[English] 日本語
Yorodumi
- PDB-8gqj: Structure of Thiolase from Pseudomonas aeruginosa PAO1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8gqj
TitleStructure of Thiolase from Pseudomonas aeruginosa PAO1
ComponentsThiolase
KeywordsTRANSFERASE / acetyl-CoA acetyltransferase thiolase
Function / homology
Function and homology information


acetyl-CoA C-acetyltransferase / acetyl-CoA C-acetyltransferase activity / fatty acid metabolic process / cytoplasm
Similarity search - Function
Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal ...Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase-like
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Acetyl-CoA acetyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsHong, J. / Son, H.F. / Kim, K.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of thiolase from Pseudomonas aeruginosa PAO1
Authors: Hong, J. / Son, H.F. / Kim, K.J.
History
DepositionAug 30, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thiolase
B: Thiolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,3718
Polymers87,3792
Non-polymers9916
Water11,584643
1
A: Thiolase
B: Thiolase
hetero molecules

A: Thiolase
B: Thiolase
hetero molecules


  • defined by author&software
  • Evidence: gel filtration
  • 177 kDa, 4 polymers
Theoretical massNumber of molelcules
Total (without water)176,74116
Polymers174,7594
Non-polymers1,98212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z1
Buried area18350 Å2
ΔGint-48 kcal/mol
Surface area48600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.201, 173.201, 139.692
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

-
Components

#1: Protein Thiolase /


Mass: 43689.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: atoB, PA2001 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9I2A8, acetyl-CoA C-acetyltransferase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL / Polyethylene glycol


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 643 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.46 Å3/Da / Density % sol: 64.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 12% (w/v) PEG 3350 4% (v/v) Tacsimate, pH 8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 113500 / % possible obs: 98.1 % / Redundancy: 13 % / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.039 / Rrim(I) all: 0.166 / Χ2: 4.306 / Net I/σ(I): 9.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.8370.29755080.7930.1010.3161.33596.3
1.83-1.867.60.2954500.8480.0950.3071.47696.3
1.86-1.98.20.28255420.8910.0880.2961.6196.8
1.9-1.948.60.27455300.9190.0840.2881.76797.3
1.94-1.989.60.26456000.9370.0770.2761.98397.5
1.98-2.0310.60.24955880.960.070.2592.25398
2.03-2.08110.23856120.9680.0650.2472.33598.1
2.08-2.1311.60.22556150.9780.060.2332.52298.1
2.13-2.212.10.21556520.980.0570.2232.68698.6
2.2-2.2712.70.20356320.9850.0520.212.88298.3
2.27-2.3513.50.19256740.9870.0480.1983.07498.7
2.35-2.4413.80.18556510.9890.0460.1913.16798.6
2.44-2.5514.20.17856970.990.0440.1843.27398.6
2.55-2.6914.90.1756960.9920.0410.1753.61798.7
2.69-2.8615.70.16357130.9920.0390.1674.09198.8
2.86-3.0816.30.15657340.9930.0360.164.81698.7
3.08-3.3917.40.14957620.9940.0340.1535.86798.8
3.39-3.8818.40.14558270.9940.0330.1497.3999.3
3.88-4.8818.70.14258740.9930.0320.1458.83898.9
4.88-5017.50.14461430.9920.0340.1488.17698.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O99

4o99


Resolution: 1.78→32.75 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.739 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1778 5678 5 %RANDOM
Rwork0.156 ---
obs0.1571 107817 97.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.49 Å2 / Biso mean: 17.436 Å2 / Biso min: 7.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.08 Å20 Å2
2--0.15 Å20 Å2
3----0.5 Å2
Refinement stepCycle: final / Resolution: 1.78→32.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5664 0 52 646 6362
Biso mean--41.22 28.51 -
Num. residues----786
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0135784
X-RAY DIFFRACTIONr_bond_other_d0.0010.0155746
X-RAY DIFFRACTIONr_angle_refined_deg1.7381.6287813
X-RAY DIFFRACTIONr_angle_other_deg1.5051.57813176
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5315784
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.98821.832262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.28415942
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7031544
X-RAY DIFFRACTIONr_chiral_restr0.0890.2766
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026678
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021242
LS refinement shellResolution: 1.784→1.831 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 363 -
Rwork0.256 6815 -
all-7178 -
obs--84.41 %

+
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