[English] 日本語
Yorodumi
- PDB-4qd8: Crystal structure of Thioesterase PA1618 from Pseudomonas aerugin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qd8
TitleCrystal structure of Thioesterase PA1618 from Pseudomonas aeruginosa in complex with phenacyl-CoA
ComponentsThioesterase PA1618
KeywordsHYDROLASE / Hotdog Fold / Thioesterase / Coenzyme A / acyl carrier protein / cytosol
Function / homology
Function and homology information


1,4-dihydroxy-2-naphthoyl-CoA thioesterase activity / Hydrolases; Acting on ester bonds; Thioester hydrolases / cytosol
Similarity search - Function
Phenylacetic acid degradation-related domain / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
phenacyl coenzyme A / Putative esterase PA1618
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.616 Å
AuthorsJi, T. / Allen, K.N. / Dunaway-Mariano, D.
CitationJournal: To be Published
Title: Design and Use of an Ester Analog of CoA to Trap the Michaelis Complex in a Thioesterase
Authors: Latham, J.A. / Ji, T. / Matthews, K. / Allen, K.N. / Dunaway-Mariano, D.
History
DepositionMay 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thioesterase PA1618
B: Thioesterase PA1618
C: Thioesterase PA1618
D: Thioesterase PA1618
E: Thioesterase PA1618
F: Thioesterase PA1618
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,30410
Polymers99,7616
Non-polymers3,5434
Water9,440524
1
A: Thioesterase PA1618

A: Thioesterase PA1618

B: Thioesterase PA1618

B: Thioesterase PA1618


Theoretical massNumber of molelcules
Total (without water)66,5074
Polymers66,5074
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation2_664-x+1,-y+1,z-1/21
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area8160 Å2
ΔGint-38 kcal/mol
Surface area21710 Å2
MethodPISA
2
C: Thioesterase PA1618
D: Thioesterase PA1618
E: Thioesterase PA1618
F: Thioesterase PA1618
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0508
Polymers66,5074
Non-polymers3,5434
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11210 Å2
ΔGint-44 kcal/mol
Surface area21380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.687, 202.005, 91.083
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein
Thioesterase PA1618


Mass: 16626.814 Da / Num. of mol.: 6 / Fragment: Hotdog domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA1618 / Plasmid: pET23-a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9I3A4, Hydrolases; Acting on ester bonds; Thioester hydrolases
#2: Chemical
ChemComp-0FQ / phenacyl coenzyme A


Mass: 885.667 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C29H42N7O17P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 524 / 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: 2.34 Å3/Da / Density % sol: 47.53 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: 45% PEG400, 0.1M Bis Tris, 10mM beta-mercaptoethanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 16, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.616→47.793 Å / Num. obs: 118644 / % possible obs: 99.18 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.62→1.7 Å / % possible all: 99.7

-
Processing

Software
NameVersionClassification
JBluIce-EPICSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.616→47.793 Å / SU ML: 0.18 / σ(F): 1.14 / Phase error: 26.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2362 2000 1.69 %RANDOM
Rwork0.2043 ---
obs0.2048 118622 99.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.616→47.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6330 0 228 524 7082
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076684
X-RAY DIFFRACTIONf_angle_d1.2149100
X-RAY DIFFRACTIONf_dihedral_angle_d18.9942458
X-RAY DIFFRACTIONf_chiral_restr0.0761034
X-RAY DIFFRACTIONf_plane_restr0.0051154
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6163-1.65670.30321420.29728264X-RAY DIFFRACTION100
1.6567-1.70150.33481420.28698286X-RAY DIFFRACTION100
1.7015-1.75150.30691420.278321X-RAY DIFFRACTION100
1.7515-1.80810.2911420.25698284X-RAY DIFFRACTION100
1.8081-1.87270.26091430.23618289X-RAY DIFFRACTION99
1.8727-1.94770.2791430.22778344X-RAY DIFFRACTION99
1.9477-2.03630.26671410.21418277X-RAY DIFFRACTION99
2.0363-2.14370.2351430.20948292X-RAY DIFFRACTION99
2.1437-2.2780.27931430.20468327X-RAY DIFFRACTION99
2.278-2.45390.24571430.20738325X-RAY DIFFRACTION99
2.4539-2.70080.25861430.20628355X-RAY DIFFRACTION99
2.7008-3.09150.22771440.20348409X-RAY DIFFRACTION99
3.0915-3.89470.20931440.18588410X-RAY DIFFRACTION99
3.8947-47.81350.19061450.17448439X-RAY DIFFRACTION96

+
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