[English] 日本語
Yorodumi
- PDB-8jg2: Crystal structure of a biosynthetic thiolase from Megasphaera hex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8jg2
TitleCrystal structure of a biosynthetic thiolase from Megasphaera hexanoica soaked with hexanoyl-CoA
ComponentsAcetyl-CoA C-acetyltransferase
KeywordsBIOSYNTHETIC PROTEIN / acetyl-coenzyme A C-acyltransferase
Function / homology
Function and homology information


acetyl-CoA C-acetyltransferase / acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase-like
Similarity search - Domain/homology
ACETATE ION / COENZYME A / Acetyl-CoA acetyltransferase
Similarity search - Component
Biological speciesMegasphaera hexanoica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsKim, E.-J. / Seo, H. / Kim, K.-J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of biosynthetic thiolase from Megasphaera hexanoica
Authors: Jeon, B.S. / Kim, E.-J. / Kim, K.-J. / Sang, B.-I.
History
DepositionMay 19, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 8, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acetyl-CoA C-acetyltransferase
B: Acetyl-CoA C-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8376
Polymers92,1832
Non-polymers1,6534
Water11,241624
1
A: Acetyl-CoA C-acetyltransferase
B: Acetyl-CoA C-acetyltransferase
hetero molecules

A: Acetyl-CoA C-acetyltransferase
B: Acetyl-CoA C-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,67312
Polymers184,3674
Non-polymers3,3068
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565x,-y+1,-z1
Buried area20290 Å2
ΔGint-17 kcal/mol
Surface area48170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.505, 111.443, 140.996
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-700-

HOH

-
Components

#1: Protein Acetyl-CoA C-acetyltransferase / Biosynthetic thiolase


Mass: 46091.727 Da / Num. of mol.: 2 / Mutation: C88S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Megasphaera hexanoica (bacteria) / Gene: HF872_02440 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A848BQU5
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 624 / 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: 2.22 Å3/Da / Density % sol: 44.67 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25 % w/v polyethylene glycol (PEG) 3350 and 0.1M HEPES pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 3, 2016
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.64→38.99 Å / Num. obs: 99877 / % possible obs: 99.61 % / Redundancy: 2 % / Biso Wilson estimate: 21.19 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.02374 / Rpim(I) all: 0.02374 / Rrim(I) all: 0.03357 / Net I/σ(I): 12.08
Reflection shellResolution: 1.64→1.699 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2768 / Mean I/σ(I) obs: 2.11 / Num. unique obs: 9827 / CC1/2: 0.853 / CC star: 0.96 / Rpim(I) all: 0.2768 / Rrim(I) all: 0.3915 / % possible all: 99.22

-
Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→38.99 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.965 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23558 4968 5 %RANDOM
Rwork0.1982 ---
obs0.2001 94895 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 mean: 22.664 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0 Å2-0 Å2
2---2.05 Å20 Å2
3---2.24 Å2
Refinement stepCycle: 1 / Resolution: 1.64→38.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5872 0 0 624 6496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125991
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165829
X-RAY DIFFRACTIONr_angle_refined_deg1.5491.6438113
X-RAY DIFFRACTIONr_angle_other_deg0.5211.56813426
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9485792
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.349534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.414101019
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0760.2945
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027018
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021248
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0212.2623167
X-RAY DIFFRACTIONr_mcbond_other2.0152.2623166
X-RAY DIFFRACTIONr_mcangle_it2.784.0623958
X-RAY DIFFRACTIONr_mcangle_other2.7814.0623959
X-RAY DIFFRACTIONr_scbond_it2.9232.6442824
X-RAY DIFFRACTIONr_scbond_other2.9222.6442825
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5334.7434156
X-RAY DIFFRACTIONr_long_range_B_refined5.59323.946749
X-RAY DIFFRACTIONr_long_range_B_other5.54123.096607
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.64→1.683 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 342 -
Rwork0.334 6917 -
obs--98.96 %

+
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