[English] 日本語
Yorodumi
- PDB-7dvv: Heme sensor protein PefR from Streptococcus agalactiae bound to o... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7dvv
TitleHeme sensor protein PefR from Streptococcus agalactiae bound to operator DNA (28-mer)
Components
  • (DNA (28-MER)) x 2
  • HTH marR-type domain-containing protein
KeywordsTRANSCRIPTION / heme-binding / helix-turn-helix
Function / homology
Function and homology information


DNA-binding transcription factor activity / metal ion binding
Similarity search - Function
Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / HTH marR-type domain-containing protein
Similarity search - Component
Biological speciesStreptococcus agalactiae serotype III
Streptococcus agalactiae NEM316 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.49 Å
Model detailsheme sensor protein
AuthorsNishinaga, M. / Nagai, S. / Nishitani, Y. / Sugimoto, H. / Shiro, Y. / Sawai, H.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP26220807 Japan
Japan Society for the Promotion of Science (JSPS)JP18H02396 Japan
Japan Society for the Promotion of Science (JSPS)JP18K05321 Japan
CitationJournal: Commun Biol / Year: 2021
Title: Heme controls the structural rearrangement of its sensor protein mediating the hemolytic bacterial survival.
Authors: Nishinaga, M. / Sugimoto, H. / Nishitani, Y. / Nagai, S. / Nagatoishi, S. / Muraki, N. / Tosha, T. / Tsumoto, K. / Aono, S. / Shiro, Y. / Sawai, H.
History
DepositionJan 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HTH marR-type domain-containing protein
B: HTH marR-type domain-containing protein
L: DNA (28-MER)
M: DNA (28-MER)


Theoretical massNumber of molelcules
Total (without water)52,8394
Polymers52,8394
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11250 Å2
ΔGint-79 kcal/mol
Surface area22590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.973, 100.973, 128.989
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212

-
Components

#1: Protein HTH marR-type domain-containing protein


Mass: 17817.852 Da / Num. of mol.: 2 / Fragment: heme sensor protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae serotype III (strain NEM316) (bacteria)
Strain: NEM316 / Gene: gbs1402 / Plasmid: pET-22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8E4J9
#2: DNA chain DNA (28-MER)


Mass: 8579.605 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptococcus agalactiae NEM316 (bacteria)
#3: DNA chain DNA (28-MER)


Mass: 8623.598 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptococcus agalactiae NEM316 (bacteria)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3.59 Å3/Da / Density % sol: 65.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25%(w/v) PEGMME 2000, 0.2 M lithium sulfate, 0.1 M MES

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 22, 2018 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.49→47.06 Å / Num. obs: 26423 / % possible obs: 99.9 % / Redundancy: 6.992 % / Biso Wilson estimate: 75.503 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.089 / Χ2: 1.321 / Net I/σ(I): 14.63 / Num. measured all: 357952
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.49-2.657.0521.769157980827082220.5621.91199.4
2.65-2.836.8520.8282.1153162775977590.8550.896100
2.83-3.056.940.5123.4750387726072600.9270.554100
3.05-3.347.3070.16110.3548581664966490.9960.173100
3.34-3.747.0650.10317.0742470601260110.9970.111100
3.74-4.316.7550.06925.1335901531553150.9980.074100
4.31-5.276.9870.05433.1931448450145010.9980.058100
5.27-7.46.8640.04737.8924053350435040.9990.051100
7.4-47.067.070.02856.813970198719760.9990.0399.4

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å47.01 Å
Translation2.5 Å47.01 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XSCALEJun 1, 2017data scaling
PHASER2.7.17phasing
PDB_EXTRACT3.25data extraction
Coot0.8.9.2model building
XDSJun 1, 2017data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DVS, 4LLN

7dvs

4lln


Resolution: 2.49→47.06 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.947 / SU B: 27.848 / SU ML: 0.256 / SU R Cruickshank DPI: 0.302 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.302 / ESU R Free: 0.231
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2463 1262 4.8 %RANDOM
Rwork0.2175 ---
obs0.2189 25129 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 229.69 Å2 / Biso mean: 86.059 Å2 / Biso min: 32.13 Å2
Baniso -1Baniso -2Baniso -3
1--1.34 Å2-0.67 Å2-0 Å2
2---1.34 Å20 Å2
3---4.34 Å2
Refinement stepCycle: final / Resolution: 2.49→47.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2267 1148 0 9 3424
Biso mean---52.05 -
Num. residues----335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0113591
X-RAY DIFFRACTIONr_angle_refined_deg1.8851.4655070
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0055277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.94522.661109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.69115482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.821512
X-RAY DIFFRACTIONr_chiral_restr0.1280.2473
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022234
LS refinement shellResolution: 2.495→2.559 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.541 98 -
Rwork0.494 1811 -
all-1909 -
obs--98.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.0835-0.63462.37391.00391.03123.55180.35960.71660.082-0.1982-0.3455-0.06620.00670.0778-0.01410.10540.14690.01650.2270.00670.2221-15.04456.2739-14.2634
22.84-1.2596-1.87071.5-0.31522.62610.49310.6161-0.0552-0.3672-0.44580.1026-0.1405-0.1935-0.04740.15370.1623-0.00790.18480.00780.2891-35.279122.7707-14.3303
34.91150.1055-0.9841.0130.11621.2893-0.0318-0.0219-0.6420.0297-0.03790.37970.2754-0.14980.06970.0707-0.03640.01090.02270.01130.3717-45.10665.8341.1693
45.16630.30421.08010.58470.08691.1557-0.0634-0.01360.5758-0.0073-0.0096-0.263-0.25580.15170.0730.0717-0.0371-0.01490.0277-0.00450.3513-5.368123.3021.1736
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 141
2X-RAY DIFFRACTION2B2 - 141
3X-RAY DIFFRACTION3L1 - 14
4X-RAY DIFFRACTION3M15 - 28
5X-RAY DIFFRACTION4L15 - 28
6X-RAY DIFFRACTION4M1 - 14

+
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