[English] 日本語
Yorodumi
- PDB-4qdb: Crystal structure of mutant Thioesterase PA1618 (Q49A) from Pseud... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qdb
TitleCrystal structure of mutant Thioesterase PA1618 (Q49A) from Pseudomonas aeruginosa
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
Putative esterase PA1618
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.023 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 1.1Jun 24, 2015Group: Other
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
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


Theoretical massNumber of molelcules
Total (without water)99,4196
Polymers99,4196
Non-polymers00
Water7,134396
1
A: Thioesterase PA1618

A: Thioesterase PA1618


Theoretical massNumber of molelcules
Total (without water)33,1402
Polymers33,1402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area2510 Å2
ΔGint-19 kcal/mol
Surface area12530 Å2
MethodPISA
2
B: Thioesterase PA1618

B: Thioesterase PA1618


Theoretical massNumber of molelcules
Total (without water)33,1402
Polymers33,1402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_567x,-y+1,-z+21
Buried area2570 Å2
ΔGint-19 kcal/mol
Surface area12470 Å2
MethodPISA
3
C: Thioesterase PA1618
D: Thioesterase PA1618


Theoretical massNumber of molelcules
Total (without water)33,1402
Polymers33,1402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-17 kcal/mol
Surface area12750 Å2
MethodPISA
4
E: Thioesterase PA1618
F: Thioesterase PA1618


Theoretical massNumber of molelcules
Total (without water)33,1402
Polymers33,1402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-17 kcal/mol
Surface area12770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.959, 201.556, 90.924
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: 16569.762 Da / Num. of mol.: 6 / Mutation: Q49A
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: pET-23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q9I3A4, Hydrolases; Acting on ester bonds; Thioester hydrolases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.33 Å3/Da / Density % sol: 47.13 %
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: 2.02→47.64 Å / Num. obs: 60156 / % possible obs: 98.99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

-
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: 2.023→47.64 Å / SU ML: 0.25 / σ(F): 1.11 / Phase error: 27.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2307 1999 3.33 %random
Rwork0.2031 ---
obs0.2041 60093 98.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.023→47.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6306 0 0 396 6702
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076420
X-RAY DIFFRACTIONf_angle_d1.1058718
X-RAY DIFFRACTIONf_dihedral_angle_d13.0652304
X-RAY DIFFRACTIONf_chiral_restr0.0771014
X-RAY DIFFRACTIONf_plane_restr0.0051128
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0233-2.07390.34921420.32184126X-RAY DIFFRACTION100
2.0739-2.130.3271420.28584131X-RAY DIFFRACTION100
2.13-2.19270.29551430.26724150X-RAY DIFFRACTION100
2.1927-2.26350.27861420.24544126X-RAY DIFFRACTION100
2.2635-2.34440.2661430.24184146X-RAY DIFFRACTION100
2.3444-2.43820.24681420.2334124X-RAY DIFFRACTION100
2.4382-2.54920.28451430.22284166X-RAY DIFFRACTION100
2.5492-2.68360.24711440.20524172X-RAY DIFFRACTION100
2.6836-2.85170.27091420.1984160X-RAY DIFFRACTION100
2.8517-3.07180.21121440.18944154X-RAY DIFFRACTION99
3.0718-3.38090.21821430.18454172X-RAY DIFFRACTION99
3.3809-3.86990.21721430.17014151X-RAY DIFFRACTION98
3.8699-4.87490.18091430.16294151X-RAY DIFFRACTION97
4.8749-47.65340.20221430.2094165X-RAY DIFFRACTION94

+
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