[English] 日本語
Yorodumi
- PDB-6abq: Crystal structure of transcription factor from Listeria monocytogenes -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6abq
TitleCrystal structure of transcription factor from Listeria monocytogenes
ComponentsPadR family transcriptional regulator
KeywordsDNA BINDING PROTEIN / Bacteria / PadR / transcription factor
Function / homology
Function and homology information


: / Transcription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PadR family transcriptional regulator
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLee, C. / Hong, M.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (Korea)2018R1A2B6001619 Korea, Republic Of
National Research Foundation (Korea)2015R1D1A1A0105757 Korea, Republic Of
CitationJournal: Plos One / Year: 2019
Title: Structure-based molecular characterization and regulatory mechanism of the LftR transcription factor from Listeria monocytogenes: Conformational flexibilities and a ligand-induced regulatory mechanism.
Authors: Lee, C. / Kim, M.I. / Park, J. / Hong, M.
History
DepositionJul 23, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: PadR family transcriptional regulator
A: PadR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9094
Polymers25,8382
Non-polymers712
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-45 kcal/mol
Surface area11800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.955, 73.955, 66.313
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein PadR family transcriptional regulator


Mass: 12918.959 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: C7K50_07245, CDR86_13565, LmNIHS28_00834 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: L8DXR9
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.07 Å3/Da / Density % sol: 40.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1 M lithium chloride, 0.1 M citric acid, pH 5.5, and 30% polyethylene glycol 6000

-
Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.0003 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Dec 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0003 Å / Relative weight: 1
ReflectionResolution: 2.3→64 Å / Num. obs: 9616 / % possible obs: 99.7 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.018 / Rrim(I) all: 0.049 / Χ2: 1.81 / Net I/σ(I): 22.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.347.30.0754580.9950.030.0812.038100
2.34-2.387.20.0714820.9960.0280.0772.078100
2.38-2.437.30.0694640.9960.0270.0741.936100
2.43-2.487.20.0644770.9960.0250.0681.894100
2.48-2.537.30.0634730.9980.0250.0681.861100
2.53-2.597.20.0634640.9970.0250.0681.889100
2.59-2.667.20.0594990.9980.0230.0641.91100
2.66-2.737.20.0564610.9980.0220.061.858100
2.73-2.817.30.0544660.9980.0210.0581.802100
2.81-2.97.20.0524820.9980.0210.0561.826100
2.9-37.20.054920.9980.020.0541.77100
3-3.127.20.0474620.9980.0190.0511.868100
3.12-3.267.20.0434790.9990.0170.0471.678100
3.26-3.447.10.0424920.9980.0170.0451.747100
3.44-3.657.10.0394740.9980.0160.0421.696100
3.65-3.937.10.0374910.9990.0150.041.612100
3.93-4.3370.0374920.9980.0150.041.705100
4.33-4.956.90.0364910.9990.0150.0391.561100
4.95-6.246.80.0385080.9980.0160.0411.553100
6.24-505.80.0415090.9970.0190.0461.93295

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.24data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ESF

4esf


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.874 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.542 / ESU R Free: 0.271 / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2533 486 5.1 %RANDOM
Rwork0.2048 ---
obs0.2072 9111 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 70.13 Å2 / Biso mean: 25.591 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å20 Å2
2--0.14 Å2-0 Å2
3----0.45 Å2
Refinement stepCycle: final / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1742 0 2 129 1873
Biso mean--13.43 10.38 -
Num. residues----217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021811
X-RAY DIFFRACTIONr_angle_refined_deg1.3142.0022434
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0635225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.78724.41677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.1215368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.891510
X-RAY DIFFRACTIONr_chiral_restr0.090.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211318
LS refinement shellResolution: 2.301→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 34 -
Rwork0.205 659 -
all-693 -
obs--100 %
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)
15.48683.32571.53822.50950.71711.3982-0.21160.06140.55820.1178-0.0310.3050.1090.01370.24250.2238-0.04330.00270.1716-0.01370.125424.02995.910.959
24.3186-0.2529-0.1341.54230.15722.621-0.19250.2543-0.0551-0.11710.1360.11650.0588-0.12340.05640.0694-0.0255-0.01080.03830.00340.012836.427105.356-4.903
31.7934-0.84360.26782.2494-0.6791.007-0.08480.05490.00970.04540.0069-0.0697-0.0148-0.05660.0780.0724-0.0158-0.00350.0762-0.01420.00841.221108.8381.437
45.92846.3853-1.406110.3952-1.16331.090.07730.1403-0.44630.10290.0358-0.3851-0.13830.0076-0.11310.11940.020.03530.0638-0.01390.114141.23988.173-2.49
57.99622.14692.65353.4168-3.06125.9428-0.12350.1954-0.0938-0.25240.11870.00220.1868-0.05650.00470.16790.0276-0.03360.0681-0.04580.167127.33877.877-2.004
64.6625-5.519-4.25226.79714.24716.51190.0315-0.00180.02870.0459-0.1332-0.0908-0.36610.26210.10170.1117-0.0094-0.02690.14610.02770.10736.93687.5837.505
76.2164-1.0507-0.56453.9233-1.00293.7651-0.16970.0087-0.263-0.09990.0466-0.39710.19910.29170.12310.05480.01560.0220.0316-0.00840.063526.28975.259.998
89.3558-1.46230.27051.7917-0.47741.01220.1124-0.46380.118-0.0315-0.0594-0.28320.06320.2645-0.05290.1153-0.0359-0.01610.1199-0.01420.067329.74580.87614.968
91.24130.37760.14024.4719-3.6244.7196-0.0012-0.0753-0.1223-0.0248-0.0452-0.04490.24550.06430.04640.0470.00740.00160.0289-0.01730.047817.7776.40714.299
1010.49033.6162-8.62961.3286-3.24438.255-0.17470.2239-0.4688-0.07380.033-0.10950.0863-0.14460.14160.11970.01890.00780.0767-0.00550.08128.73891.987-7.544
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-4 - 13
2X-RAY DIFFRACTION2A14 - 38
3X-RAY DIFFRACTION3A39 - 81
4X-RAY DIFFRACTION4A82 - 99
5X-RAY DIFFRACTION5A100 - 105
6X-RAY DIFFRACTION6B3 - 9
7X-RAY DIFFRACTION7B10 - 36
8X-RAY DIFFRACTION8B37 - 56
9X-RAY DIFFRACTION9B57 - 90
10X-RAY DIFFRACTION10B91 - 108

+
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