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- PDB-4ass: TubR bound to tubC - 26 bp - from Bacillus thuringiensis serovar ... -

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Basic information

Entry
Database: PDB / ID: 4ass
TitleTubR bound to tubC - 26 bp - from Bacillus thuringiensis serovar israelensis pBtoxis
Components
  • (TUBC FROM BACILLUS THURINGIENSIS PBTOXIS 26 BP) x 2
  • TUBR FROM BACILLUS THURINGIENSIS PBTOXIS
KeywordsSTRUCTURAL PROTEIN/DNA / STRUCTURAL PROTEIN-DNA COMPLEX / SEGREGATION / PARTITIONING
Function / homologyplasmid partitioning / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / DNA binding / identical protein binding / DNA / DNA (> 10) / DNA-binding transcriptional repressor TubR
Function and homology information
Biological speciesBACILLUS THURINGIENSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7 Å
AuthorsAylett, C.H.S. / Lowe, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Superstructure of the Centromeric Complex of Tubzrc Plasmid Partitioning Systems.
Authors: Aylett, C.H.S. / Lowe, J.
History
DepositionMay 2, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TUBR FROM BACILLUS THURINGIENSIS PBTOXIS
B: TUBR FROM BACILLUS THURINGIENSIS PBTOXIS
C: TUBR FROM BACILLUS THURINGIENSIS PBTOXIS
D: TUBR FROM BACILLUS THURINGIENSIS PBTOXIS
E: TUBR FROM BACILLUS THURINGIENSIS PBTOXIS
F: TUBR FROM BACILLUS THURINGIENSIS PBTOXIS
G: TUBR FROM BACILLUS THURINGIENSIS PBTOXIS
H: TUBR FROM BACILLUS THURINGIENSIS PBTOXIS
I: TUBR FROM BACILLUS THURINGIENSIS PBTOXIS
Y: TUBC FROM BACILLUS THURINGIENSIS PBTOXIS 26 BP
Z: TUBC FROM BACILLUS THURINGIENSIS PBTOXIS 26 BP


Theoretical massNumber of molelcules
Total (without water)125,04811
Polymers125,04811
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13950 Å2
ΔGint-100.3 kcal/mol
Surface area43490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.561, 162.352, 285.394
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
TUBR FROM BACILLUS THURINGIENSIS PBTOXIS


Mass: 12119.912 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS THURINGIENSIS (bacteria) / Strain: SEROVAR ISRAELENSIS / Plasmid: PHIS17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): C41 / References: UniProt: Q8KNP2
#2: DNA chain TUBC FROM BACILLUS THURINGIENSIS PBTOXIS 26 BP


Mass: 7917.136 Da / Num. of mol.: 1 / Fragment: SENSE STRAND / Source method: obtained synthetically / Source: (synth.) BACILLUS THURINGIENSIS (bacteria)
#3: DNA chain TUBC FROM BACILLUS THURINGIENSIS PBTOXIS 26 BP


Mass: 8051.268 Da / Num. of mol.: 1 / Fragment: ANTISENSE STRAND / Source method: obtained synthetically / Source: (synth.) BACILLUS THURINGIENSIS (bacteria)
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: 4.14 Å3/Da / Density % sol: 70.3 %
Description: RIGID BODY ON VERY LOW RESOLUTION DATA. STRUCTURE CONFIRMED BY MSE SAD ANOMALOUS DIFFERENCE MAP. REGISTER OF DNA WAS INFERRED FROM CRYSTALLOGRAPHIC SYMMETRY.
Crystal growpH: 7.5
Details: BT TUBR-TUBC CRYSTALS WERE PRODUCED IN 500 NL TO 500 NL PROTEIN TO PRECIPITANT DROPS: 10 MG/ML BT TUBR, 500 UM TUBC-26, 100 MM NA-HEPES PH 7.5, 5 MM MGCL2, 25 % (W/V) POLYACRYLIC ACID 5100 SODIUM SALT.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9794
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 29, 2011
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 6.7→142.7 Å / Num. obs: 3906 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 12.4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.2
Reflection shellResolution: 6.7→7.06 Å / Redundancy: 13.3 % / Rmerge(I) obs: 1.586 / Mean I/σ(I) obs: 2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3M9A

3m9a


Resolution: 7→67.81 Å / SU ML: 1.64 / σ(F): 1.41 / Phase error: 51.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.4839 156 5 %
Rwork0.408 --
obs0.4117 3906 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 7→67.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6543 1066 0 0 7609
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0157825
X-RAY DIFFRACTIONf_angle_d1.37610785
X-RAY DIFFRACTIONf_dihedral_angle_d21.9092920
X-RAY DIFFRACTIONf_chiral_restr0.0971243
X-RAY DIFFRACTIONf_plane_restr0.0041204
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
7.0005-8.81680.46351670.43492923X-RAY DIFFRACTION100
8.8168-67.81270.49221440.39912941X-RAY DIFFRACTION100

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