[English] 日本語
Yorodumi
- PDB-3b7k: Human Acyl-coenzyme A thioesterase 12 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3b7k
TitleHuman Acyl-coenzyme A thioesterase 12
ComponentsAcyl-coenzyme A thioesterase 12
KeywordsHYDROLASE / Hotdog fold / Structural Genomics / Structural Genomics Consortium / SGC / Fatty acid metabolism / Lipid metabolism / Serine esterase
Function / homology
Function and homology information


acetyl-CoA hydrolase / acetyl-CoA hydrolase activity / acyl-CoA metabolic process / acetyl-CoA metabolic process / Mitochondrial Fatty Acid Beta-Oxidation / carboxylic ester hydrolase activity / intercellular bridge / fatty acid metabolic process / lipid binding / nucleoplasm ...acetyl-CoA hydrolase / acetyl-CoA hydrolase activity / acyl-CoA metabolic process / acetyl-CoA metabolic process / Mitochondrial Fatty Acid Beta-Oxidation / carboxylic ester hydrolase activity / intercellular bridge / fatty acid metabolic process / lipid binding / nucleoplasm / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Hotdog acyl-CoA thioesterase (ACOT)-type domain / Cytosolic acyl coenzyme A thioester hydrolase / Hotdog acyl-CoA thioesterase (ACOT)-type domain profile. / START domain / START domain / START domain profile. / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A ...Hotdog acyl-CoA thioesterase (ACOT)-type domain / Cytosolic acyl coenzyme A thioester hydrolase / Hotdog acyl-CoA thioesterase (ACOT)-type domain profile. / START domain / START domain / START domain profile. / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / START-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Acetyl-coenzyme A thioesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLehtio, L. / Busam, R.D. / Arrowsmith, C.H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. ...Lehtio, L. / Busam, R.D. / Arrowsmith, C.H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Herman, M.D. / Johansson, A. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Moche, M. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Sundstrom, M. / Svensson, L. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Berglund, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Human Acyl-coenzyme A thioesterase 12.
Authors: Lehtio, L. / Busam, R.D. / Arrowsmith, C.H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Herman, M.D. / ...Authors: Lehtio, L. / Busam, R.D. / Arrowsmith, C.H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Herman, M.D. / Johansson, A. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Moche, M. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Sundstrom, M. / Svensson, L. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Berglund, H.
History
DepositionOct 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Acyl-coenzyme A thioesterase 12
B: Acyl-coenzyme A thioesterase 12
C: Acyl-coenzyme A thioesterase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,8106
Polymers111,5083
Non-polymers2,3033
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.700, 126.050, 185.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Acyl-coenzyme A thioesterase 12 / Acyl-CoA thioesterase 12 / Acyl-CoA thioester hydrolase 12 / Cytoplasmic acetyl-CoA hydrolase 1 / ...Acyl-CoA thioesterase 12 / Acyl-CoA thioester hydrolase 12 / Cytoplasmic acetyl-CoA hydrolase 1 / CACH-1 / hCACH-1 / START domain-containing protein 12 / StARD12


Mass: 37169.176 Da / Num. of mol.: 3
Fragment: Acyl coenzyme A hydrolase domains 1 and 2: Residues 7-316
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACOT12, CACH, CACH1, STARD12 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) gold pRARE / References: UniProt: Q8WYK0, acetyl-CoA hydrolase
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H36N7O16P3S

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 350mM NaSCN, 25% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 10, 2006 / Details: mirrors
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 26807 / Num. obs: 26807 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.16 % / Biso Wilson estimate: 69.8 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 12.5
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 7.33 % / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 3.37 / Num. unique all: 2737 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.3.0040refinement
ProDCdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1VPM

1vpm


Resolution: 2.7→19.89 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.884 / SU B: 36.952 / SU ML: 0.359 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.428 / ESU R Free: 0.382 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28479 1339 5 %RANDOM
Rwork0.23362 ---
all0.2362 25467 --
obs0.2362 25467 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.179 Å2
Baniso -1Baniso -2Baniso -3
1-2.77 Å20 Å20 Å2
2--2.01 Å20 Å2
3----4.79 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5917 0 144 0 6061
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226174
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.111.9578384
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5345760
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.87623.922255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.721151033
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5641536
X-RAY DIFFRACTIONr_chiral_restr0.0690.2977
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024486
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.190.22432
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2920.24106
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2163
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.231
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2680.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2581.53933
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.45526159
X-RAY DIFFRACTIONr_scbond_it0.63732506
X-RAY DIFFRACTIONr_scangle_it1.0654.52225
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 96 -
Rwork0.29 1829 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.60240.2699-1.43310.93370.31073.36260.22460.1720.1184-0.6303-0.1280.0721-0.8978-0.0165-0.09660.1393-0.1487-0.1174-0.49450.0401-0.2828-0.4112-23.345210.6726
25.0925-3.21730.83194.9726-0.63933.1780.1855-0.1492-0.3651-0.0823-0.32680.6529-0.258-0.67150.1413-0.1626-0.1359-0.1416-0.24710.0463-0.0935-14.0595-29.07213.8294
33.7436-0.7631-1.90492.96720.41964.1734-0.1061-0.0229-0.4248-0.3825-0.1180.05980.0959-0.05780.2241-0.2901-0.1465-0.1181-0.42280.1295-0.12482.6999-41.11314.7519
43.0304-2.2603-1.94362.25181.47735.1060.0761-0.4090.4846-0.35490.2458-0.6568-0.32560.7249-0.3220.0549-0.62620.15810.1715-0.2753-0.044226.1847-13.250128.1908
53.55780.17630.61731.66770.9943.45710.0185-0.82630.9126-0.32730.2046-0.4531-0.99340.6227-0.22310.2773-0.50830.13270.1515-0.36920.176721.2616-1.943836.8903
62.9912-0.4056-0.5932.8041-0.38042.89130.4244-0.34750.3578-0.4968-0.1093-0.0698-0.84610.1931-0.31520.2406-0.36130.0539-0.2665-0.1108-0.2159.2463-9.391621.7631
72.4294-0.6829-1.93592.2927-1.37087.6019-0.0348-0.4324-0.5015-0.07890.0121-0.15590.03920.83870.0226-0.2807-0.0781-0.08190.00340.1468-0.177920.1153-46.255524.8832
82.17962.0495-1.06736.6353-0.45041.5853-0.0982-1.1292-0.4110.55170.0013-0.20120.44340.69140.0969-0.03390.2023-0.08940.43330.3203-0.077320.2545-52.227739.2199
92.4278-0.6921-1.09384.7985-0.39862.90290.0524-0.9183-0.1051-0.16840.1551-0.54140.02321.1364-0.2076-0.2306-0.2441-0.09850.5563-0.054-0.192428.8407-32.895334.4022
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 11322 - 130
2X-RAY DIFFRACTION2AA114 - 187131 - 204
3X-RAY DIFFRACTION3AA188 - 298205 - 315
4X-RAY DIFFRACTION4BB9 - 11326 - 130
5X-RAY DIFFRACTION5BB114 - 187131 - 204
6X-RAY DIFFRACTION6BB188 - 290205 - 307
7X-RAY DIFFRACTION7CC6 - 11323 - 130
8X-RAY DIFFRACTION8CC114 - 187131 - 204
9X-RAY DIFFRACTION9CC188 - 290205 - 307

+
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