[English] 日本語
Yorodumi
- PDB-6yr1: TetR(D) soaked with Tigecycline I4(1)22 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6yr1
TitleTetR(D) soaked with Tigecycline I4(1)22
ComponentsTetracycline repressor protein class D
KeywordsTRANSCRIPTION
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. / Tetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily
Similarity search - Domain/homology
TIGECYCLINE / Tetracycline repressor protein class D
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHinrichs, W. / Stary, K.
CitationJournal: to be published
Title: TetR(D) soaked with Tigecycline
Authors: Hinrichs, W. / Stary, K.
History
DepositionApr 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Tetracycline repressor protein class D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0076
Polymers23,2881
Non-polymers7185
Water45025
1
AAA: Tetracycline repressor protein class D
hetero molecules

AAA: Tetracycline repressor protein class D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,01312
Polymers46,5772
Non-polymers1,43710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area6430 Å2
ΔGint-102 kcal/mol
Surface area18680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.459, 68.459, 180.440
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

-
Components

#1: Protein Tetracycline repressor protein class D


Mass: 23288.334 Da / Num. of mol.: 1 / Mutation: A2S
Source method: isolated from a genetically manipulated source
Details: RA1 plasmid / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tetR / Details (production host): pWH1950 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0ACT4
#2: Chemical ChemComp-T1C / TIGECYCLINE


Mass: 587.665 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H41N5O8 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antibiotic*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Native crystal soaked in 1M (NH4)2SO4, 0.2M NaCl, 0.05M Tris/HCl, pH 7.0, 0.0142 mM Tigecycline, 2mM MgCl2, 22days

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 70 / Detector: CCD / Date: Oct 21, 2009 / Details: mirror
RadiationMonochromator: Osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→31 Å / Num. obs: 9565 / % possible obs: 96 % / Redundancy: 5.83 % / Biso Wilson estimate: 59 Å2 / Rmerge(I) obs: 0.081 / Χ2: 0.97 / Net I/σ(I): 11
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.56 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 863 / Χ2: 0.82 / % possible all: 88.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2xpv

2xpv


Resolution: 2.3→30.2 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.93 / SU B: 26.982 / SU ML: 0.284 / Cross valid method: FREE R-VALUE / ESU R: 0.464 / ESU R Free: 0.286
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2792 704 7.364 %
Rwork0.2333 --
all0.237 --
obs-9560 95.849 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 66.175 Å2
Baniso -1Baniso -2Baniso -3
1-1.301 Å2-0 Å2-0 Å2
2--1.301 Å2-0 Å2
3----2.601 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1555 0 46 25 1626
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121626
X-RAY DIFFRACTIONr_angle_refined_deg1.7651.6762210
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7875194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.64621.38394
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.51715277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7411515
X-RAY DIFFRACTIONr_chiral_restr0.1290.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021260
X-RAY DIFFRACTIONr_nbd_refined0.2530.2747
X-RAY DIFFRACTIONr_nbtor_refined0.3190.21107
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.261
X-RAY DIFFRACTIONr_metal_ion_refined0.1190.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.240.282
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1740.25
X-RAY DIFFRACTIONr_mcbond_it4.2855.526782
X-RAY DIFFRACTIONr_mcangle_it6.0998.266974
X-RAY DIFFRACTIONr_scbond_it5.0085.877843
X-RAY DIFFRACTIONr_scangle_it6.9598.6491235
X-RAY DIFFRACTIONr_lrange_it9.04774.3042454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.297540.33576X-RAY DIFFRACTION87.0166
2.36-2.4240.334540.305609X-RAY DIFFRACTION94.5792
2.424-2.4950.367330.285617X-RAY DIFFRACTION96.7262
2.495-2.5710.399490.313596X-RAY DIFFRACTION96.8468
2.571-2.6560.391380.299580X-RAY DIFFRACTION96.5625
2.656-2.7490.392430.271557X-RAY DIFFRACTION95.3895
2.749-2.8520.387330.298554X-RAY DIFFRACTION94.8304
2.852-2.9680.32470.295491X-RAY DIFFRACTION95.2212
2.968-3.10.373360.297494X-RAY DIFFRACTION94.3061
3.1-3.2510.385420.312466X-RAY DIFFRACTION95.3096
3.251-3.4260.43280.277470X-RAY DIFFRACTION94.8571
3.426-3.6330.299380.287436X-RAY DIFFRACTION98.75
3.633-3.8830.252280.264423X-RAY DIFFRACTION98.6871
3.883-4.1930.225330.227390X-RAY DIFFRACTION98.1439
4.193-4.5920.234410.173362X-RAY DIFFRACTION99.5062
4.592-5.130.307300.158334X-RAY DIFFRACTION98.913
5.13-5.9180.281240.208301X-RAY DIFFRACTION99.3884
5.918-7.2320.249240.219261X-RAY DIFFRACTION100
7.232-10.1630.159160.155216X-RAY DIFFRACTION98.7234
10.163-30.20.19130.176123X-RAY DIFFRACTION91.2752
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)
12.5851-0.57911.44310.1555-0.50322.34440.04030.16790.166-0.0088-0.0144-0.03150.17210.0427-0.02590.09070.0073-0.03540.1251-0.02250.039618.878428.155713.2917
20.76910.34390.39290.33140.60651.39230.10280.01060.00440.0021-0.06420.00560.0015-0.0755-0.03860.10110.0466-0.01530.0888-0.00630.022924.665633.085839.8311
36.42921.4114-0.31223.4552-4.2055.47740.30230.0375-0.6646-0.3829-0.3158-0.13420.6490.41420.01350.30020.0775-0.00380.0454-0.00550.075349.126319.585835.6353
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA2 - 63
2X-RAY DIFFRACTION2ALLAAA64 - 152
3X-RAY DIFFRACTION2ALLAAA182 - 208
4X-RAY DIFFRACTION2ALLAAA1209 - 1210
5X-RAY DIFFRACTION3ALLAAA160 - 181

+
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