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- PDB-6bje: Crystal Structure of Lysophospholipase A2 Conjugated with Phenylm... -

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Basic information

Entry
Database: PDB / ID: 6bje
TitleCrystal Structure of Lysophospholipase A2 Conjugated with Phenylmethylsulfonyl Fluoride
ComponentsAcyl-protein thioesterase 2
KeywordsPROTEIN BINDING / Lysophospholipases / PMSF / inhibitor / complex
Function / homology
Function and homology information


prostaglandin catabolic process / protein depalmitoylation / palmitoyl[protein] hydrolase / palmitoyl-(protein) hydrolase activity / L1CAM interactions / acylglycerol catabolic process / Hydrolases; Acting on ester bonds; Thioester hydrolases / Golgi stack / carboxylic ester hydrolase activity / phosphatidylcholine lysophospholipase activity ...prostaglandin catabolic process / protein depalmitoylation / palmitoyl[protein] hydrolase / palmitoyl-(protein) hydrolase activity / L1CAM interactions / acylglycerol catabolic process / Hydrolases; Acting on ester bonds; Thioester hydrolases / Golgi stack / carboxylic ester hydrolase activity / phosphatidylcholine lysophospholipase activity / axon guidance / fatty acid metabolic process / cadherin binding / extracellular exosome / nucleoplasm / cytoplasm / cytosol
Similarity search - Function
: / Phospholipase/carboxylesterase/thioesterase / Phospholipase/Carboxylesterase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
phenylmethanesulfonic acid / Acyl-protein thioesterase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsXu, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F31GM120879 United States
CitationJournal: J. Lipid Res. / Year: 2019
Title: Lysophospholipases cooperate to mediate lipid homeostasis and lysophospholipid signaling.
Authors: Wepy, J.A. / Galligan, J.J. / Kingsley, P.J. / Xu, S. / Goodman, M.C. / Tallman, K.A. / Rouzer, C.A. / Marnett, L.J.
History
DepositionNov 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyl-protein thioesterase 2
B: Acyl-protein thioesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0324
Polymers47,6882
Non-polymers3442
Water57632
1
A: Acyl-protein thioesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0162
Polymers23,8441
Non-polymers1721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Acyl-protein thioesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0162
Polymers23,8441
Non-polymers1721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Acyl-protein thioesterase 2
B: Acyl-protein thioesterase 2
hetero molecules

A: Acyl-protein thioesterase 2
B: Acyl-protein thioesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,0648
Polymers95,3754
Non-polymers6894
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area8360 Å2
ΔGint-19 kcal/mol
Surface area34150 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-10 kcal/mol
Surface area18830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.769, 54.769, 279.619
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Acyl-protein thioesterase 2 / APT-2 / Lysophospholipase II / LysoPLA II


Mass: 23843.840 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LYPLA2, APT2 / Production host: Escherichia coli (E. coli) / Strain (production host): rosetta 2 (DE3)
References: UniProt: O95372, Hydrolases; Acting on ester bonds; Thioester hydrolases
#2: Chemical ChemComp-PMS / phenylmethanesulfonic acid


Mass: 172.202 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 44.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M NaCitric pH 5.6, 15% PEG-3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.66→139.81 Å / Num. obs: 12993 / % possible obs: 98.4 % / Redundancy: 12 % / CC1/2: 0.988 / Rpim(I) all: 0.145 / Net I/σ(I): 7.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) all% possible allRmerge(I) obsRrim(I) all
2.66-2.819.916180.5650.50788.7
8.42-139.8110.35350.9980.0391000.1250.131

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
Aimless0.1.27data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementResolution: 2.7→69.905 Å / SU ML: 0.39 / σ(F): 0 / Phase error: 26.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2641 1259 9.99 %
Rwork0.2213 --
obs0.2256 12607 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→69.905 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3295 0 20 32 3347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033450
X-RAY DIFFRACTIONf_angle_d0.6954696
X-RAY DIFFRACTIONf_dihedral_angle_d13.7952084
X-RAY DIFFRACTIONf_chiral_restr0.046538
X-RAY DIFFRACTIONf_plane_restr0.008604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.80820.46571350.37281212X-RAY DIFFRACTION100
2.8082-2.9360.36281360.30071225X-RAY DIFFRACTION100
2.936-3.09080.30271370.2491230X-RAY DIFFRACTION100
3.0908-3.28440.30371340.24311224X-RAY DIFFRACTION100
3.2844-3.5380.2781390.22131249X-RAY DIFFRACTION100
3.538-3.8940.23981390.2031251X-RAY DIFFRACTION100
3.894-4.45740.24681380.18361251X-RAY DIFFRACTION100
4.4574-5.61550.23531450.19041301X-RAY DIFFRACTION100
5.6155-69.92820.21071560.21341405X-RAY DIFFRACTION100
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)
1-0.03160.2755-0.15682.24360.2091.68750.01810.57660.0168-0.259-0.16390.29690.10410.13180.03830.28950.05850.04360.37670.07130.4624-44.575645.50872.678
22.5429-1.0051.11110.9732-0.17211.4443-0.0474-0.00390.0191-0.0428-0.01740.0204-0.14920.00160.06380.21620.02190.01260.19230.02890.2341-33.886243.055313.0067
33.2365-0.58220.71722.1655-0.8772.8964-0.0418-0.33610.34610.1555-0.0158-0.0301-0.207-0.05970.03570.2416-0.00510.05290.2021-0.03390.1975-36.20345.775424.5543
41.2710.2047-0.81030.35550.40291.4090.0302-0.1730.5249-0.0515-0.1048-0.055-0.07830.2016-0.06320.53930.0427-0.00020.6604-0.00360.3514-35.778242.864332.951
52.07450.38-0.38631.3762-0.34020.9377-0.2894-0.1141-0.22510.51040.21150.46250.1783-0.08010.02540.38990.05330.04780.27620.02290.3021-47.377937.768123.0888
62.61971.3324-0.30011.22310.16651.57510.08970.1799-0.15060.05130.049-0.31240.12890.2064-0.07270.3693-0.003-0.0560.2848-0.03380.2618-6.163719.77746.8314
70.93610.4158-0.19741.319-0.44391.1874-0.1206-0.2436-0.41170.07640.15360.14550.0829-0.1648-0.08710.35450.0727-0.02940.3380.05260.3136-22.371121.510711.616
80.0310.1065-0.05580.26130.09040.3720.87870.5349-0.44930.95290.6914-0.7111.79490.4361-0.29560.757-0.1087-0.25170.5774-0.01170.51-26.971717.480825.3922
92.2672-0.0536-0.94252.42140.76630.61390.246-0.1115-0.41880.1827-0.299-0.01860.55950.0228-0.00940.54790.0594-0.04910.340.04560.2993-12.320712.220519.4736
102.3011.32650.46130.8412-0.08071.7840.554-0.5181-0.27921.0881-0.4808-0.06190.24470.0568-0.16760.5507-0.0557-0.13520.37370.06790.4543-8.586920.764429.3869
112.705-0.4495-0.28670.8217-0.92172.1128-0.01460.015-0.20890.0299-0.0748-0.4681-0.15940.7392-0.06170.43760.0707-0.06750.51790.04760.39533.000620.013317.6835
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 122 )
3X-RAY DIFFRACTION3chain 'A' and (resid 123 through 180 )
4X-RAY DIFFRACTION4chain 'A' and (resid 181 through 194 )
5X-RAY DIFFRACTION5chain 'A' and (resid 195 through 231 )
6X-RAY DIFFRACTION6chain 'B' and (resid 10 through 51 )
7X-RAY DIFFRACTION7chain 'B' and (resid 52 through 78 )
8X-RAY DIFFRACTION8chain 'B' and (resid 79 through 90 )
9X-RAY DIFFRACTION9chain 'B' and (resid 91 through 180 )
10X-RAY DIFFRACTION10chain 'B' and (resid 181 through 213 )
11X-RAY DIFFRACTION11chain 'B' and (resid 214 through 231 )

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