[English] 日本語
Yorodumi
- PDB-1lx6: Crystal Structure of E. Coli Enoyl Reductase-NAD+ with a Bound Be... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1lx6
TitleCrystal Structure of E. Coli Enoyl Reductase-NAD+ with a Bound Benzamide Inhibitor
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / FABI / ENOYL REDUCTASE
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / 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 activity (NAD(P)H) / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-ZAM / 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: 2.4 Å
AuthorsSmith, W.W. / Qiu, X. / Janson, C.A.
CitationJournal: J.Med.Chem. / Year: 2002
Title: Discovery of aminopyridine-based inhibitors of bacterial enoyl-ACP reductase (FabI).
Authors: Miller, W.H. / Seefeld, M.A. / Newlander, K.A. / Uzinskas, I.N. / Burgess, W.J. / Heerding, D.A. / Yuan, C.C. / Head, M.S. / Payne, D.J. / Rittenhouse, S.F. / Moore, T.D. / Pearson, S.C. / ...Authors: Miller, W.H. / Seefeld, M.A. / Newlander, K.A. / Uzinskas, I.N. / Burgess, W.J. / Heerding, D.A. / Yuan, C.C. / Head, M.S. / Payne, D.J. / Rittenhouse, S.F. / Moore, T.D. / Pearson, S.C. / Berry, V. / DeWolf Jr., W.E. / Keller, P.M. / Polizzi, B.J. / Qiu, X. / Janson, C.A. / Huffman, W.F.
History
DepositionJun 4, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8706
Polymers55,7862
Non-polymers2,0844
Water4,450247
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,73912
Polymers111,5724
Non-polymers4,1688
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area21840 Å2
ΔGint-150 kcal/mol
Surface area28380 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)79.440, 79.440, 327.080
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein Enoyl-[acyl-carrier-protein] reductase [NADH] / NADH-dependent enoyl-ACP reductase


Mass: 27892.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P29132, UniProt: P0AEK4*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-ZAM / 3-[(ACETYL-METHYL-AMINO)-METHYL]-4-AMINO-N-METHYL-N-(1-METHYL-1H-INDOL-2-YLMETHYL)-BENZAMIDE


Mass: 378.467 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H26N4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.67 Å3/Da / Density % sol: 53.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES, 2M(NH4)2SO4,5% PEG400, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5 / Details: Qiu, X., (1999) Protein Sci., 8, 2529.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
20.1 MHEPES1reservoirpH7.5
32 Mammonium sulfate1reservoir
45 %PEG4001reservoir
520 %ammonium sulfate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1 / Wavelength: 1 Å
DetectorType: BRANDEIS / Detector: CCD / Date: Feb 11, 1999
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 2.4→50 Å / Num. all: 22357 / Num. obs: 20345 / % possible obs: 91 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 18.5
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 1.58 % / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.198 / % possible all: 83
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 50 Å / Num. obs: 22357 / % possible obs: 90.6 % / Redundancy: 3 % / Num. measured all: 66826 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 82.8 % / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 2.8

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 1C14

1c14


Resolution: 2.4→50 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 590722.01 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 981 5 %RANDOM
Rwork0.188 ---
all-22357 --
obs-20345 86.9 %-
Displacement parametersBiso mean: 21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3598 0 144 247 3989
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.94
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.45
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.4→2.5 Å / Rfactor Rfree error: 0.12 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.34 72 5 %
Rwork0.25 1442 -
obs--83 %
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 7 Å / Num. reflection obs: 19077 / σ(F): 2 / Rfactor Rfree: 0.251 / Rfactor Rwork: 0.188 / σ(I): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.45
LS refinement shell
*PLUS
Rfactor Rfree: 0.34 / Rfactor Rwork: 0.25

+
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