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- PDB-5gw8: Crystal structure of a putative DAG-like lipase (MgMDL2) from Mal... -

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Basic information

Entry
Database: PDB / ID: 5gw8
TitleCrystal structure of a putative DAG-like lipase (MgMDL2) from Malassezia globosa
ComponentsHypothetical secretory lipase (Family 3)
KeywordsHYDROLASE / DAG-like lipase / N-linked glycosylation
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / lipid catabolic process / hydrolase activity / extracellular region / metal ion binding
Similarity search - Function
: / Fungal lipase-like domain / Lipase (class 3) / Lipases, serine active site. / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / FORMIC ACID / MALONIC ACID / Secreted mono- and diacylglycerol lipase MDL2
Similarity search - Component
Biological speciesMalassezia globosa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsXu, J. / Xu, H. / Liu, J.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Malassezia globosa MgMDL2 lipase: Crystal structure and rational modification of substrate specificity.
Authors: Lan, D. / Xu, H. / Xu, J. / Dubin, G. / Liu, J. / Iqbal Khan, F. / Wang, Y.
History
DepositionSep 9, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references
Category: citation / citation_author / pdbx_database_related
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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical secretory lipase (Family 3)
B: Hypothetical secretory lipase (Family 3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,57715
Polymers63,6532
Non-polymers1,92413
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-2 kcal/mol
Surface area21000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.970, 82.320, 116.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Hypothetical secretory lipase (Family 3)


Mass: 31826.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Malassezia globosa (strain ATCC MYA-4612 / CBS 7966) (fungus)
Strain: ATCC MYA-4612 / CBS 7966 / Gene: MGL_0799 / Production host: Pichia pastoris (fungus) / Strain (production host): X33 / References: UniProt: A8PUY5

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Sugars , 2 types, 4 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 188 molecules

#4: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O4
#5: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C2H4O2
#6: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: CH2O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.91 Å3/Da / Density % sol: 57.8 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS
Mosaicity: 0.73 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6 / Details: 8% (v/v) tacsimate (pH 6.0), 20% PEG 5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→67.3 Å / Num. obs: 50908 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.038 / Rrim(I) all: 0.1 / Net I/σ(I): 13.3 / Num. measured all: 351167 / Scaling rejects: 259
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.056.90.6852564237000.9120.2790.74399.9
8.94-67.35.90.02838666500.9990.0130.03130.898.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
Aimless0.5.1data scaling
MOLREPphasing
PDB_EXTRACT3.2data extraction
Aimlessdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UUE

3uue


Resolution: 2→67.3 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 8.38 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2470 4.9 %RANDOM
Rwork0.18831 ---
obs0.18983 48369 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.321 Å2
Baniso -1Baniso -2Baniso -3
1-2.12 Å20 Å2-0 Å2
2---1.21 Å20 Å2
3----0.91 Å2
Refinement stepCycle: 1 / Resolution: 2→67.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4491 0 126 179 4796
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194749
X-RAY DIFFRACTIONr_bond_other_d0.0020.024383
X-RAY DIFFRACTIONr_angle_refined_deg1.6051.9626452
X-RAY DIFFRACTIONr_angle_other_deg1.012310057
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7445572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.88823.966232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.21415720
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8721529
X-RAY DIFFRACTIONr_chiral_restr0.0920.2698
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025437
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021152
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_it0.8241.6862286
X-RAY DIFFRACTIONr_mcbond_other0.8241.6882287
X-RAY DIFFRACTIONr_mcangle_it1.3852.5142850
X-RAY DIFFRACTIONr_mcangle_other1.3852.5142851
X-RAY DIFFRACTIONr_scbond_it1.3021.942463
X-RAY DIFFRACTIONr_scbond_other1.3021.9362460
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0782.8523601
X-RAY DIFFRACTIONr_long_range_B_refined4.65414.3995403
X-RAY DIFFRACTIONr_long_range_B_other4.65314.4075404
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 188 -
Rwork0.274 3505 -
obs--99.86 %
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)
11.10950.0446-0.36412.1322-1.0362.95430.00230.0692-0.0045-0.0814-0.0793-0.0634-0.43-0.04480.07690.27190.0338-0.03770.0273-0.01120.0132-16.395130.0703-33.0745
20.8093-0.08290.02381.884-0.76223.7482-0.104-0.0764-0.06040.1194-0.0208-0.0339-0.2127-0.05520.12480.0444-0.0007-0.0160.05610.00110.0404-16.699511.02286.0082
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 304
2X-RAY DIFFRACTION2B19 - 304

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