[English] 日本語
Yorodumi
- PDB-9i1x: Crystal structure of the E. coli TetR family regulator CecR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9i1x
TitleCrystal structure of the E. coli TetR family regulator CecR
ComponentsHTH-type transcriptional dual regulator CecR
KeywordsTRANSCRIPTION / TetR family regulators / antimicrobial resistance / cephalosporin-binding protein
Function / homology
Function and homology information


negative regulation of DNA-templated transcription initiation / positive regulation of DNA-templated transcription initiation / transcription cis-regulatory region binding / DNA-binding transcription factor activity / DNA-templated transcription / regulation of DNA-templated transcription / identical protein binding / cytoplasm
Similarity search - Function
Transcription regulator YbiH, C-terminal / HTH-type transcriptional dual regulator CecR, 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
ACETATE ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / HTH-type transcriptional dual regulator CecR
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsPietrzyk-Brzezinska, A.J. / Koczurowska, A. / Nielipinski, M. / Nielipinska, D. / Sekula, B.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science CentreDEC-2023/07/X/NZ1/00577 Poland
CitationJournal: Febs J. / Year: 2025
Title: Molecular basis of antibiotic sensing by the TetR family regulator CecR - a structural perspective.
Authors: Pietrzyk-Brzezinska, A.J. / Koczurowska, A. / Orlikowska, M. / Nielipinski, M. / Nielipinska, D. / Sekula, B.
History
DepositionJan 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HTH-type transcriptional dual regulator CecR
B: HTH-type transcriptional dual regulator CecR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,16811
Polymers50,4962
Non-polymers6739
Water6,720373
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7130 Å2
ΔGint-44 kcal/mol
Surface area19450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.960, 95.010, 110.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein HTH-type transcriptional dual regulator CecR / Regulator of cefoperazone and chloramphenicol sensitivity


Mass: 25247.939 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The first two residues (MA) are the remainings from the His-Tag.
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: cecR, ybiH, b0796, JW0780 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ACU0

-
Non-polymers , 6 types, 382 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.15 M magnesium chloride, 0.05 M sodium acetate, 0.1 M Bis-Tris pH 6.5, 25% (v/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.976264 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976264 Å / Relative weight: 1
ReflectionResolution: 1.91→47.66 Å / Num. obs: 51101 / % possible obs: 99.6 % / Redundancy: 13.57 % / CC1/2: 0.998 / Net I/σ(I): 11.24
Reflection shellResolution: 1.91→2.02 Å / Num. unique obs: 8127 / CC1/2: 0.653

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→47.66 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2088 2101 4.11 %
Rwork0.1752 --
obs0.1766 51081 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.91→47.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3452 0 42 373 3867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083725
X-RAY DIFFRACTIONf_angle_d0.8985077
X-RAY DIFFRACTIONf_dihedral_angle_d4.928540
X-RAY DIFFRACTIONf_chiral_restr0.049584
X-RAY DIFFRACTIONf_plane_restr0.008657
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.950.30831380.29723210X-RAY DIFFRACTION99
1.95-20.32461380.27983224X-RAY DIFFRACTION100
2-2.060.29041380.25263214X-RAY DIFFRACTION100
2.06-2.120.26431380.22473213X-RAY DIFFRACTION100
2.12-2.190.22651370.19683215X-RAY DIFFRACTION99
2.19-2.260.20121400.18183251X-RAY DIFFRACTION100
2.26-2.350.20421380.17263234X-RAY DIFFRACTION100
2.35-2.460.19811400.16473252X-RAY DIFFRACTION100
2.46-2.590.22961400.16583272X-RAY DIFFRACTION100
2.59-2.750.18381400.1633258X-RAY DIFFRACTION100
2.75-2.970.18631400.1643275X-RAY DIFFRACTION100
2.97-3.260.19171400.17183256X-RAY DIFFRACTION99
3.26-3.740.19951410.16383294X-RAY DIFFRACTION100
3.74-4.710.18091430.15163348X-RAY DIFFRACTION100
4.71-47.660.21731500.17163464X-RAY DIFFRACTION99
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)
10.0793-0.2908-0.5133.15712.21362.4353-0.02460.06340.0144-0.1528-0.05940.2654-0.086-0.15970.09990.2116-0.016-0.0040.24230.00590.22676.18343.207219.8596
22.4692-1.15970.56514.8363-1.7743.8980.0343-0.14350.13520.08620.07860.26870.0071-0.3034-0.10250.1369-0.04070.01240.2432-0.05470.18457.106215.957636.189
30.7156-0.995-1.71632.96252.36932.47460.0843-0.20220.0254-0.15730.2893-0.5567-0.13760.4212-0.40230.2160.0251-0.00410.2688-0.05430.297534.8579-1.916235.2089
40.9481-0.22920.28681.51540.14452.10010.0468-0.06040.080.1135-0.0379-0.0921-0.10.1171-0.00680.2004-0.04390.01450.2297-0.01560.223920.306313.43140.6723
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid -1:143)
2X-RAY DIFFRACTION2(chain A and resid 144:222)
3X-RAY DIFFRACTION3(chain B and resid 7:88)
4X-RAY DIFFRACTION4(chain B and resid 89:220)

+
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