[English] 日本語
Yorodumi
- PDB-5h20: X-ray structure of PadR-like Transcription factor from bacteroid ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5h20
TitleX-ray structure of PadR-like Transcription factor from bacteroid fragilis
ComponentsPutative PadR-family transcriptional regulatory protein
KeywordsTRANSCRIPTION REGULATOR / bacteroid fragilis / transcription factor / PadR
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
alpha-D-glucopyranose / ISOPROPYL ALCOHOL / PHOSPHATE ION / Putative PadR-family transcriptional regulatory protein
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLee, C. / Hong, M.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National research foundation of korea2015R1D1A1A01057574 Korea, Republic Of
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Structural and functional analysis of BF2549, a PadR-like transcription factor from Bacteroides fragilis.
Authors: Lee, C. / Kim, M.I. / Hong, M.
History
DepositionOct 13, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative PadR-family transcriptional regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4487
Polymers12,8631
Non-polymers5856
Water36020
1
A: Putative PadR-family transcriptional regulatory protein
hetero molecules

A: Putative PadR-family transcriptional regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,89614
Polymers25,7262
Non-polymers1,17112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area5540 Å2
ΔGint-44 kcal/mol
Surface area11980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.890, 72.890, 84.141
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Putative PadR-family transcriptional regulatory protein


Mass: 12862.837 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: ATCC 25285 / DSM 2151 / JCM 11019 / NCTC 9343 / Gene: BF9343_2549 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5LC36
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 5.02 Å3/Da
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 1.5 M Ammonium sulfate, 4 % Isopropanol

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.00002 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Dec 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 10398 / % possible obs: 98.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.063 / Net I/av σ(I): 19.121 / Net I/σ(I): 13.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.4-2.443.90.3920.925199.8
2.44-2.493.90.3320.961100
2.49-2.533.90.3020.9391100
2.53-2.5940.2240.9771100
2.59-2.643.90.2190.9761100
2.64-2.740.1950.977199.8
2.7-2.773.90.170.971100
2.77-2.8540.1390.9761100
2.85-2.933.90.130.9861100
2.93-3.023.90.1120.9841100
3.02-3.133.90.1020.979199.8
3.13-3.263.90.0950.9821100
3.26-3.413.90.0810.991199.8
3.41-3.583.90.0750.9881100
3.58-3.813.80.0590.994199.6
3.81-4.13.80.0520.995199.5
4.1-4.523.80.0470.995199.4
4.52-5.173.80.0450.993198.7
5.17-6.513.70.0430.993198.2
2.5-2.553.90.0630.977199.8

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.2data extraction
DENZOdata reduction
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ejo

4ejo


Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.916 / SU B: 8.933 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.284 / ESU R Free: 0.226 / Details: U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2749 472 5.1 %RANDOM
Rwork0.2643 ---
obs0.2648 8721 98.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 221.01 Å2 / Biso mean: 76 Å2 / Biso min: 45.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20.32 Å20 Å2
2--0.65 Å2-0 Å2
3----2.1 Å2
Refinement stepCycle: final / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms833 0 35 20 888
Biso mean--76.88 66.59 -
Num. residues----103
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.019895
X-RAY DIFFRACTIONr_angle_refined_deg1.4832.0271210
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.045106
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.30424.47438
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.44415171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.993155
X-RAY DIFFRACTIONr_chiral_restr0.0820.2137
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021632
X-RAY DIFFRACTIONr_mcbond_it0.812.08415
X-RAY DIFFRACTIONr_mcangle_it1.493.111518
X-RAY DIFFRACTIONr_scbond_it0.7732.422479
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 45 -
Rwork0.253 630 -
all-675 -
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)
112.7109-14.8012-5.728917.49889.630437.0207-0.7069-0.5983-0.14330.89570.67420.16680.9733-0.69890.03270.4173-0.04570.00880.4260.04090.056731.674-3.35718.271
21.9104-3.0874-3.233110.85764.416111.7249-0.2213-0.13010.4372-0.05230.4308-1.32540.63270.8955-0.20950.5014-0.00540.06350.6557-0.13130.364140.255-12.2853.665
39.2929-1.47270.33753.983-3.959412.882-0.2462-0.2054-1.02220.37460.34980.57590.15790.114-0.10360.647-0.04750.00310.5249-0.05870.259733.96-13.3777.939
46.69068.08315.5326.305210.46895.44290.0090.18670.004-0.7812-0.01520.0178-0.1490.12770.00620.584-0.14160.10880.5026-0.03080.055831.974-17.385-5.034
510.93087.94352.783412.051810.60313.209-0.366-0.2201-0.1873-0.57650.5461-0.394-0.76061.0719-0.18010.6285-0.12340.07310.6197-0.01650.291641.6662.8784.681
641.56287.816138.86511.48317.303936.3876-0.9973-0.95631.7854-0.1528-0.47270.41-0.4676-0.78111.46992.75820.3588-0.22232.0853-0.73231.189249.1459.73120.017
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 14
2X-RAY DIFFRACTION2A15 - 35
3X-RAY DIFFRACTION3A36 - 60
4X-RAY DIFFRACTION4A61 - 81
5X-RAY DIFFRACTION5A82 - 97
6X-RAY DIFFRACTION6A98 - 106

+
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://pdbjlvh1.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