[English] 日本語
Yorodumi
- PDB-8jfn: Crystal structure of enoyl-ACP reductase FabI in complex with NAD... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8jfn
TitleCrystal structure of enoyl-ACP reductase FabI in complex with NAD+ and crotonyl-ACP from Helicobacter pylori
Components
  • Acyl carrier protein
  • Enoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsBIOSYNTHETIC PROTEIN / enoyl-ACP reductase / FabI / NAD+ / crotonyl-ACP / Helicobacter pylori
Function / homology
Function and homology information


Kdo2-lipid A biosynthetic process / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / lipid A biosynthetic process / acyl binding / acyl carrier activity / phosphopantetheine binding / fatty acid biosynthetic process / membrane / cytosol
Similarity search - Function
Enoyl-[acyl-carrier-protein] reductase (NADH) / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Acyl carrier protein (ACP) / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily ...Enoyl-[acyl-carrier-protein] reductase (NADH) / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Acyl carrier protein (ACP) / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-PSR / Enoyl-[acyl-carrier-protein] reductase [NADH] / Acyl carrier protein
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsSong, W.Y. / Zhang, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22077081 China
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: The Molecular Basis of Catalysis by SDR Family Members Ketoacyl-ACP Reductase FabG and Enoyl-ACP Reductase FabI in Type-II Fatty Acid Biosynthesis.
Authors: Zhou, J. / Zhang, L. / Wang, Y. / Song, W. / Huang, Y. / Mu, Y. / Schmitz, W. / Zhang, S.Y. / Lin, H. / Chen, H.Z. / Ye, F. / Zhang, L.
History
DepositionMay 18, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)39,5794
Polymers38,4872
Non-polymers1,0922
Water1,74797
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Acyl carrier protein
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)158,31516
Polymers153,9488
Non-polymers4,3678
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-x-1,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area29520 Å2
ΔGint-169 kcal/mol
Surface area47720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.272, 101.816, 126.329
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-408-

HOH

21A-432-

HOH

31A-472-

HOH

-
Components

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


Mass: 29746.154 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: fabI / Production host: Escherichia coli (E. coli) / References: UniProt: A0A086RSH0
#2: Protein Acyl carrier protein


Mass: 8740.794 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: acpP / Production host: Escherichia coli (E. coli) / References: UniProt: Q5EDC8
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-PSR / THIOBUTYRIC ACID S-{2-[3-(2-HYDROXY-3,3-DIMETHYL-4-PHOSPHONOOXY-BUTYRYLAMINO)-PROPIONYLAMINO]-ETHYL} ESTER


Mass: 428.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H29N2O8PS / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.22 Å3/Da / Density % sol: 61.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium citrate pH 5.5, 15% w/v PEG 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9875 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9875 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 19566 / % possible obs: 99.4 % / Redundancy: 12.1 % / CC1/2: 0.979 / CC star: 0.995 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.051 / Rrim(I) all: 0.18 / Χ2: 0.987 / Net I/σ(I): 6.2 / Num. measured all: 235980
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.4-2.497.70.90618460.8980.9730.3110.9610.93493.8
2.49-2.5910.30.71919070.9670.9910.220.7530.94299.8
2.59-2.711.90.60519360.9790.9950.1770.6310.952100
2.7-2.8512.60.49619480.9830.9960.1430.5170.972100
2.85-3.0213.10.38919500.9880.9970.1110.4050.966100
3.02-3.2612.20.29119490.9860.9970.0880.3050.998100
3.26-3.5813.70.219700.9910.9980.0560.2081.02100
3.58-4.113.50.15319790.9920.9980.0430.1590.97100
4.1-5.1712.40.12419860.9910.9980.0370.130.88100
5.17-5012.70.16320950.9720.9930.0490.171.18100

-
Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8JFM

8jfm


Resolution: 2.41→40.29 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2353 803 4.9 %
Rwork0.1833 --
obs0.1858 16395 83.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.41→40.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2707 0 44 97 2848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082798
X-RAY DIFFRACTIONf_angle_d1.1193793
X-RAY DIFFRACTIONf_dihedral_angle_d21.36441
X-RAY DIFFRACTIONf_chiral_restr0.057440
X-RAY DIFFRACTIONf_plane_restr0.007477
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.560.2862670.22811119X-RAY DIFFRACTION37
2.56-2.760.2812910.22581991X-RAY DIFFRACTION64
2.76-3.030.27181860.22212984X-RAY DIFFRACTION98
3.03-3.470.24131470.19923101X-RAY DIFFRACTION100
3.47-4.370.20371530.16833135X-RAY DIFFRACTION100
4.37-40.290.22641590.16053262X-RAY DIFFRACTION100

+
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