[English] 日本語
Yorodumi
- PDB-7bka: Crystal structure of 3-hydroxydecanoyl-acyl carrier protein dehyd... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7bka
TitleCrystal structure of 3-hydroxydecanoyl-acyl carrier protein dehydratase (FabA) from Pseudomonas aeruginosa in complex with DDD01870824
Components3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
KeywordsLYASE / FabA / PA1610 / Complex
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
4-ethylbenzenesulfonamide / 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsMoynie, L. / Naismith, J.H.
Funding support1items
OrganizationGrant numberCountry
European Communitys Seventh Framework Programme
CitationJournal: To Be Published
Title: Crystal structures of 3-hydroxydecanoyl-acyl carrier protein dehydratase (FabA) from Pseudomonas aeruginosa
Authors: Moynie, L. / Naismith, J.H. / Robinson, D.A.
History
DepositionJan 15, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
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)95,16015
Polymers93,8435
Non-polymers1,31710
Water3,243180
1
A: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
hetero molecules

A: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0646
Polymers37,5372
Non-polymers5274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3940 Å2
ΔGint-15 kcal/mol
Surface area13120 Å2
MethodPISA
2
B: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
C: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0646
Polymers37,5372
Non-polymers5274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-12 kcal/mol
Surface area13180 Å2
MethodPISA
3
D: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
E: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0646
Polymers37,5372
Non-polymers5274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-12 kcal/mol
Surface area13160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.670, 142.030, 77.900
Angle α, β, γ (deg.)90.000, 114.140, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

21A-341-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15B
25C
16B
26D
17B
27E
18C
28D
19C
29E
110D
210E

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRPHEPHEAA2 - 1712 - 171
21THRTHRPHEPHEBB2 - 1712 - 171
12LYSLYSPHEPHEAA3 - 1713 - 171
22LYSLYSPHEPHECC3 - 1713 - 171
13LYSLYSPHEPHEAA3 - 1713 - 171
23LYSLYSPHEPHEDD3 - 1713 - 171
14THRTHRPHEPHEAA2 - 1712 - 171
24THRTHRPHEPHEEE2 - 1712 - 171
15LYSLYSPHEPHEBB3 - 1713 - 171
25LYSLYSPHEPHECC3 - 1713 - 171
16LYSLYSPHEPHEBB3 - 1713 - 171
26LYSLYSPHEPHEDD3 - 1713 - 171
17THRTHRSERSERBB2 - 1702 - 170
27THRTHRSERSEREE2 - 1702 - 170
18LYSLYSPHEPHECC3 - 1713 - 171
28LYSLYSPHEPHEDD3 - 1713 - 171
19LYSLYSPHEPHECC3 - 1713 - 171
29LYSLYSPHEPHEEE3 - 1713 - 171
110LYSLYSPHEPHEDD3 - 1713 - 171
210LYSLYSPHEPHEEE3 - 1713 - 171

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

-
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 (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (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-4JC / 4-ethylbenzenesulfonamide


Mass: 185.243 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C8H11NO2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.88→43.07 Å / Num. obs: 91024 / % possible obs: 99.63 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Net I/σ(I): 10.2
Reflection shellResolution: 1.88→1.91 Å / Rmerge(I) obs: 1.249 / Num. unique obs: 17404 / CC1/2: 0.371

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CL6

4cl6


Resolution: 1.88→43.07 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.433 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2172 4486 4.9 %RANDOM
Rwork0.1962 ---
obs0.1972 86537 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 111.59 Å2 / Biso mean: 35.994 Å2 / Biso min: 22.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20 Å2-0.34 Å2
2--0.49 Å20 Å2
3----0.51 Å2
Refinement stepCycle: final / Resolution: 1.88→43.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6509 0 80 180 6769
Biso mean--35.99 37.62 -
Num. residues----844
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0136736
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176301
X-RAY DIFFRACTIONr_angle_refined_deg1.6141.6479108
X-RAY DIFFRACTIONr_angle_other_deg1.3671.59314536
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.765836
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.75121.483344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.478151080
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7131547
X-RAY DIFFRACTIONr_chiral_restr0.0760.2822
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027614
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021511
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A50880.07
12B50880.07
21A50220.08
22C50220.08
31A50040.07
32D50040.07
41A50180.09
42E50180.09
51B51220.05
52C51220.05
61B51090.05
62D51090.05
71B51380.07
72E51380.07
81C50990.05
82D50990.05
91C50550.07
92E50550.07
101D50580.07
102E50580.07
LS refinement shellResolution: 1.88→1.929 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 355 -
Rwork0.32 6376 -
all-6731 -
obs--99.97 %

+
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