[English] 日本語
Yorodumi
- PDB-5xs9: Crystal structure of Mycobacterium smegmatis BioQ -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xs9
TitleCrystal structure of Mycobacterium smegmatis BioQ
ComponentsTetR family transcriptional regulator
KeywordsTRANSCRIPTION / Biotin / Transcriptional regulator
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / response to antibiotic / negative regulation of DNA-templated transcription
Similarity search - Function
Tetracycline transcriptional regulator, TetR / Tetracycline repressor TetR, C-terminal / Tetracyclin repressor-like, C-terminal domain / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / : / Tetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily
Similarity search - Domain/homology
Transcriptional regulator, TetR family protein / Transcriptional regulator, TetR family protein
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsZhang, Y. / Ji, Q. / Feng, Y.
CitationJournal: To Be Published
Title: Structural analysis of BioQ suggests a distinct regulatory mechanism for biotin, a nutritional virulence factor in Mycobacterium
Authors: Wei, W. / Zhang, Y. / Gao, R. / Li, J. / Xu, Y. / Wang, S. / Ji, Q. / Feng, Y.
History
DepositionJun 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TetR family transcriptional regulator
B: TetR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)44,4092
Polymers44,4092
Non-polymers00
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-21 kcal/mol
Surface area16120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.041, 190.179, 83.413
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein TetR family transcriptional regulator / BioQ


Mass: 22204.717 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEI_3111 / Production host: Escherichia coli (E. coli) / References: UniProt: I7FDJ0, UniProt: A0QX69*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.73 Å3/Da / Density % sol: 54.87 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.15 M DL-malic acid (pH 7.0), 0.1 M imidazole (pH 7.0), 22% (v/v) PEG mono-methyl ether 550

-
Data collection

DiffractionMean temperature: 195 K
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 38389 / % possible obs: 99.7 % / Redundancy: 12.7 % / Net I/σ(I): 41.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementResolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.886 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.126 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22908 1907 5 %RANDOM
Rwork0.17913 ---
obs0.1816 36482 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 48.456 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å2-0 Å20 Å2
2---3.39 Å2-0 Å2
3---4.13 Å2
Refinement stepCycle: 1 / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2718 0 0 198 2916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192760
X-RAY DIFFRACTIONr_bond_other_d0.0020.022650
X-RAY DIFFRACTIONr_angle_refined_deg1.7961.9363746
X-RAY DIFFRACTIONr_angle_other_deg1.07336024
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0035351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.16422.985134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.31715438
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.611529
X-RAY DIFFRACTIONr_chiral_restr0.120.2437
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023182
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02667
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.1854.3991416
X-RAY DIFFRACTIONr_mcbond_other4.1324.3961415
X-RAY DIFFRACTIONr_mcangle_it5.3546.551763
X-RAY DIFFRACTIONr_mcangle_other5.3556.5521764
X-RAY DIFFRACTIONr_scbond_it5.7525.1771342
X-RAY DIFFRACTIONr_scbond_other5.7515.1791343
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.347.5171984
X-RAY DIFFRACTIONr_long_range_B_refined9.55636.7583371
X-RAY DIFFRACTIONr_long_range_B_other9.54536.4793310
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.903→1.952 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 129 -
Rwork0.317 2543 -
obs--94.32 %

+
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