[English] 日本語
Yorodumi
- PDB-4aso: TubR bound to 24 bp of tubC from Bacillus thuringiensis serovar i... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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)
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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.

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more