[English] 日本語
Yorodumi
- PDB-2y7r: DntR Inducer Binding Domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2y7r
TitleDntR Inducer Binding Domain
ComponentsLYSR-TYPE REGULATORY PROTEIN
KeywordsTRANSCRIPTION REGULATOR / TRANSCRIPTION / LYSR TYPE TRANSCRIPTION FACTOR
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
LysR-type regulatory protein
Similarity search - Component
Biological speciesBURKHOLDERIA SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsDevesse, L. / Smirnova, I. / Lonneborg, R. / Kapp, U. / Brzezinski, P. / Leonard, G.A. / Dian, C.
CitationJournal: Mol.Microbiol. / Year: 2011
Title: Crystal Structures of Dntr Inducer Binding Domains in Complex with Salicylate Offer Insights Into the Activation of Lysr-Type Transcriptional Regulators.
Authors: Devesse, L. / Smirnova, I. / Lonneborg, R. / Kapp, U. / Brzezinski, P. / Leonard, G.A. / Dian, C.
History
DepositionFeb 1, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LYSR-TYPE REGULATORY PROTEIN
B: LYSR-TYPE REGULATORY PROTEIN
C: LYSR-TYPE REGULATORY PROTEIN
D: LYSR-TYPE REGULATORY PROTEIN
E: LYSR-TYPE REGULATORY PROTEIN
F: LYSR-TYPE REGULATORY PROTEIN
G: LYSR-TYPE REGULATORY PROTEIN
H: LYSR-TYPE REGULATORY PROTEIN


Theoretical massNumber of molelcules
Total (without water)198,7038
Polymers198,7038
Non-polymers00
Water0
1
D: LYSR-TYPE REGULATORY PROTEIN
H: LYSR-TYPE REGULATORY PROTEIN


Theoretical massNumber of molelcules
Total (without water)49,6762
Polymers49,6762
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-27.4 kcal/mol
Surface area18430 Å2
MethodPISA
2
B: LYSR-TYPE REGULATORY PROTEIN
F: LYSR-TYPE REGULATORY PROTEIN


Theoretical massNumber of molelcules
Total (without water)49,6762
Polymers49,6762
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-27.1 kcal/mol
Surface area18100 Å2
MethodPISA
3
C: LYSR-TYPE REGULATORY PROTEIN
G: LYSR-TYPE REGULATORY PROTEIN


Theoretical massNumber of molelcules
Total (without water)49,6762
Polymers49,6762
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-25.9 kcal/mol
Surface area18310 Å2
MethodPISA
4
A: LYSR-TYPE REGULATORY PROTEIN
E: LYSR-TYPE REGULATORY PROTEIN


Theoretical massNumber of molelcules
Total (without water)49,6762
Polymers49,6762
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-22.2 kcal/mol
Surface area18130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.473, 125.003, 184.841
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99995, 0.00469, 0.00905), (0.00577, 0.99232, 0.1236), (-0.0084, 0.12365, -0.99229)1.9652, 0.12432, -3.47784
2given(-0.99834, -0.03353, 0.04688), (0.05052, -0.11753, 0.99178), (-0.02774, 0.9925, 0.11903)24.4923, 35.29449, -31.30251
3given(0.87558, 0.40568, -0.26226), (0.40668, -0.91203, -0.05307), (-0.26072, -0.06019, -0.96354)4.61094, -17.38171, 7.05825
4given(-0.8734, 0.36291, 0.32477), (-0.40616, -0.91076, -0.07456), (0.26873, -0.19703, 0.94285)7.09424, -16.50521, 9.92107
5given(-0.85007, -0.27382, 0.44988), (-0.48048, 0.05343, -0.87538), (0.21566, -0.96029, -0.17699)47.77568, -38.20033, 29.71514
6given(0.86453, 0.26231, 0.42871), (0.42396, 0.07747, -0.90236), (-0.26991, 0.96187, -0.04424)-6.60652, -57.13587, -18.43282

-
Components

#1: Protein
LYSR-TYPE REGULATORY PROTEIN / DNTR


Mass: 24837.824 Da / Num. of mol.: 8 / Fragment: INDUCER BINDING DOMAIN, RESIDUES 90-301 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA SP. (bacteria) / Strain: DNT / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q7WT50

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47 % / Description: RD1 AND RD2 USED AS SEPARATE SEARCH MODELS
Crystal growDetails: 0.2 M NA/K TARTRATE, 0.1 M TRIS PH 8.0-8.5; PEG 8000 28-30%

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 3→44 Å / Num. obs: 37607 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 40.2 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 6.8
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.3 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UTB, CHAIN A

1utb


Resolution: 2.99→43.9 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.843 / SU B: 19.915 / SU ML: 0.373 / Cross valid method: THROUGHOUT / ESU R Free: 0.486 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1883 5 %RANDOM
Rwork0.19364 ---
obs0.1972 35722 98.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.876 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å20 Å2
2---0.23 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 2.99→43.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12995 0 0 0 12995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02213355
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.96118157
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.64451684
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.44322.458541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.74152084
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4061592
X-RAY DIFFRACTIONr_chiral_restr0.10.22033
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02210176
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.5231.58474
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.013213634
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.35934881
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3934.54523
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.987→3.064 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 142 -
Rwork0.272 2546 -
obs--96.38 %

+
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