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- PDB-4ord: Crystal Structure of Zebra Fish Thioesterase Superfamily Member 2 -

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Basic information

Entry
Database: PDB / ID: 4ord
TitleCrystal Structure of Zebra Fish Thioesterase Superfamily Member 2
ComponentsThioesterase Superfamily Member 2
KeywordsHYDROLASE / Hotdog / thioesterase / Acyl-CoA
Function / homology
Function and homology information


: / fatty acyl-CoA hydrolase activity
Similarity search - Function
Acyl-coenzyme A thioesterase 13 / Phenylacetic acid degradation-related domain / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Acyl-CoA thioesterase 13
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYu, S.S. / Li, H. / Gao, F. / Xu, H. / Gong, W.M.
CitationJournal: To be Published
Title: Crystal Structure and Potential Physiological Role of Zebra Fish Thioesterase Superfamily Member 2 (fTHEM2)
Authors: Yu, S.S. / Li, H. / Gao, F. / Wang, Y. / Miao, L.Y. / Zhang, J. / Xu, H. / Gong, W.M.
History
DepositionFeb 11, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioesterase Superfamily Member 2
B: Thioesterase Superfamily Member 2
C: Thioesterase Superfamily Member 2
D: Thioesterase Superfamily Member 2


Theoretical massNumber of molelcules
Total (without water)64,6114
Polymers64,6114
Non-polymers00
Water5,603311
1
A: Thioesterase Superfamily Member 2
D: Thioesterase Superfamily Member 2

A: Thioesterase Superfamily Member 2
D: Thioesterase Superfamily Member 2


Theoretical massNumber of molelcules
Total (without water)64,6114
Polymers64,6114
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8220 Å2
ΔGint-27 kcal/mol
Surface area21370 Å2
MethodPISA
2
B: Thioesterase Superfamily Member 2
C: Thioesterase Superfamily Member 2

B: Thioesterase Superfamily Member 2
C: Thioesterase Superfamily Member 2


Theoretical massNumber of molelcules
Total (without water)64,6114
Polymers64,6114
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area8560 Å2
ΔGint-30 kcal/mol
Surface area20920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.064, 74.350, 96.590
Angle α, β, γ (deg.)90.00, 93.72, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-251-

HOH

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Components

#1: Protein
Thioesterase Superfamily Member 2 / fTHEM2 / Uncharacterized protein


Mass: 16152.664 Da / Num. of mol.: 4 / Fragment: UNP residues 6-146
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: acot13 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: F6P1Y9, Hydrolases; Acting on ester bonds; Thioester hydrolases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.14 Å3/Da / Density % sol: 42.44 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Ammonium Acetate, 0.1M Bis-Tris, 17%(w/v) PEG10000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9716 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 10, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9716 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 50707 / Num. obs: 50707 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 15.5
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F0X

2f0x


Resolution: 1.8→35.02 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.085 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.136 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22505 2569 5.1 %RANDOM
Rwork0.19347 ---
obs0.19516 48094 99.54 %-
all-50707 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.401 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.01 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→35.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4116 0 0 311 4427
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224202
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.11.9665666
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1925560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.76324.545154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.32315796
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4191524
X-RAY DIFFRACTIONr_chiral_restr0.0730.2686
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023004
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.4731.52734
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.94324396
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.70231468
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8144.51264
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.795→1.842 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 180 -
Rwork0.27 3453 -
obs--96.42 %
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)
10.591-0.0826-0.04561.3346-0.17671.88850.0559-0.0291-0.00880.0564-0.05860.0280.2519-0.0390.00270.0556-0.0319-0.00380.0477-0.00210.0404-0.4434-9.378111.1718
21.2042-0.2325-0.17111.41270.03512.3411-0.04860.08640.00940.0180.0256-0.1030.09920.27280.0230.0381-0.01110.00040.0543-0.00290.03947.1741-8.285434.6947
32.03410.1574-0.2230.7721-0.09091.3486-0.09390.116-0.1298-0.12640.05570.11980.2554-0.33630.03820.0864-0.0807-0.00790.0927-0.00790.0379-19.1414-15.342741.588
41.43420.40790.14841.77870.29981.39390.0351-0.09270.25340.119-0.078-0.0861-0.23180.1450.04290.0602-0.0449-0.00370.0461-0.01640.08886.14517.9419.102
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 140
2X-RAY DIFFRACTION2B3 - 140
3X-RAY DIFFRACTION3C3 - 140
4X-RAY DIFFRACTION4D3 - 140

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