[English] 日本語
Yorodumi
- PDB-6ihc: Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ihc
TitleCrystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase(FabZ) Y100A mutant in complex with holo-ACP from Helicobacter pylori
Components
  • 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
  • holo-form acyl carrier protein (holo-ACP)
KeywordsBIOSYNTHETIC PROTEIN / Dehydrotase / fatty acid biosynthesis
Function / homology
Function and homology information


(3R)-3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity / (3R)-3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / (3R)-3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity / (3R)-3-hydroxymyristoyl-[acyl-carrier-protein] dehydratase activity / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / lipid A biosynthetic process / phosphopantetheine binding / acyl carrier activity / fatty acid biosynthetic process / cytoplasm
Similarity search - Function
Beta-hydroxyacyl-(acyl-carrier-protein) dehydratase FabZ / Beta-hydroxydecanoyl thiol ester dehydrase, FabA/FabZ / FabA-like domain / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Acyl carrier protein (ACP) / Phosphopantetheine attachment site ...Beta-hydroxyacyl-(acyl-carrier-protein) dehydratase FabZ / Beta-hydroxydecanoyl thiol ester dehydrase, FabA/FabZ / FabA-like domain / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Roll / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Chem-PN7 / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ / Acyl carrier protein / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsShen, S.Q. / Zhang, L. / Zhang, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China21722802 China
CitationJournal: Int. J. Biol. Macromol. / Year: 2019
Title: A back-door Phenylalanine coordinates the stepwise hexameric loading of acyl carrier protein by the fatty acid biosynthesis enzyme beta-hydroxyacyl-acyl carrier protein dehydratase (FabZ).
Authors: Shen, S.Q. / Hang, X.D. / Zhuang, J.J. / Zhang, L. / Bi, H.K. / Zhang, L.
History
DepositionSep 29, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
B: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
C: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
D: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
E: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
F: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
G: holo-form acyl carrier protein (holo-ACP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,24311
Polymers111,3087
Non-polymers9354
Water5,459303
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17510 Å2
ΔGint-68 kcal/mol
Surface area36370 Å2
Unit cell
Length a, b, c (Å)272.528, 76.900, 72.991
Angle α, β, γ (deg.)90.00, 99.23, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ / (3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase / (3R)-hydroxymyristoyl-ACP dehydrase / ...(3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase / (3R)-hydroxymyristoyl-ACP dehydrase / Beta-hydroxyacyl-ACP dehydratase


Mass: 17372.229 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: fabZ, AOD77_0202395 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1Q4MZN5, UniProt: Q5G940*PLUS, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase
#2: Protein holo-form acyl carrier protein (holo-ACP)


Mass: 7074.954 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: B6JLE2
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-PN7 / N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-sulfanylethyl)-beta-alaninamide


Mass: 358.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H23N2O7PS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 3.42 Å3/Da / Density % sol: 63.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.05M tri-Sodium citrate dehydrate

-
Data collection

DiffractionMean temperature: 185 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å
DetectorType: MACSCIENCE DIP100S / Detector: IMAGE PLATE / Date: Sep 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 56174 / % possible obs: 96.1 % / Redundancy: 3.2 % / Net I/σ(I): 14.9
Reflection shellResolution: 2.4→2.49 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.4→45.644 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2138 2847 5.07 %
Rwork0.1754 --
obs0.1774 56174 96.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→45.644 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7739 0 60 303 8102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097980
X-RAY DIFFRACTIONf_angle_d0.97510802
X-RAY DIFFRACTIONf_dihedral_angle_d9.9464751
X-RAY DIFFRACTIONf_chiral_restr0.0611202
X-RAY DIFFRACTIONf_plane_restr0.0061382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.44140.2651010.21711970X-RAY DIFFRACTION72
2.4414-2.48580.33351010.21912275X-RAY DIFFRACTION81
2.4858-2.53360.2621150.22132399X-RAY DIFFRACTION87
2.5336-2.58540.29431220.22332555X-RAY DIFFRACTION92
2.5854-2.64160.25271590.20642608X-RAY DIFFRACTION95
2.6416-2.7030.26081490.20372726X-RAY DIFFRACTION98
2.703-2.77060.2361320.19962720X-RAY DIFFRACTION99
2.7706-2.84550.23231470.1942808X-RAY DIFFRACTION100
2.8455-2.92920.22951560.19012744X-RAY DIFFRACTION100
2.9292-3.02370.24461430.19982767X-RAY DIFFRACTION100
3.0237-3.13180.2341330.19512774X-RAY DIFFRACTION100
3.1318-3.25720.24411510.19532737X-RAY DIFFRACTION100
3.2572-3.40530.22491550.18672774X-RAY DIFFRACTION100
3.4053-3.58480.19741460.17622772X-RAY DIFFRACTION100
3.5848-3.80930.20791470.15852784X-RAY DIFFRACTION100
3.8093-4.10330.19031560.1512764X-RAY DIFFRACTION100
4.1033-4.51590.16961630.13482774X-RAY DIFFRACTION100
4.5159-5.16850.1751710.14332765X-RAY DIFFRACTION100
5.1685-6.50880.19621440.1742798X-RAY DIFFRACTION99
6.5088-45.65180.22251560.18032813X-RAY DIFFRACTION98

+
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