[English] 日本語
Yorodumi
- PDB-8b72: Crystal structure of 3-hydroxydecanoyl-acyl carrier protein dehyd... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8b72
TitleCrystal structure of 3-hydroxydecanoyl-acyl carrier protein dehydratase (FabA) from Pseudomonas aeruginosa in complex with Z30857828
Components3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
KeywordsLYASE / FABA / PA1610
Function / homology
Function and homology information


trans-2-decenoyl-[acyl-carrier protein] isomerase / trans-2-decenoyl-acyl-carrier-protein isomerase activity / unsaturated fatty acid biosynthetic process / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / cytoplasm
Similarity search - Function
Beta-hydroxyacyl-(acyl-carrier-protein) dehydratase FabA / Beta-hydroxydecanoyl thiol ester dehydrase, FabA/FabZ / FabA-like domain / HotDog domain superfamily
Similarity search - Domain/homology
N-{2-[4-(AMINOSULFONYL)PHENYL]ETHYL}ACETAMIDE / 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsRobinson, D.A. / Moynie, L. / Naismith, J.H. / Gray, D.W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of 3-hydroxydecanoyl-acyl carrier protein dehydratase (FabA) from Pseudomonas aeruginosa in complex with Z30857828
Authors: Robinson, D.A. / Gray, D.W.G.
History
DepositionSep 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
B: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
C: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
D: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
E: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,2418
Polymers93,8435
Non-polymers3993
Water10,971609
1
A: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
B: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8574
Polymers37,5372
Non-polymers3202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-5 kcal/mol
Surface area13320 Å2
MethodPISA
2
C: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
D: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6153
Polymers37,5372
Non-polymers781
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-13 kcal/mol
Surface area13600 Å2
MethodPISA
3
E: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase

E: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase


Theoretical massNumber of molelcules
Total (without water)37,5372
Polymers37,5372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3220 Å2
ΔGint-18 kcal/mol
Surface area13660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.254, 142.382, 78.236
Angle α, β, γ (deg.)90.000, 114.050, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabA / Beta-hydroxydecanoyl thioester dehydrase / ...3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabA / Beta-hydroxydecanoyl thioester dehydrase / Trans-2-decenoyl-[acyl-carrier-protein] isomerase


Mass: 18768.533 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: fabA, PA1610 / Production host: Escherichia coli (E. coli)
References: UniProt: O33877, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase, trans-2-decenoyl-[acyl-carrier protein] isomerase
#2: Chemical ChemComp-M25 / N-{2-[4-(AMINOSULFONYL)PHENYL]ETHYL}ACETAMIDE


Mass: 242.295 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N2O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 609 / 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: 3.08 Å3/Da / Density % sol: 60.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: PEG 4000, Ammonium sulfate, sodium citrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.87→71.55 Å / Num. obs: 92452 / % possible obs: 99.7 % / Redundancy: 3.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.046 / Net I/σ(I): 10.8
Reflection shellResolution: 1.87→1.97 Å / Rmerge(I) obs: 1.115 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 13512 / CC1/2: 0.46

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CL6

4cl6


Resolution: 1.87→71.55 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.523 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2259 4533 4.9 %RANDOM
Rwork0.1864 ---
obs0.1883 87917 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 235.91 Å2 / Biso mean: 45.488 Å2 / Biso min: 27.55 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20 Å20.83 Å2
2---1.5 Å20 Å2
3----0.38 Å2
Refinement stepCycle: final / Resolution: 1.87→71.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6551 0 24 609 7184
Biso mean--58.9 63.17 -
Num. residues----849
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136727
X-RAY DIFFRACTIONr_bond_other_d0.0010.0156385
X-RAY DIFFRACTIONr_angle_refined_deg1.6021.6399098
X-RAY DIFFRACTIONr_angle_other_deg1.3181.58314655
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.65843
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.621.351348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.76151089
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.491549
X-RAY DIFFRACTIONr_chiral_restr0.070.2825
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027753
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021625
LS refinement shellResolution: 1.873→1.922 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 322 -
Rwork0.35 6537 -
all-6859 -
obs--99.62 %

+
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