[English] 日本語
Yorodumi
- PDB-2y2z: ligand-free form of TetR-like repressor SimR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2y2z
Titleligand-free form of TetR-like repressor SimR
ComponentsPUTATIVE REPRESSOR SIMREG2
KeywordsTRANSCRIPTION / SIMOCYCLINONE REGULATOR / TETR-FAMILY
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / metal ion binding
Similarity search - Function
Tetracycline repressor TetR, C-terminal / Tetracyclin repressor-like, C-terminal domain / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeodomain-like / Homeobox-like domain superfamily ...Tetracycline repressor TetR, C-terminal / Tetracyclin repressor-like, C-terminal domain / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Putative repressor SimReg2
Similarity search - Component
Biological speciesSTREPTOMYCES ANTIBIOTICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsLe, T.B.K. / Stevenson, C.E.M. / Fiedler, H.-P. / Maxwell, A. / Lawson, D.M. / Buttner, M.J.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structures of the Tetr-Like Simocyclinone Efflux Pump Repressor, Simr, and the Mechanism of Ligand-Mediated Derepression.
Authors: Le, T.B.K. / Stevenson, C.E.M. / Fiedler, H.-P. / Maxwell, A. / Lawson, D.M. / Buttner, M.J.
History
DepositionDec 17, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1May 19, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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: PUTATIVE REPRESSOR SIMREG2


Theoretical massNumber of molelcules
Total (without water)30,2401
Polymers30,2401
Non-polymers00
Water2,180121
1
A: PUTATIVE REPRESSOR SIMREG2

A: PUTATIVE REPRESSOR SIMREG2


Theoretical massNumber of molelcules
Total (without water)60,4802
Polymers60,4802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_444-x-2/3,-x+y-1/3,-z-1/31
Buried area4950 Å2
ΔGint-36.1 kcal/mol
Surface area23380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.060, 116.060, 109.381
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-2007-

HOH

21A-2008-

HOH

31A-2061-

HOH

-
Components

#1: Protein PUTATIVE REPRESSOR SIMREG2 / SIM16 / SIMR


Mass: 30240.215 Da / Num. of mol.: 1 / Fragment: RESIDUES 3-261
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES ANTIBIOTICUS (bacteria) / Strain: TU 6040 / Plasmid: PIJ10499 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q9AMH9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.35 Å3/Da / Density % sol: 48 %
Description: A PARTIAL MOLECULAR REPLACEMENT SOLUTION USING PDB ENTRY 2HX AS THE SEARCH MODEL WAS USED AS A SECONDARY SOURCE OF PHASE INFORMATION.
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.5
Details: HANGING DROP VAPOUR DIFFUSION. PROTEIN AT 5MG/ML IN 25MM TRIS-HCL PH8.4, 300MM NACL MIXED WITH 2% PEG 10000, 0.2M AMMONIUM ACETATE IN 0.1M BIS-TRIS PH5.5 IN 1 TO 1 RATIO.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.95→48.04 Å / Num. obs: 20761 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 31.8 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.6
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3.8 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.5.0091refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.95→37 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.94 / SU B: 9.09 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23366 1044 5 %RANDOM
Rwork0.20486 ---
obs0.20634 19717 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.312 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å2-0.34 Å20 Å2
2---0.67 Å20 Å2
3---1.01 Å2
Refinement stepCycle: LAST / Resolution: 1.95→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1881 0 0 121 2002
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211976
X-RAY DIFFRACTIONr_bond_other_d0.0010.021367
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.9582694
X-RAY DIFFRACTIONr_angle_other_deg0.95933294
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6965249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.55922.44794
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.1615326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8981523
X-RAY DIFFRACTIONr_chiral_restr0.10.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212236
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02427
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_it0.9371.51214
X-RAY DIFFRACTIONr_mcbond_other0.2511.5492
X-RAY DIFFRACTIONr_mcangle_it1.62821952
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5363762
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8964.5739
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: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 72 -
Rwork0.28 1447 -
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)
19.7051.30680.56874.5101-0.22182.56090.00780.1184-0.4356-0.26850.0145-0.27580.04790.1806-0.02230.10980.0367-0.02060.10640.02850.1061-11.058-7.1022-28.8398
26.9909-3.88580.68413.0685-1.21871.30680.0711-0.2627-0.0775-0.0715-0.0113-0.06260.0511-0.0005-0.05980.0437-0.0047-0.0070.1540.00070.0903-23.5739-1.3354-27.8549
34.9319-1.27610.57258.5426-1.592910.30990.0476-0.0634-0.01050.4010.08870.41080.4173-0.5737-0.13630.1151-0.03080.03050.1388-0.08010.093-23.6284.5153-20.3326
44.12713.08510.71025.21231.02582.08450.2778-0.43550.32860.2482-0.0179-0.05130.0215-0.072-0.25990.1016-0.00530.04530.221-0.04840.1003-35.7067.2957-21.9564
53.82811.1354-1.07381.8234-1.691.63030.13020.0710.0883-0.27540.17540.37450.2046-0.1209-0.30560.1438-0.0206-0.06110.2170.04380.1538-52.3853-3.4392-25.8323
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 45
2X-RAY DIFFRACTION2A46 - 119
3X-RAY DIFFRACTION3A120 - 134
4X-RAY DIFFRACTION4A135 - 179
5X-RAY DIFFRACTION5A180 - 244

+
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