[English] 日本語
Yorodumi
- PDB-3qao: The crystal structure of the N-terminal domain of a MerR-like tra... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qao
TitleThe crystal structure of the N-terminal domain of a MerR-like transcriptional regulator from Listeria monocytogenes EGD-e
ComponentsMerR-like transcriptional regulator
Keywordstranscription regulator / structural genomics / The Center for Structural Genomics of Infectious Diseases / CSGID / MerR family / DNA-binding / All-alpha / MerR/DNA-binding / cytoplasmic
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
TipA-like multidrug resistance regulator, antibiotic-recognition domain / TipAS antibiotic-recognition domain / TipAS antibiotic-recognition domain / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 - #10 / MerR family regulatory protein / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 / MerR HTH family regulatory protein / MerR-type HTH domain profile. / helix_turn_helix, mercury resistance / MerR-type HTH domain ...TipA-like multidrug resistance regulator, antibiotic-recognition domain / TipAS antibiotic-recognition domain / TipAS antibiotic-recognition domain / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 - #10 / MerR family regulatory protein / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 / MerR HTH family regulatory protein / MerR-type HTH domain profile. / helix_turn_helix, mercury resistance / MerR-type HTH domain / Putative DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.874 Å
AuthorsTan, K. / Gu, M. / Peterson, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: The crystal structure of the N-terminal domain of a MerR-like transcriptional regulator from Listeria monocytogenes EGD-e
Authors: Tan, K. / Gu, M. / Peterson, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MerR-like transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0477
Polymers29,4941
Non-polymers5536
Water1,946108
1
A: MerR-like transcriptional regulator
hetero molecules

A: MerR-like transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,09414
Polymers58,9882
Non-polymers1,10512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Buried area8030 Å2
ΔGint-41 kcal/mol
Surface area15310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.769, 56.769, 113.108
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-275-

HOH

DetailsExperimentally unknown. It is predicted that the chain A and its symmetry-related molecule by the operator ( x-y+1,-y+2,-z+1/3 ) form a dimer.

-
Components

#1: Protein MerR-like transcriptional regulator / Lmo0526 protein


Mass: 29494.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD-e / Gene: lmo0526 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8Y9K1
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 1.78 Å3/Da / Density % sol: 31.05 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M Potassium Acetate, 20% (w/v) 3350, 10ug/ml chemtrypsin, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2010 / Details: mirror
RadiationMonochromator: SI 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.874→45.1 Å / Num. all: 17734 / Num. obs: 17734 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 42.5
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 3.5 / Num. unique all: 875 / % possible all: 100

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.874→45.088 Å / SU ML: 0.23 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2279 893 5.11 %random
Rwork0.1934 ---
all0.1951 17474 --
obs0.1951 17474 97.27 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.997 Å2 / ksol: 0.348 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.1922 Å2-0 Å2-0 Å2
2--1.1922 Å20 Å2
3----2.3843 Å2
Refinement stepCycle: LAST / Resolution: 1.874→45.088 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1160 0 36 108 1304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071252
X-RAY DIFFRACTIONf_angle_d0.9111679
X-RAY DIFFRACTIONf_dihedral_angle_d14.198498
X-RAY DIFFRACTIONf_chiral_restr0.061180
X-RAY DIFFRACTIONf_plane_restr0.004212
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8743-1.99180.26451560.22892558X-RAY DIFFRACTION93
1.9918-2.14560.26071380.19452755X-RAY DIFFRACTION97
2.1456-2.36150.24971600.19322780X-RAY DIFFRACTION99
2.3615-2.70310.2131520.20362799X-RAY DIFFRACTION99
2.7031-3.40550.24361500.18272822X-RAY DIFFRACTION99
3.4055-45.10130.211370.19272867X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: -7.5649 Å / Origin y: 42.2498 Å / Origin z: 15.3471 Å
111213212223313233
T0.2479 Å2-0.0416 Å2-0.0008 Å2-0.162 Å20.0175 Å2--0.2041 Å2
L0.5964 °2-0.3573 °2-0.206 °2-1.2293 °20.7953 °2--1.1864 °2
S-0.1031 Å °-0.0796 Å °0.1038 Å °0.073 Å °0.1499 Å °0.0992 Å °-0.0375 Å °0.1018 Å °-0.0102 Å °
Refinement TLS groupSelection details: chain A

+
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