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- PDB-4aso: TubR bound to 24 bp of tubC from Bacillus thuringiensis serovar i... -

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Basic information

Entry
Database: PDB / ID: 4aso
TitleTubR bound to 24 bp of tubC from Bacillus thuringiensis serovar israelensis pBtoxis
Components
  • (TUBC FROM BACILLUS THURINGIENSIS PBTOXIS 24 BP) x 2
  • TUBR FROM BACILLUS THURINGIENSIS PBTOXIS
KeywordsSTRUCTURAL PROTEIN/DNA / STRUCTURAL PROTEIN-DNA COMPLEX / PARTITION / SEGREGATION
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 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
J: TUBR FROM BACILLUS THURINGIENSIS PBTOXIS
K: TUBR FROM BACILLUS THURINGIENSIS PBTOXIS
L: TUBR FROM BACILLUS THURINGIENSIS PBTOXIS
M: TUBR FROM BACILLUS THURINGIENSIS PBTOXIS
N: TUBR FROM BACILLUS THURINGIENSIS PBTOXIS
O: TUBR FROM BACILLUS THURINGIENSIS PBTOXIS
P: TUBR FROM BACILLUS THURINGIENSIS PBTOXIS
S: TUBC FROM BACILLUS THURINGIENSIS PBTOXIS 24 BP
T: TUBC FROM BACILLUS THURINGIENSIS PBTOXIS 24 BP
U: TUBC FROM BACILLUS THURINGIENSIS PBTOXIS 24 BP
V: TUBC FROM BACILLUS THURINGIENSIS PBTOXIS 24 BP
W: TUBC FROM BACILLUS THURINGIENSIS PBTOXIS 24 BP
X: TUBC FROM BACILLUS THURINGIENSIS PBTOXIS 24 BP
Y: TUBC FROM BACILLUS THURINGIENSIS PBTOXIS 24 BP
Z: TUBC FROM BACILLUS THURINGIENSIS PBTOXIS 24 BP


Theoretical massNumber of molelcules
Total (without water)252,84924
Polymers252,84924
Non-polymers00
Water00
1
A: TUBR FROM BACILLUS THURINGIENSIS PBTOXIS
B: TUBR FROM BACILLUS THURINGIENSIS PBTOXIS
S: TUBC FROM BACILLUS THURINGIENSIS PBTOXIS 24 BP
T: TUBC FROM BACILLUS THURINGIENSIS PBTOXIS 24 BP


Theoretical massNumber of molelcules
Total (without water)38,9724
Polymers38,9724
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-44.5 kcal/mol
Surface area17570 Å2
MethodPISA
2
C: TUBR FROM BACILLUS THURINGIENSIS PBTOXIS
D: TUBR FROM BACILLUS THURINGIENSIS PBTOXIS
S: TUBC FROM BACILLUS THURINGIENSIS PBTOXIS 24 BP
T: TUBC FROM BACILLUS THURINGIENSIS PBTOXIS 24 BP


Theoretical massNumber of molelcules
Total (without water)38,9724
Polymers38,9724
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-40.5 kcal/mol
Surface area17860 Å2
MethodPISA
3
E: TUBR FROM BACILLUS THURINGIENSIS PBTOXIS
F: TUBR FROM BACILLUS THURINGIENSIS PBTOXIS
U: TUBC FROM BACILLUS THURINGIENSIS PBTOXIS 24 BP
V: TUBC FROM BACILLUS THURINGIENSIS PBTOXIS 24 BP


Theoretical massNumber of molelcules
Total (without water)38,9724
Polymers38,9724
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6280 Å2
ΔGint-51.5 kcal/mol
Surface area16920 Å2
MethodPISA
4
G: TUBR FROM BACILLUS THURINGIENSIS PBTOXIS
H: TUBR FROM BACILLUS THURINGIENSIS PBTOXIS
U: TUBC FROM BACILLUS THURINGIENSIS PBTOXIS 24 BP
V: TUBC FROM BACILLUS THURINGIENSIS PBTOXIS 24 BP


Theoretical massNumber of molelcules
Total (without water)38,9724
Polymers38,9724
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-47.4 kcal/mol
Surface area17340 Å2
MethodPISA
5
I: TUBR FROM BACILLUS THURINGIENSIS PBTOXIS
J: TUBR FROM BACILLUS THURINGIENSIS PBTOXIS
W: TUBC FROM BACILLUS THURINGIENSIS PBTOXIS 24 BP
X: TUBC FROM BACILLUS THURINGIENSIS PBTOXIS 24 BP


Theoretical massNumber of molelcules
Total (without water)38,9724
Polymers38,9724
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6230 Å2
ΔGint-51 kcal/mol
Surface area17080 Å2
MethodPISA
6
K: TUBR FROM BACILLUS THURINGIENSIS PBTOXIS
L: TUBR FROM BACILLUS THURINGIENSIS PBTOXIS
W: TUBC FROM BACILLUS THURINGIENSIS PBTOXIS 24 BP
X: TUBC FROM BACILLUS THURINGIENSIS PBTOXIS 24 BP


Theoretical massNumber of molelcules
Total (without water)38,9724
Polymers38,9724
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-53.2 kcal/mol
Surface area17160 Å2
MethodPISA
7
M: TUBR FROM BACILLUS THURINGIENSIS PBTOXIS
N: TUBR FROM BACILLUS THURINGIENSIS PBTOXIS
Y: TUBC FROM BACILLUS THURINGIENSIS PBTOXIS 24 BP
Z: TUBC FROM BACILLUS THURINGIENSIS PBTOXIS 24 BP


Theoretical massNumber of molelcules
Total (without water)38,9724
Polymers38,9724
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6180 Å2
ΔGint-46.2 kcal/mol
Surface area17160 Å2
MethodPISA
8
O: TUBR FROM BACILLUS THURINGIENSIS PBTOXIS
P: TUBR FROM BACILLUS THURINGIENSIS PBTOXIS
Y: TUBC FROM BACILLUS THURINGIENSIS PBTOXIS 24 BP
Z: TUBC FROM BACILLUS THURINGIENSIS PBTOXIS 24 BP


Theoretical massNumber of molelcules
Total (without water)38,9724
Polymers38,9724
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-49.6 kcal/mol
Surface area17240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)519.251, 63.657, 167.263
Angle α, β, γ (deg.)90.00, 96.66, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
TUBR FROM BACILLUS THURINGIENSIS PBTOXIS


Mass: 12119.912 Da / Num. of mol.: 16
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 24 BP


Mass: 7323.761 Da / Num. of mol.: 4 / Fragment: SENSE STRAND / Source method: obtained synthetically / Source: (synth.) BACILLUS THURINGIENSIS (bacteria)
#3: DNA chain
TUBC FROM BACILLUS THURINGIENSIS PBTOXIS 24 BP


Mass: 7408.855 Da / Num. of mol.: 4 / Fragment: ANTISENSE STRAND / Source method: obtained synthetically / Source: (synth.) BACILLUS THURINGIENSIS (bacteria)
Has protein modificationY
Sequence detailsBP 126549-126514 DNA IS CONTINUOUS IN THE CRYSTALS, BUT HAS BEEN CUT FOR REFINEMENT TO CENTRE THE ...BP 126549-126514 DNA IS CONTINUOUS IN THE CRYSTALS, BUT HAS BEEN CUT FOR REFINEMENT TO CENTRE THE TUBC SITE ON THE TUBR DIMERS BP 126514-126549 DNA IS CONTINUOUS IN THE CRYSTALS, BUT HAS BEEN CUT FOR REFINEMENT TO CENTRE THE TUBC SITE ON THE TUBR DIMERS

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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: 4.81 Å3/Da / Density % sol: 74.54 %
Description: RIGID BODY ON VERY LOW RESOLUTION DATA. STRUCTURE CONFIRMED BY MSE SAD ANOMALOUS DIFFERENCE MAP. REGISTER OF DNA WAS INFERRED BY MICROARRAY EXPERIMENT.
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-24, 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: 7→257.87 Å / Num. obs: 8779 / % possible obs: 98.1 % / Observed criterion σ(I): 1.3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.9
Reflection shellResolution: 7→7.38 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.642 / Mean I/σ(I) obs: 1.3 / % possible all: 98.5

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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→64.469 Å / SU ML: 1.48 / σ(F): 1.34 / Phase error: 42.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3712 431 5.3 %
Rwork0.3443 --
obs0.3456 8097 96.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 7→64.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11632 3936 0 0 15568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01416192
X-RAY DIFFRACTIONf_angle_d1.44922672
X-RAY DIFFRACTIONf_dihedral_angle_d24.3686160
X-RAY DIFFRACTIONf_chiral_restr0.0942608
X-RAY DIFFRACTIONf_plane_restr0.0042240
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
7.0001-7.43810.45571390.45592480X-RAY DIFFRACTION95
7.4381-8.01140.43161880.40462590X-RAY DIFFRACTION98
8.0114-8.81580.42791310.33472566X-RAY DIFFRACTION98
8.8158-10.08730.33661220.34912623X-RAY DIFFRACTION98
10.0873-12.6930.33981380.34112627X-RAY DIFFRACTION97
12.693-64.47120.36011430.31982446X-RAY DIFFRACTION94

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