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- PDB-8axc: Crystal structure of mouse Ces2c -

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Basic information

Entry
Database: PDB / ID: 8axc
TitleCrystal structure of mouse Ces2c
ComponentsAcylcarnitine hydrolase
KeywordsHYDROLASE / carboxylesterase 2c / protein structure / lipid metabolism / X-ray crystallography / alpha/beta-hydrolase fold / biochemistry / lipid hydrolysis / non-alcoholic fatty liver disease / molnupiravir
Function / homology
Function and homology information


acylcarnitine hydrolase / acylcarnitine hydrolase activity / all-trans-retinyl-palmitate hydrolase, all-trans-retinol forming activity / response to bile acid / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / carboxylic ester hydrolase activity / prostaglandin metabolic process / intracellular membrane-bounded organelle / endoplasmic reticulum
Similarity search - Function
Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
NICOTINAMIDE / Acylcarnitine hydrolase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsEisner, H. / Riegler-Berket, L. / Rodriguez Gamez, C. / Sagmeister, T. / Chalhoub, G. / Darnhofer, B. / Panikkaveetil Jawaharlal, J. / Birner-Gruenberger, R. / Pavkov-Keller, T. / Haemmerle, G. ...Eisner, H. / Riegler-Berket, L. / Rodriguez Gamez, C. / Sagmeister, T. / Chalhoub, G. / Darnhofer, B. / Panikkaveetil Jawaharlal, J. / Birner-Gruenberger, R. / Pavkov-Keller, T. / Haemmerle, G. / Schoiswohl, G. / Oberer, M.
Funding support Austria, 2items
OrganizationGrant numberCountry
Austrian Science FundF73 Austria
Austrian Science FundDOC50 Austria
CitationJournal: Int J Mol Sci / Year: 2022
Title: The Crystal Structure of Mouse Ces2c, a Potential Ortholog of Human CES2, Shows Structural Similarities in Substrate Regulation and Product Release to Human CES1.
Authors: Eisner, H. / Riegler-Berket, L. / Gamez, C.F.R. / Sagmeister, T. / Chalhoub, G. / Darnhofer, B. / Jazleena, P.J. / Birner-Gruenberger, R. / Pavkov-Keller, T. / Haemmerle, G. / Schoiswohl, G. / Oberer, M.
History
DepositionAug 31, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acylcarnitine hydrolase
B: Acylcarnitine hydrolase
C: Acylcarnitine hydrolase
D: Acylcarnitine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)251,10015
Polymers250,1294
Non-polymers97111
Water27,3291517
1
A: Acylcarnitine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8124
Polymers62,5321
Non-polymers2803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Acylcarnitine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8124
Polymers62,5321
Non-polymers2803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Acylcarnitine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7864
Polymers62,5321
Non-polymers2543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Acylcarnitine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6903
Polymers62,5321
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.052, 143.595, 183.756
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
32A
42C
53A
63D
74B
84C
95B
105D
116C
126D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERGLNGLNAA29 - 54929 - 549
211SERSERGLNGLNBB29 - 54929 - 549
322GLUGLUGLUGLUAA31 - 55031 - 550
422GLUGLUGLUGLUCC31 - 55031 - 550
533PROPROGLNGLNAA30 - 54930 - 549
633PROPROGLNGLNDD30 - 54930 - 549
744GLUGLUGLUGLUBB31 - 55031 - 550
844GLUGLUGLUGLUCC31 - 55031 - 550
955PROPROGLUGLUBB30 - 56030 - 560
1055PROPROGLUGLUDD30 - 56030 - 560
1166GLUGLUGLNGLNCC31 - 54931 - 549
1266GLUGLUGLNGLNDD31 - 54931 - 549

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

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Components

#1: Protein
Acylcarnitine hydrolase / ACH M1 / Carboxylesterase 2 / CES 2 / Carboxylic ester hydrolase / Peroxisome proliferator- ...ACH M1 / Carboxylesterase 2 / CES 2 / Carboxylic ester hydrolase / Peroxisome proliferator-inducible acylcarnitine hydrolase


Mass: 62532.340 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ces2c, Ces2 / Production host: Homo sapiens (human)
References: UniProt: Q91WG0, acylcarnitine hydrolase, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-NCA / NICOTINAMIDE


Mass: 122.125 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H6N2O / Comment: medication*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1517 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: Crystallisation condition 0.5 ul with PEG 8000, 0.2 M Ammonium sulfate 0.1 M Sodium cacodylate, pH-6.5, 30 % w/v and 0.5 ul 10mg/ml Protein in 150mM NaCl, 20mM Tris HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0121 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0121 Å / Relative weight: 1
ReflectionResolution: 2.12→49.05 Å / Num. obs: 145761 / % possible obs: 98.99 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.0906 / Net I/σ(I): 15.23
Reflection shellResolution: 2.12→2.196 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.5328 / Num. unique obs: 14158 / CC1/2: 0.881 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MX9

1mx9


Resolution: 2.12→49.05 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.183 / WRfactor Rwork: 0.151 / Average fsc free: 0.9437 / Average fsc work: 0.9526 / Cross valid method: FREE R-VALUE / ESU R: 0.184 / ESU R Free: 0.153
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1959 7342 5.037 %
Rwork0.163 138415 -
all0.165 --
obs-145757 99.004 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 33.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.009 Å20 Å20 Å2
2--0.008 Å2-0 Å2
3----0.017 Å2
Refinement stepCycle: LAST / Resolution: 2.12→49.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16161 0 63 1517 17741
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01316996
X-RAY DIFFRACTIONr_bond_other_d0.0350.01515644
X-RAY DIFFRACTIONr_angle_refined_deg1.5341.63523158
X-RAY DIFFRACTIONr_angle_other_deg2.3031.56936170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.68552132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.5422.985861
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.596152737
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7781579
X-RAY DIFFRACTIONr_chiral_restr0.0830.22143
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219500
X-RAY DIFFRACTIONr_gen_planes_other0.0110.023868
X-RAY DIFFRACTIONr_nbd_refined0.2210.23337
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2070.213467
X-RAY DIFFRACTIONr_nbtor_refined0.1630.28130
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0660.26729
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.21126
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2560.215
X-RAY DIFFRACTIONr_nbd_other0.2650.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1320.211
X-RAY DIFFRACTIONr_mcbond_it2.9513.1828435
X-RAY DIFFRACTIONr_mcbond_other2.9483.1828434
X-RAY DIFFRACTIONr_mcangle_it4.2464.7510582
X-RAY DIFFRACTIONr_mcangle_other4.2474.75110583
X-RAY DIFFRACTIONr_scbond_it4.0973.6878561
X-RAY DIFFRACTIONr_scbond_other4.0963.6888560
X-RAY DIFFRACTIONr_scangle_it6.3585.31412559
X-RAY DIFFRACTIONr_scangle_other6.3575.31412559
X-RAY DIFFRACTIONr_lrange_it8.1638.27219043
X-RAY DIFFRACTIONr_lrange_other8.09337.9818717
X-RAY DIFFRACTIONr_ncsr_local_group_10.090.0516858
X-RAY DIFFRACTIONr_ncsr_local_group_20.0780.0516699
X-RAY DIFFRACTIONr_ncsr_local_group_30.0780.0516756
X-RAY DIFFRACTIONr_ncsr_local_group_40.0780.0516671
X-RAY DIFFRACTIONr_ncsr_local_group_50.0690.0517251
X-RAY DIFFRACTIONr_ncsr_local_group_60.0740.0516768
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.089950.05008
12BX-RAY DIFFRACTIONLocal ncs0.089950.05008
23AX-RAY DIFFRACTIONLocal ncs0.078390.05008
24CX-RAY DIFFRACTIONLocal ncs0.078390.05008
35AX-RAY DIFFRACTIONLocal ncs0.077580.05008
36DX-RAY DIFFRACTIONLocal ncs0.077580.05008
47BX-RAY DIFFRACTIONLocal ncs0.07840.05008
48CX-RAY DIFFRACTIONLocal ncs0.07840.05008
59BX-RAY DIFFRACTIONLocal ncs0.068920.05009
510DX-RAY DIFFRACTIONLocal ncs0.068920.05009
611CX-RAY DIFFRACTIONLocal ncs0.074460.05008
612DX-RAY DIFFRACTIONLocal ncs0.074460.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.1750.2375280.219992X-RAY DIFFRACTION97.3804
2.175-2.2350.2225620.1949797X-RAY DIFFRACTION98.8171
2.235-2.2990.2085070.1759647X-RAY DIFFRACTION99.5197
2.299-2.370.2254250.1789450X-RAY DIFFRACTION99.5564
2.37-2.4480.2014700.1679163X-RAY DIFFRACTION99.5145
2.448-2.5340.2044440.1638853X-RAY DIFFRACTION99.6997
2.534-2.6290.1894850.1598477X-RAY DIFFRACTION99.744
2.629-2.7370.2074390.1638223X-RAY DIFFRACTION99.7237
2.737-2.8580.2124360.1667869X-RAY DIFFRACTION99.4968
2.858-2.9980.1893700.167494X-RAY DIFFRACTION98.4477
2.998-3.160.193690.1696954X-RAY DIFFRACTION96.2034
3.16-3.3510.2083980.1746744X-RAY DIFFRACTION99.5401
3.351-3.5820.2123550.1686410X-RAY DIFFRACTION99.5732
3.582-3.8690.2083220.1555973X-RAY DIFFRACTION99.4628
3.869-4.2380.1712880.1375516X-RAY DIFFRACTION99.3495
4.238-4.7370.1472680.1265017X-RAY DIFFRACTION99.3982
4.737-5.4680.1752210.1444454X-RAY DIFFRACTION99.3624
5.468-6.6930.2071770.1763669X-RAY DIFFRACTION95.6716
6.693-9.450.1831640.1682992X-RAY DIFFRACTION100

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