[English] 日本語
Yorodumi
- PDB-5ifl: Crystal structure of B. pseudomallei FabI in complex with NAD and... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ifl
TitleCrystal structure of B. pseudomallei FabI in complex with NAD and triclosan
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / enoyl-ACP reductase / Burkholderia pseudomallei / diphenyl ethers / slow-binding inhibitors
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / nucleotide binding
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 / TRICLOSAN / Enoyl-[acyl-carrier-protein] reductase [NADH] / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHirschbeck, M.W. / Eltschkner, S. / Tonge, P.J. / Kisker, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB 630 Germany
CitationJournal: Biochemistry / Year: 2017
Title: Rationalizing the Binding Kinetics for the Inhibition of the Burkholderia pseudomallei FabI1 Enoyl-ACP Reductase.
Authors: Neckles, C. / Eltschkner, S. / Cummings, J.E. / Hirschbeck, M. / Daryaee, F. / Bommineni, G.R. / Zhang, Z. / Spagnuolo, L. / Yu, W. / Davoodi, S. / Slayden, R.A. / Kisker, C. / Tonge, P.J.
History
DepositionFeb 26, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Apr 19, 2017Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
F: Enoyl-[acyl-carrier-protein] reductase [NADH]
G: Enoyl-[acyl-carrier-protein] reductase [NADH]
H: Enoyl-[acyl-carrier-protein] reductase [NADH]
I: Enoyl-[acyl-carrier-protein] reductase [NADH]
J: Enoyl-[acyl-carrier-protein] reductase [NADH]
K: Enoyl-[acyl-carrier-protein] reductase [NADH]
L: Enoyl-[acyl-carrier-protein] reductase [NADH]
M: Enoyl-[acyl-carrier-protein] reductase [NADH]
N: Enoyl-[acyl-carrier-protein] reductase [NADH]
O: Enoyl-[acyl-carrier-protein] reductase [NADH]
P: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)484,45448
Polymers469,20616
Non-polymers15,24732
Water10,251569
1
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,11312
Polymers117,3024
Non-polymers3,8128
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20890 Å2
ΔGint-217 kcal/mol
Surface area30000 Å2
MethodPISA
2
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
F: Enoyl-[acyl-carrier-protein] reductase [NADH]
G: Enoyl-[acyl-carrier-protein] reductase [NADH]
H: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,11312
Polymers117,3024
Non-polymers3,8128
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20960 Å2
ΔGint-217 kcal/mol
Surface area30030 Å2
MethodPISA
3
I: Enoyl-[acyl-carrier-protein] reductase [NADH]
J: Enoyl-[acyl-carrier-protein] reductase [NADH]
K: Enoyl-[acyl-carrier-protein] reductase [NADH]
L: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,11312
Polymers117,3024
Non-polymers3,8128
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20920 Å2
ΔGint-216 kcal/mol
Surface area30070 Å2
MethodPISA
4
M: Enoyl-[acyl-carrier-protein] reductase [NADH]
N: Enoyl-[acyl-carrier-protein] reductase [NADH]
O: Enoyl-[acyl-carrier-protein] reductase [NADH]
P: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,11312
Polymers117,3024
Non-polymers3,8128
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20600 Å2
ΔGint-211 kcal/mol
Surface area30240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.360, 99.920, 139.860
Angle α, β, γ (deg.)82.87, 89.20, 78.13
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Enoyl-[acyl-carrier-protein] reductase [NADH]


Mass: 29325.391 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria)
Gene: fabI, fabI_2, ACT79_25590, AM256_11615, AM257_11635, AMS56_08605, DP46_2957, DP49_6839, ERS012314_03793, ERS012372_03823, SY87_14645, TR70_1075, VU09_13745
Production host: Escherichia coli (E. coli)
References: UniProt: A0A069B9A4, UniProt: A0A0H3HP34*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical
ChemComp-TCL / TRICLOSAN


Mass: 289.542 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C12H7Cl3O2
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 569 / 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: 2.03 Å3/Da / Density % sol: 39.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 8 % PEG 1000, 8 % PEG 8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Aug 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.6→51.39 Å / Num. obs: 112071 / % possible obs: 98.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 8.9
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 3.2 / % possible all: 97.9

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EK2

3ek2


Resolution: 2.6→48.584 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 28.97
RfactorNum. reflection% reflection
Rfree0.2624 5629 5.02 %
Rwork0.2214 --
obs0.2235 112038 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→48.584 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30400 0 976 569 31945
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00331984
X-RAY DIFFRACTIONf_angle_d0.72943424
X-RAY DIFFRACTIONf_dihedral_angle_d10.78811584
X-RAY DIFFRACTIONf_chiral_restr0.0264976
X-RAY DIFFRACTIONf_plane_restr0.0035840
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.62950.35941990.30733527X-RAY DIFFRACTION98
2.6295-2.66050.36291780.30573472X-RAY DIFFRACTION98
2.6605-2.69290.35671970.29533563X-RAY DIFFRACTION98
2.6929-2.7270.35031790.29993550X-RAY DIFFRACTION98
2.727-2.76290.35091940.28813482X-RAY DIFFRACTION98
2.7629-2.80070.32781810.28283564X-RAY DIFFRACTION98
2.8007-2.84070.35611800.29293534X-RAY DIFFRACTION98
2.8407-2.88310.33291790.28093528X-RAY DIFFRACTION98
2.8831-2.92820.35131910.28383587X-RAY DIFFRACTION98
2.9282-2.97620.33551770.2853498X-RAY DIFFRACTION98
2.9762-3.02750.31131680.27853604X-RAY DIFFRACTION98
3.0275-3.08250.3361950.27753490X-RAY DIFFRACTION98
3.0825-3.14180.31752010.26753514X-RAY DIFFRACTION98
3.1418-3.20590.30041750.25753590X-RAY DIFFRACTION99
3.2059-3.27560.32512040.263508X-RAY DIFFRACTION98
3.2756-3.35180.2891760.25653644X-RAY DIFFRACTION99
3.3518-3.43560.3131660.2443525X-RAY DIFFRACTION99
3.4356-3.52850.2941880.24863568X-RAY DIFFRACTION99
3.5285-3.63230.26272040.23773481X-RAY DIFFRACTION99
3.6323-3.74950.28131810.22023583X-RAY DIFFRACTION99
3.7495-3.88340.25272050.21133552X-RAY DIFFRACTION99
3.8834-4.03880.2591940.21263549X-RAY DIFFRACTION99
4.0388-4.22260.22921890.19613551X-RAY DIFFRACTION99
4.2226-4.4450.23481810.18493580X-RAY DIFFRACTION99
4.445-4.72330.24042130.18413541X-RAY DIFFRACTION99
4.7233-5.08760.20931710.18213574X-RAY DIFFRACTION99
5.0876-5.5990.21322000.17463558X-RAY DIFFRACTION99
5.599-6.40760.20781820.18933581X-RAY DIFFRACTION99
6.4076-8.06690.20241940.1663561X-RAY DIFFRACTION99
8.0669-48.59230.16111870.15613550X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 15.3552 Å / Origin y: 25.9931 Å / Origin z: 17.2357 Å
111213212223313233
T0.4744 Å2-0.0491 Å20.0654 Å2-0.2978 Å2-0.0052 Å2--0.374 Å2
L0.0738 °2-0.1013 °2-0.0243 °2-0.1861 °20.0586 °2--0.2525 °2
S-0.0531 Å °0.0132 Å °0.033 Å °0.1896 Å °-0.027 Å °0.0187 Å °-0.0058 Å °0.0379 Å °0.0861 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