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- PDB-5fv4: Pig liver esterase 5 (PLE5) -

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Basic information

Entry
Database: PDB / ID: 5fv4
TitlePig liver esterase 5 (PLE5)
ComponentsCARBOXYLIC ESTER HYDROLASECarboxylesterase
KeywordsHYDROLASE / ESTERASE / ESTERASE-LIPASE SUPERFAMILY / CARBOXYLESTERASE
Function / homology
Function and homology information


methyl indole-3-acetate esterase activity / sterol esterase activity / carboxylesterase / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / triglyceride lipase activity / carboxylic ester hydrolase activity / lipid catabolic process / hydrolase activity / endoplasmic reticulum lumen / extracellular space
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, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Carboxylic ester hydrolase / Liver carboxylesterase
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWerten, S. / Palm, G.J. / Berndt, L. / Hinrichs, W.
CitationJournal: To be Published
Title: Pig Liver Esterase 5
Authors: Werten, S. / Palm, G.J. / Berndt, L. / Hinrichs, W.
History
DepositionFeb 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.temp
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: CARBOXYLIC ESTER HYDROLASE
B: CARBOXYLIC ESTER HYDROLASE
C: CARBOXYLIC ESTER HYDROLASE
D: CARBOXYLIC ESTER HYDROLASE
E: CARBOXYLIC ESTER HYDROLASE
F: CARBOXYLIC ESTER HYDROLASE


Theoretical massNumber of molelcules
Total (without water)357,2156
Polymers357,2156
Non-polymers00
Water9,314517
1
A: CARBOXYLIC ESTER HYDROLASE


Theoretical massNumber of molelcules
Total (without water)59,5361
Polymers59,5361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CARBOXYLIC ESTER HYDROLASE


Theoretical massNumber of molelcules
Total (without water)59,5361
Polymers59,5361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: CARBOXYLIC ESTER HYDROLASE


Theoretical massNumber of molelcules
Total (without water)59,5361
Polymers59,5361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: CARBOXYLIC ESTER HYDROLASE


Theoretical massNumber of molelcules
Total (without water)59,5361
Polymers59,5361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: CARBOXYLIC ESTER HYDROLASE


Theoretical massNumber of molelcules
Total (without water)59,5361
Polymers59,5361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: CARBOXYLIC ESTER HYDROLASE


Theoretical massNumber of molelcules
Total (without water)59,5361
Polymers59,5361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.860, 188.020, 109.500
Angle α, β, γ (deg.)90.00, 96.44, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / Auth seq-ID: 5 - 534 / Label seq-ID: 5 - 534

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16BB
26CC
17BB
27DD
18BB
28EE
19BB
29FF
110CC
210DD
111CC
211EE
112CC
212FF
113DD
213EE
114DD
214FF
115EE
215FF

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

NCS oper:
IDCodeMatrixVector
1given(-0.97402, -0.22224, 0.04353), (-0.22629, 0.94766, -0.22525), (0.00881, -0.22925, -0.97333)9.2611, 41.3708, 197.43523
2given(-0.97009, -0.24251, 0.01078), (0.10661, -0.4655, -0.87861), (0.21809, -0.85118, 0.47742)11.23982, 261.7403, 140.72946
3given(-0.99936, 0.00869, 0.03472), (0.03094, -0.27809, 0.96006), (0.018, 0.96052, 0.27764)-37.88942, 64.84949, -59.24981
4given(0.98274, 0.08407, -0.16476), (-0.06096, -0.69379, -0.71759), (-0.17463, 0.71525, -0.67669)17.75239, 275.16031, 70.20776
5given(0.97227, 0.03849, -0.23066), (0.21744, -0.51176, 0.83116), (-0.08605, -0.85827, -0.50594)39.43866, 119.08277, 240.81943

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Components

#1: Protein
CARBOXYLIC ESTER HYDROLASE / Carboxylesterase / PLE5


Mass: 59535.801 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Organ: LIVER / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): SHUFFLE T7 EXPRESS
References: UniProt: A9GYW6, UniProt: Q29550*PLUS, carboxylesterase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 517 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE DIFFERENCES BETWEEN UNIPROT AND THE SAMPLE ARE DUE TO A LOCAL CLONE BEING USED.

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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: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growTemperature: 295 K / pH: 7.5 / Details: 100 MM HEPES PH 7.5, 18% PEG 4000 AT 295 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2015 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.4→71.14 Å / Num. obs: 144950 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 62.262 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.8
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 2.02 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MX9

1mx9


Resolution: 2.4→71.14 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 17.945 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.359 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2051 7248 5 %RANDOM
Rwork0.17912 ---
obs0.18043 137701 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20 Å2-0.33 Å2
2---1.01 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.4→71.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24570 0 0 517 25087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01925254
X-RAY DIFFRACTIONr_bond_other_d0.0080.0223880
X-RAY DIFFRACTIONr_angle_refined_deg1.5621.96434368
X-RAY DIFFRACTIONr_angle_other_deg1.282355176
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.03653174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.05524.2941062
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.055154038
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.05915108
X-RAY DIFFRACTIONr_chiral_restr0.0850.23762
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02128560
X-RAY DIFFRACTIONr_gen_planes_other0.0070.025628
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_it2.0033.80812714
X-RAY DIFFRACTIONr_mcbond_other2.0023.80712713
X-RAY DIFFRACTIONr_mcangle_it3.2015.70615882
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3794.0512540
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A659560.04
12B659560.04
21A662700.03
22C662700.03
31A659520.04
32D659520.04
41A663520.03
42E663520.03
51A660700.04
52F660700.04
61B662360.04
62C662360.04
71B659300.04
72D659300.04
81B661240.03
82E661240.03
91B662360.04
92F662360.04
101C661840.04
102D661840.04
111C664160.03
112E664160.03
121C663140.04
122F663140.04
131D662120.03
132E662120.03
141D660800.04
142F660800.04
151E663380.03
152F663380.03
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 534 -
Rwork0.3 10152 -
obs--99.59 %
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)
10.9714-0.295-0.47561.04850.47121.17990.02390.19590.0227-0.13-0.0318-0.03610.0206-0.00320.00790.02690.03890.00760.27450.01360.00744.3369146.5089110.4509
21.32050.2764-0.2420.8905-0.16551.29750.0429-0.4293-0.05220.1499-0.1249-0.04710.05180.04240.0820.0305-0.0291-0.00540.39590.03310.1845-22.7178154.357256.2409
30.8455-0.3445-0.011.7606-0.01931.17730.01990.0460.3-0.077-0.0838-0.1897-0.2305-0.06050.06390.04920.0221-0.00270.1365-0.01470.2327-27.27496.786569.7522
41.93090.04541.17631.17920.08192.48810.32640.4432-0.5249-0.11210.09430.1280.59050.046-0.42080.1627-0.0105-0.13520.3425-0.19930.3671-37.096130.3568112.2242
50.98880.23670.15072.1139-0.2172.0673-0.057-0.24570.42330.3215-0.0632-0.0158-0.6580.26410.12010.2557-0.1157-0.08910.2868-0.1660.583616.110993.8899.428
61.2649-0.33630.55220.9915-0.30442.29070.0952-0.1613-0.2429-0.00940.01980.15590.4210.1237-0.11490.08550.0626-0.00370.30780.10720.080423.8107136.979758.775
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 534
2X-RAY DIFFRACTION2B5 - 534
3X-RAY DIFFRACTION3C5 - 534
4X-RAY DIFFRACTION4D5 - 534
5X-RAY DIFFRACTION5E5 - 534
6X-RAY DIFFRACTION6F5 - 534

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