[English] 日本語
Yorodumi
- PDB-3zqh: Structure of Tetracycline repressor in complex with inducer pepti... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zqh
TitleStructure of Tetracycline repressor in complex with inducer peptide- TIP3
Components
  • INDUCER PEPTIDE TIP3
  • TETRACYCLINE REPRESSOR PROTEIN CLASS B FROM TRANSPOSON TN10, TETRACYCLINE REPRESSOR PROTEIN CLASS D
KeywordsTRANSCRIPTION / TETR / PEPTIDIC EFFECTORS / ALLOSTERY
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / response to antibiotic / negative regulation of DNA-templated transcription / metal ion binding
Similarity search - Function
Tetracycline transcriptional regulator, TetR / Tetracycline repressor TetR, C-terminal / Tetracyclin repressor-like, C-terminal domain / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / : / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family ...Tetracycline transcriptional regulator, TetR / Tetracycline repressor TetR, C-terminal / Tetracyclin repressor-like, C-terminal domain / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / : / 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
Tetracycline repressor protein class B from transposon Tn10 / Tetracycline repressor protein class D
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSevvana, M. / Goeke, D. / Stoeckle, C. / Kaspar, D. / Grubmueller, S. / Goetz, C. / Wimmer, C. / Berens, C. / Klotzsche, M. / Muller, Y.A. / Hillen, W.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: An Exclusive Alpha/Beta Code Directs Allostery in Tetr-Peptide Complexes.
Authors: Sevvana, M. / Goetz, C. / Goeke, D. / Wimmer, C. / Berens, C. / Hillen, W. / Muller, Y.A.
History
DepositionJun 9, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2012Group: Other
Revision 1.2Mar 15, 2017Group: Source and taxonomy
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TETRACYCLINE REPRESSOR PROTEIN CLASS B FROM TRANSPOSON TN10, TETRACYCLINE REPRESSOR PROTEIN CLASS D
C: INDUCER PEPTIDE TIP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5054
Polymers25,3812
Non-polymers1242
Water3,279182
1
A: TETRACYCLINE REPRESSOR PROTEIN CLASS B FROM TRANSPOSON TN10, TETRACYCLINE REPRESSOR PROTEIN CLASS D
C: INDUCER PEPTIDE TIP3
hetero molecules

A: TETRACYCLINE REPRESSOR PROTEIN CLASS B FROM TRANSPOSON TN10, TETRACYCLINE REPRESSOR PROTEIN CLASS D
C: INDUCER PEPTIDE TIP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0108
Polymers50,7624
Non-polymers2484
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area10830 Å2
ΔGint-54.2 kcal/mol
Surface area18730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.350, 57.340, 57.810
Angle α, β, γ (deg.)90.00, 112.29, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-2001-

HOH

-
Components

#1: Protein TETRACYCLINE REPRESSOR PROTEIN CLASS B FROM TRANSPOSON TN10, TETRACYCLINE REPRESSOR PROTEIN CLASS D


Mass: 23531.662 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-187,188-208 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: CHIMERIC PROTEIN, RESIDUES 1-187 ARE FROM VARIANT B, RESIDUES 188-208 ARE FROM VARIANT D
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04483, UniProt: P0ACT4
#2: Protein/peptide INDUCER PEPTIDE TIP3


Mass: 1849.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ESCHERICHIA COLI (E. coli)
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 68 TO SER ENGINEERED RESIDUE IN CHAIN A, CYS 88 TO ASN ...ENGINEERED RESIDUE IN CHAIN A, CYS 68 TO SER ENGINEERED RESIDUE IN CHAIN A, CYS 88 TO ASN ENGINEERED RESIDUE IN CHAIN A, CYS 121 TO THR ENGINEERED RESIDUE IN CHAIN A, CYS 144 TO SER

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.9 % / Description: NONE
Crystal growpH: 9 / Details: 0.2 M NACL, 0.1 M TRIS PH 9.0, 25% PEG 3350.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184
DetectorType: MARRESEARCH MX-225 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 28325 / % possible obs: 96.1 % / Observed criterion σ(I): 2 / Redundancy: 3.47 % / Biso Wilson estimate: 33.3 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.8
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.71 / % possible all: 80.1

-
Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NS8

2ns8


Resolution: 1.6→24.72 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.222 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22401 1416 5 %RANDOM
Rwork0.18048 ---
obs0.18273 26893 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.144 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å2-0.28 Å2
2--0.89 Å20 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 1.6→24.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1730 0 8 182 1920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0211845
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2221.9622508
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9635233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.9123.58792
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.52615331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1341516
X-RAY DIFFRACTIONr_chiral_restr0.1710.2281
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211409
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_it1.3851.51112
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.1721799
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3813733
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.2214.5701
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: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 78 -
Rwork0.253 1474 -
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)
11.7904-0.29580.73851.0738-1.05182.3971-0.0076-0.2968-0.2921-0.09650.10070.220.2574-0.0315-0.09310.15530.0598-0.00140.17730.06350.15812.3991-20.70812.0368
20.4411-0.6220.21522.3297-0.26481.04090.0188-0.12190.11690.02260.0476-0.151-0.0580.1366-0.06650.1153-0.0173-0.00180.1741-0.02050.162211.09420.55238.0739
30.970.18640.11620.94010.58862.27220.0116-0.0940.0571-0.00890.0696-0.0836-0.07660.1656-0.08120.10860.010.02280.1082-0.02090.10674.09383.76756.6177
40.7776-0.1374-0.06240.75980.96622.4917-0.02740.17170.2588-0.09620.05160.001-0.29090.1808-0.02410.1789-0.0290.0140.13410.04510.16694.540711.473-9.6467
51.0721.525-0.82962.1698-1.195319.30960.0047-0.0311-0.07980.011-0.0401-0.11570.57220.4450.03540.05590.0233-0.01650.152-0.03370.0191-8.5585-2.6324.6746
67.37535.95570.8454.82540.68270.09880.1186-0.23420.55110.0525-0.18850.42390.0141-0.01390.06990.10740.02340.0310.1046-0.02130.08620.31121.410312.0924
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 46
2X-RAY DIFFRACTION2A47 - 102
3X-RAY DIFFRACTION3A103 - 161
4X-RAY DIFFRACTION4A162 - 205
5X-RAY DIFFRACTION5C4 - 9
6X-RAY DIFFRACTION6C10 - 15

+
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