of type III plasmid segregation TubR
ComponentsPutative DNA-binding protein
KeywordsDNA BINDING PROTEIN / TubR / winged helix-turn-helix / plasmid segregation
Function / homology
Function and homology information


plasmid partitioning / 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 / MOLECULAR REPLACEMENT / Resolution: 2.5 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 21, 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 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: Putative DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)14,0101
Polymers14,0101
Non-polymers00
Water34219
1
A: Putative DNA-binding protein

A: Putative DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)28,0202
Polymers28,0202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area2290 Å2
ΔGint-17 kcal/mol
Surface area10080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.494, 69.546, 114.217
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Putative DNA-binding protein


Mass: 14009.907 Da / Num. of mol.: 1
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.: 19 / 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: 2.3 Å3/Da / Density % sol: 46.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 40 mM Na/K phosphate pH 6.2, 2.5 M NaCl, 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: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 30, 2008 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: KHOZU Double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.5→59.4 Å / Num. all: 4741 / Num. obs: 4637 / % possible obs: 97.8 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.066 / Net I/σ(I): 11.4
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 3 / % possible all: 99.3

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3M3E

3m3e


Resolution: 2.5→57.11 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.902 / SU B: 20.087 / SU ML: 0.228 / Cross valid method: THROUGHOUT / ESU R: 0.45 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26395 448 9.7 %RANDOM
Rwork0.21916 ---
obs0.2234 4189 97.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.069 Å2
Baniso -1Baniso -2Baniso -3
1--4.09 Å20 Å20 Å2
2---0.31 Å20 Å2
3---4.39 Å2
Refinement stepCycle: LAST / Resolution: 2.5→57.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms727 0 0 19 746
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022737
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2671.953995
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.554592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.71425.42935
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.6515130
X-RAY DIFFRACTIONr_dihedral_angle_4_deg32.334153
X-RAY DIFFRACTIONr_chiral_restr0.10.2115
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02550
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.2320
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.2518
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.222
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3090.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.441.5471
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.6582740
X-RAY DIFFRACTIONr_scbond_it1.0673298
X-RAY DIFFRACTIONr_scangle_it1.7654.5255
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 37 -
Rwork0.303 298 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 0.794 Å / Origin y: 25.3 Å / Origin z: 20.114 Å
111213212223313233
T0.1087 Å20.0041 Å2-0.0064 Å2-0.0722 Å2-0.0264 Å2--0.1859 Å2
L9.389 °20.6423 °20.3037 °2-7.3145 °20.3923 °2--2.3383 °2
S-0.0306 Å °0.5725 Å °-0.8226 Å °-0.4478 Å °0.2613 Å °-0.2864 Å °0.1682 Å °0.1162 Å °-0.2306 Å °

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