[English] 日本語
Yorodumi
- PDB-7um8: Crystal structure of E. Coli FabI in complex with NAD and (R,E)-3... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7um8
TitleCrystal structure of E. Coli FabI in complex with NAD and (R,E)-3-(7-amino-8-oxo-6,7,8,9-tetrahydro-5H-pyrido[2,3-b]azepin-3-yl)-N-methyl-N-((3-methylbenzofuran-2-yl)methyl)acrylamide
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH] FabI
KeywordsANTIBIOTIC / enoyl reductase / FabI / antimicrobial resistance
Function / homology
Function and homology information


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 ...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 domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-NQF / Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
Similarity search - Component
Biological speciesEscherichia coli str. K-12 substr. MG1655 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHajian, B.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Acs Cent.Sci. / Year: 2022
Title: An Iterative Approach Guides Discovery of the FabI Inhibitor Fabimycin, a Late-Stage Antibiotic Candidate with In Vivo Efficacy against Drug-Resistant Gram-Negative Infections
Authors: Parker, E.N. / Cain, B.N. / Hajian, B. / Ulrich, R.J. / Geddes, E.J. / Barkho, S. / Lee, H.Y. / Williams, J.D. / Raynor, M. / Caridha, D. / Zaino, A. / Rohde, J.M. / Zak, M. / Shekhar, M. / ...Authors: Parker, E.N. / Cain, B.N. / Hajian, B. / Ulrich, R.J. / Geddes, E.J. / Barkho, S. / Lee, H.Y. / Williams, J.D. / Raynor, M. / Caridha, D. / Zaino, A. / Rohde, J.M. / Zak, M. / Shekhar, M. / Munoz, K.A. / Rzasa, K.M. / Temple, E.R. / Hunt, D. / Jin, X. / Vuong, C. / Pannone, K. / Kelly, A.M. / Mulligan, M.P. / Lee, K.K. / Lau, G.W. / Hung, D.T. / Hergenrother, P.J.
History
DepositionApr 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Source and taxonomy / Category: chem_comp_atom / chem_comp_bond / entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,6566
Polymers56,5212
Non-polymers2,1364
Water9,332518
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
B: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)117,31312
Polymers113,0414
Non-polymers4,2728
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Unit cell
Length a, b, c (Å)79.630, 79.630, 323.680
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-539-

HOH

21B-527-

HOH

-
Components

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


Mass: 28260.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria)
Gene: fabI / Production host: Escherichia coli (E. coli)
References: UniProt: P0AEK4, 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 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-NQF / (2E)-3-[(7R)-7-amino-8-oxo-6,7,8,9-tetrahydro-5H-pyrido[2,3-b]azepin-3-yl]-N-methyl-N-[(3-methyl-1-benzofuran-2-yl)methyl]prop-2-enamide


Mass: 404.462 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H24N4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 518 / 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: 2.62 Å3/Da / Density % sol: 53.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM Tris pH 7.5-8.5 0.5-1.5 M sodium citrate tribasic.

-
Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→47.2 Å / Num. obs: 69000 / % possible obs: 99.98 % / Redundancy: 2 % / Biso Wilson estimate: 22.85 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.018 / Net I/σ(I): 19.55
Reflection shellResolution: 1.7→1.761 Å / Num. unique obs: 6632 / CC1/2: 0.896

-
Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.19.2_4158refinement
XDSdata reduction
Cootmodel building
PDB_EXTRACTdata extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JQC

4jqc


Resolution: 1.7→47.2 Å / SU ML: 0.2111 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.3292
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1898 1999 2.92 %
Rwork0.1654 66571 -
obs0.1661 68570 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.92 Å2
Refinement stepCycle: LAST / Resolution: 1.7→47.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3825 0 148 518 4491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01884051
X-RAY DIFFRACTIONf_angle_d1.68435498
X-RAY DIFFRACTIONf_chiral_restr0.104617
X-RAY DIFFRACTIONf_plane_restr0.0135704
X-RAY DIFFRACTIONf_dihedral_angle_d6.4266574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.3051390.28284639X-RAY DIFFRACTION99.79
1.74-1.790.28081400.23894628X-RAY DIFFRACTION100
1.79-1.840.26781400.22154669X-RAY DIFFRACTION100
1.84-1.90.23791410.1934704X-RAY DIFFRACTION100
1.9-1.970.22281390.18214629X-RAY DIFFRACTION100
1.97-2.040.22981410.18644721X-RAY DIFFRACTION100
2.04-2.140.21951410.18984660X-RAY DIFFRACTION100
2.14-2.250.19681420.17214717X-RAY DIFFRACTION100
2.25-2.390.20851410.16434729X-RAY DIFFRACTION100
2.39-2.570.191430.16444755X-RAY DIFFRACTION99.98
2.58-2.830.18541440.16884770X-RAY DIFFRACTION100
2.83-3.240.18611450.16284819X-RAY DIFFRACTION100
3.24-4.090.15581470.14734902X-RAY DIFFRACTION100
4.09-47.20.15871560.13815229X-RAY DIFFRACTION99.94
Refinement TLS params.Method: refined / Origin x: -36.4388821674 Å / Origin y: 35.6519143368 Å / Origin z: -18.804627356 Å
111213212223313233
T0.124146256702 Å20.023417575478 Å2-0.0203398346831 Å2-0.158922795663 Å2-0.0454683750497 Å2--0.129274226289 Å2
L0.172502061345 °20.278760660408 °20.293783298214 °2-0.451343564373 °20.475060460549 °2--0.495541086847 °2
S-0.031666927309 Å °0.0044583445055 Å °0.0445545948399 Å °-0.075406028945 Å °0.0140156296253 Å °0.0302884682948 Å °-0.0787300650181 Å °0.0278057281492 Å °-0.0637670984864 Å °
Refinement TLS groupSelection details: all

+
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