[English] 日本語
Yorodumi
- PDB-1qsg: CRYSTAL STRUCTURE OF ENOYL REDUCTASE INHIBITION BY TRICLOSAN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qsg
TitleCRYSTAL STRUCTURE OF ENOYL REDUCTASE INHIBITION BY TRICLOSAN
ComponentsENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
KeywordsOXIDOREDUCTASE / ENOYL REDUCTASE
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase [NAD(P)H] activity / NADH binding / biotin biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / lipid biosynthetic process / catalytic complex / protein homotetramerization / response to antibiotic ...enoyl-[acyl-carrier-protein] reductase [NAD(P)H] activity / NADH binding / biotin biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / lipid biosynthetic process / catalytic complex / protein homotetramerization / response to antibiotic / protein-containing complex / identical protein binding / membrane / cytosol
Similarity search - Function
Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-D-glucopyranose / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / TRICLOSAN / Enoyl-[acyl-carrier-protein] reductase [NADH] FabI / Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsStewart, M.J. / Parikh, S. / Xiao, G. / Tonge, P.J. / Kisker, C.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Structural basis and mechanism of enoyl reductase inhibition by triclosan.
Authors: Stewart, M.J. / Parikh, S. / Xiao, G. / Tonge, P.J. / Kisker, C.
History
DepositionJun 21, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
B: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
C: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
D: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
E: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
F: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
G: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
H: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,46732
Polymers225,4028
Non-polymers9,06524
Water24,3201350
1
A: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
B: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
C: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
D: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,23316
Polymers112,7014
Non-polymers4,53212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22690 Å2
ΔGint-201 kcal/mol
Surface area32310 Å2
MethodPISA, PQS
2
E: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
F: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
G: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
H: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,23316
Polymers112,7014
Non-polymers4,53212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22820 Å2
ΔGint-201 kcal/mol
Surface area32010 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)73.733, 82.077, 84.177
Angle α, β, γ (deg.)89.54, 87.43, 77.77
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE / NADH-DEPENDENT ENOYL-ACP REDUCTASE


Mass: 28175.201 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET15B / Production host: Escherichia coli (E. coli)
References: UniProt: P29132, UniProt: P0AEK4*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Sugar
ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-TCL / TRICLOSAN


Mass: 289.542 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C12H7Cl3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1350 / 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: 2.2 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4000, AMMONIUM ACETATE, SODIUM ACETATE, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Feb 7, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. obs: 183224 / % possible obs: 94.2 % / Observed criterion σ(I): 0 / Redundancy: 1.85 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 13.2
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 1.64 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 1.6 / % possible all: 90.5
Reflection shell
*PLUS
% possible obs: 90.5 %

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DFI

1dfi


Resolution: 1.75→20 Å / SU B: 3.26 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.12
RfactorNum. reflection% reflectionSelection details
Rfree0.215 3664 2 %RANDOM
Rwork0.172 ---
obs-182903 94.2 %-
Displacement parametersBiso mean: 27.18 Å2
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15353 0 584 1350 17287
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d0.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.035
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.456
X-RAY DIFFRACTIONp_mcangle_it3.04
X-RAY DIFFRACTIONp_scbond_it3.038
X-RAY DIFFRACTIONp_scangle_it4.308
X-RAY DIFFRACTIONp_plane_restr0.022
X-RAY DIFFRACTIONp_chiral_restr0.109
X-RAY DIFFRACTIONp_singtor_nbd0.166
X-RAY DIFFRACTIONp_multtor_nbd0.258
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.157
X-RAY DIFFRACTIONp_planar_tor4
X-RAY DIFFRACTIONp_staggered_tor13.8
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor27.3
X-RAY DIFFRACTIONp_special_tor

+
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