[English] 日本語
Yorodumi
- PDB-1bow: MULTIDRUG-BINDING DOMAIN OF TRANSCRIPTION ACTIVATOR BMRR (APO FORM) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bow
TitleMULTIDRUG-BINDING DOMAIN OF TRANSCRIPTION ACTIVATOR BMRR (APO FORM)
ComponentsMULTIDRUG-EFFLUX TRANSPORTER 1 REGULATOR BMRR
KeywordsTRANSCRIPTION ACTIVATOR / MULTIDRUG BINDING
Function / homology
Function and homology information


DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
GyrI-like small molecule binding domain / GyrI-like small molecule binding domain / Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A / Regulatory factor, effector binding domain / Regulatory factor, effector binding domain superfamily / MerR-type HTH domain signature. / : / MerR HTH family regulatory protein / helix_turn_helix, mercury resistance / MerR-type HTH domain profile. ...GyrI-like small molecule binding domain / GyrI-like small molecule binding domain / Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A / Regulatory factor, effector binding domain / Regulatory factor, effector binding domain superfamily / MerR-type HTH domain signature. / : / MerR HTH family regulatory protein / helix_turn_helix, mercury resistance / MerR-type HTH domain profile. / MerR-type HTH domain / Putative DNA-binding domain superfamily / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / Multidrug-efflux transporter 1 regulator
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.7 Å
AuthorsZheleznova, E.E. / Markham, P.N. / Neyfakh, A.A. / Brennan, R.G.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1999
Title: Structural basis of multidrug recognition by BmrR, a transcription activator of a multidrug transporter.
Authors: Zheleznova, E.E. / Markham, P.N. / Neyfakh, A.A. / Brennan, R.G.
History
DepositionAug 6, 1998Processing site: BNL
Revision 1.0Aug 6, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MULTIDRUG-EFFLUX TRANSPORTER 1 REGULATOR BMRR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5472
Polymers18,4921
Non-polymers551
Water54030
1
A: MULTIDRUG-EFFLUX TRANSPORTER 1 REGULATOR BMRR
hetero molecules

A: MULTIDRUG-EFFLUX TRANSPORTER 1 REGULATOR BMRR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0944
Polymers36,9842
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)76.300, 76.300, 96.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-160-

MN

-
Components

#1: Protein MULTIDRUG-EFFLUX TRANSPORTER 1 REGULATOR BMRR / BRC


Mass: 18492.049 Da / Num. of mol.: 1 / Fragment: MULTIDRUG-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P39075
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.78 Å3/Da / Density % sol: 67.43 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Zheleznova, E.E., (1997) Protein Sci., 6, 2465.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
14.3 M1reservoirNaCl
220 mMTris-HCl1reservoirpH8.5
32 mM1reservoirMnCl2

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: ADSC / Detector: AREA DETECTOR
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→24 Å / Num. obs: 8264 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Rsym value: 0.06 / Net I/σ(I): 10.3
Reflection shellResolution: 2.7→2.8 Å / Mean I/σ(I) obs: 1.6 / % possible all: 100
Reflection
*PLUS
Num. measured all: 65480 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 100 %

-
Processing

Software
NameVersionClassification
PHASESphasing
TNT5Drefinement
ADSCdata collection
LOSCALEdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.7→20 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: RFREE / σ(F): 0 / Stereochemistry target values: TNT CSDX_PROTGEO
RfactorNum. reflection% reflectionSelection details
Rfree0.27 -10 %RANDOM
all0.202 ---
obs0.202 8250 100 %-
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1166 0 1 30 1197
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.011
X-RAY DIFFRACTIONt_angle_deg1.29
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it4.7
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Version: 5D / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.274
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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