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- PDB-6ny9: Alpha/beta hydrolase domain-containing protein 10 from mouse -

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Basic information

Entry
Database: PDB / ID: 6ny9
TitleAlpha/beta hydrolase domain-containing protein 10 from mouse
ComponentsMycophenolic acid acyl-glucuronide esterase, mitochondrial
KeywordsHYDROLASE / Alpha/beta hydrolase / Depalmitoylase / Mitochondria
Function / homology
Function and homology information


mycophenolic acid acyl-glucuronide esterase / mycophenolic acid acyl-glucuronide esterase activity / Glucuronidation / protein depalmitoylation / palmitoyl[protein] hydrolase / palmitoyl-(protein) hydrolase activity / glucuronoside catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / mitochondrion / cytosol
Similarity search - Function
Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
STRONTIUM ION / Palmitoyl-protein thioesterase ABHD10, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsCao, Y. / Rice, P.A. / Dickinson, B.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM119840 United States
CitationJournal: Nat.Chem.Biol. / Year: 2019
Title: ABHD10 is an S-depalmitoylase affecting redox homeostasis through peroxiredoxin-5.
Authors: Cao, Y. / Qiu, T. / Kathayat, R.S. / Azizi, S.A. / Thorne, A.K. / Ahn, D. / Fukata, Y. / Fukata, M. / Rice, P.A. / Dickinson, B.C.
History
DepositionFeb 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Mycophenolic acid acyl-glucuronide esterase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2906
Polymers27,8211
Non-polymers4695
Water3,693205
1
B: Mycophenolic acid acyl-glucuronide esterase, mitochondrial
hetero molecules

B: Mycophenolic acid acyl-glucuronide esterase, mitochondrial
hetero molecules

B: Mycophenolic acid acyl-glucuronide esterase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,87018
Polymers83,4643
Non-polymers1,40615
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area6030 Å2
ΔGint-189 kcal/mol
Surface area29940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.388, 99.388, 149.597
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2
Components on special symmetry positions
IDModelComponents
11B-305-

SR

21B-405-

HOH

31B-600-

HOH

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Components

#1: Protein Mycophenolic acid acyl-glucuronide esterase, mitochondrial / Alpha/beta hydrolase domain-containing protein 10 / Abhydrolase domain-containing protein 10


Mass: 27821.311 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Abhd10 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q6PE15, mycophenolic acid acyl-glucuronide esterase
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Sr
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O

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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: 3.83 Å3/Da / Density % sol: 67.91 %
Crystal growTemperature: 277.15 K / Method: liquid diffusion / pH: 6.4
Details: 0.08 M strontium chloride hexahydrate, 0.04 M sodium cacodylate trihydrate pH 6.4, 25% v/v (+/-)-2-methyl-2,4-pentanediol (MPD), 0.012 M spermine tetrahydrochloride
PH range: 6.0-6.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.657→56.46 Å / Num. obs: 52270 / % possible obs: 92.82 % / Redundancy: 12.9 % / Biso Wilson estimate: 16.57 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1082 / Net I/σ(I): 20.82
Reflection shellResolution: 1.657→1.717 Å / Redundancy: 12.8 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4994 / CC1/2: 0.686 / % possible all: 76.98

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIX1.13-2998phasing
Coot0.8.9model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LLC

3llc


Resolution: 1.66→56.46 Å / SU ML: 0.1917 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.0141
RfactorNum. reflection% reflection
Rfree0.2188 1879 3.86 %
Rwork0.1954 --
obs0.1963 48620 92.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.19 Å2
Refinement stepCycle: LAST / Resolution: 1.66→56.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1954 0 12 205 2171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112004
X-RAY DIFFRACTIONf_angle_d1.0342714
X-RAY DIFFRACTIONf_chiral_restr0.0583307
X-RAY DIFFRACTIONf_plane_restr0.0067343
X-RAY DIFFRACTIONf_dihedral_angle_d12.50681209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.70.35341180.3092880X-RAY DIFFRACTION75.98
1.7-1.750.35141220.29473052X-RAY DIFFRACTION80.21
1.75-1.810.25311220.28093098X-RAY DIFFRACTION81.58
1.81-1.870.27171380.23773395X-RAY DIFFRACTION88.9
1.87-1.950.27771470.23383499X-RAY DIFFRACTION91.89
1.95-2.040.23061450.20483607X-RAY DIFFRACTION94.68
2.04-2.140.23161490.19793747X-RAY DIFFRACTION97.42
2.14-2.280.19421480.19373721X-RAY DIFFRACTION96.89
2.28-2.460.18481540.18413817X-RAY DIFFRACTION98.71
2.46-2.70.20051540.18183848X-RAY DIFFRACTION99.43
2.7-3.090.17821570.1783917X-RAY DIFFRACTION99.78
3.09-3.90.19111580.16393951X-RAY DIFFRACTION99.73
3.9-74.680.23161670.18944209X-RAY DIFFRACTION99.93
Refinement TLS params.Method: refined / Origin x: 29.4150756586 Å / Origin y: -34.2369923944 Å / Origin z: 17.0271591659 Å
111213212223313233
T0.0840196755691 Å2-0.0177117528344 Å20.0195104481202 Å2-0.166980730707 Å2-0.01372011656 Å2--0.117167095443 Å2
L1.25373227372 °20.117727781811 °20.617945279542 °2-1.42996274185 °20.0097615648983 °2--1.82174236856 °2
S-0.0540392989986 Å °-0.117346249124 Å °0.0370595617151 Å °0.0557155182448 Å °0.0151882969493 Å °0.158560768983 Å °0.006794386401 Å °-0.270239267195 Å °0.0242724436552 Å °
Refinement TLS groupSelection details: all

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