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- PDB-6hw1: ROOM TEMPERATURE STRUCTURE OF LIPASE FROM T. LANUGINOSA AT 2.5 A ... -

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Basic information

Entry
Database: PDB / ID: 6hw1
TitleROOM TEMPERATURE STRUCTURE OF LIPASE FROM T. LANUGINOSA AT 2.5 A RESOLUTION IN CHIPX MICROFLUIDIC DEVICE
ComponentsLipase
KeywordsHYDROLASE / LIPASE
Function / homology
Function and homology information


triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process
Similarity search - Function
Mono-/di-acylglycerol lipase, N-terminal / Lipase 3 N-terminal region / : / 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
PHOSPHATE ION / Lipase
Similarity search - Component
Biological speciesThermomyces lanuginosus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGavira, J.A. / Fernadez-Penas, R. / Martinez-Rodriguez, S. / Verdugo-Escamilla, C.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBIO2016-74875-P Spain
CitationJournal: Iucrj / Year: 2019
Title: A simple and versatile microfluidic device for efficient biomacromolecule crystallization and structural analysis by serial crystallography.
Authors: de Wijn, R. / Hennig, O. / Roche, J. / Engilberge, S. / Rollet, K. / Fernandez-Millan, P. / Brillet, K. / Betat, H. / Morl, M. / Roussel, A. / Girard, E. / Mueller-Dieckmann, C. / Fox, G.C. ...Authors: de Wijn, R. / Hennig, O. / Roche, J. / Engilberge, S. / Rollet, K. / Fernandez-Millan, P. / Brillet, K. / Betat, H. / Morl, M. / Roussel, A. / Girard, E. / Mueller-Dieckmann, C. / Fox, G.C. / Olieric, V. / Gavira, J.A. / Lorber, B. / Sauter, C.
History
DepositionOct 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Structure summary
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _exptl_crystal_grow.pdbx_details / _struct.title
Revision 1.2May 29, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr2_auth_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 24, 2024Group: 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 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipase
B: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2717
Polymers58,6852
Non-polymers5865
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-29 kcal/mol
Surface area21430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.652, 142.652, 80.721
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Lipase / Triacylglycerol lipase


Mass: 29342.484 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus) / References: UniProt: O59952, triacylglycerol lipase
#2: 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
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 3.92 Å3/Da / Density % sol: 68.62 % / Description: Bi-pyramidal hexagon
Crystal growTemperature: 293 K / Method: counter-diffusion / pH: 7.5
Details: 300 mM Na/K Phosphate, 50 mM NaAc pH 4.5. COUNTER-DIFFUSION IN CHIPX MICROFLUIDIC DEVICE
PH range: 4.0-7.5

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Data collection

DiffractionMean temperature: 295 K / Ambient temp details: Room Temperature / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 4, 2017
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.5→49.06 Å / Num. obs: 31982 / % possible obs: 98.5 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 3.2 % / Biso Wilson estimate: 63.3 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.075 / Rrim(I) all: 0.114 / Χ2: 0.99 / Net I/σ(I): 6.3
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 3668 / CC1/2: 0.5 / Rpim(I) all: 0.8 / Rrim(I) all: 1.2 / Χ2: 1.07 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GWL

4gwl


Resolution: 2.5→49.055 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.93
RfactorNum. reflection% reflection
Rfree0.1994 1573 4.99 %
Rwork0.172 --
obs0.1733 31516 96.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 61.63 Å2
Displacement parametersBiso mean: 83.83 Å2
Refinement stepCycle: LAST / Resolution: 2.5→49.055 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4142 0 35 47 4224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034567
X-RAY DIFFRACTIONf_angle_d0.5186248
X-RAY DIFFRACTIONf_dihedral_angle_d12.073891
X-RAY DIFFRACTIONf_chiral_restr0.04663
X-RAY DIFFRACTIONf_plane_restr0.003849
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.58080.36671270.3472662X-RAY DIFFRACTION95
2.5808-2.67310.37131490.32312676X-RAY DIFFRACTION96
2.6731-2.78010.32741520.28322673X-RAY DIFFRACTION96
2.7801-2.90660.30961710.25842667X-RAY DIFFRACTION97
2.9066-3.05980.26251510.23412713X-RAY DIFFRACTION98
3.0598-3.25150.2221440.20682760X-RAY DIFFRACTION98
3.2515-3.50250.2091390.17422724X-RAY DIFFRACTION97
3.5025-3.85480.16941140.15332791X-RAY DIFFRACTION98
3.8548-4.41230.18071640.13592735X-RAY DIFFRACTION98
4.4123-5.55780.16791340.12812766X-RAY DIFFRACTION98
5.5578-49.06450.14141280.15032776X-RAY DIFFRACTION95
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)
17.05526.38564.28159.32532.91542.91380.1059-0.2813-0.08780.2671-0.43250.6451-0.01770.11060.38620.4910.09220.00020.4771-0.09310.5221-36.2907-50.62313.4025
24.7872-4.6779-5.17484.82535.11566.01930.59030.19420.9131-0.38930.5102-1.6515-1.48852.0427-0.94470.6409-0.02710.08091.1729-0.02280.9134-18.5234-47.51992.0224
37.7685-1.8828-0.89757.8963-2.00938.6693-0.00620.36880.1885-0.4516-0.1179-1.2365-0.73240.86950.02320.5822-0.01290.00750.7628-0.00020.4363-23.7566-44.4516-3.2985
45.3348-2.3277-2.84962.14983.46136.41250.3611-0.05060.4807-0.1268-0.17-0.6705-0.94740.5035-0.32190.7603-0.0093-0.11450.5110.04060.5223-28.7813-38.78742.4042
55.2794-0.1130.14237.55681.63612.56310.44271.55591.1385-1.1501-0.5296-0.033-2.19260.190.18441.47170.29320.11670.99250.23920.8359-40.1999-23.4427-5.203
64.0993-3.5211-4.19957.00485.29365.83540.87881.27320.372-1.8361-0.92470.049-1.68830.1023-0.16941.07760.1902-0.05221.09330.21570.64-31.152-34.5299-12.2677
73.4868-0.7096-0.08023.17780.16293.03960.05050.5772-0.0019-0.3592-0.30280.505-0.7233-0.55970.22210.57740.1908-0.10980.5495-0.05790.4756-41.944-39.35942.9923
87.46354.6698-0.9484.4389-3.30764.9508-0.3643-0.2696-0.77650.51130.3330.0624-0.6722-0.7491-0.12750.47460.22530.06260.74540.16420.6351-29.8235-53.618132.8207
96.9339-5.0948-4.11253.86393.49954.3104-0.3415-1.45321.49260.76781.0187-0.8682-3.3858-0.1525-0.54081.77350.50920.16571.193-0.07930.9461-32.8807-34.389736.1547
106.6752-0.85932.15074.1320.42697.4773-0.9196-1.08090.62240.47950.31760.2273-1.8648-0.79810.50711.09410.347-0.04860.82360.02810.5195-28.1882-39.253836.6942
112.1878-2.195-0.06583.8883-1.10986.1823-0.5057-0.44120.40740.59440.1835-0.6308-1.16930.83910.3460.8369-0.041-0.14610.94190.05230.5904-13.0847-45.229236.5024
123.9601-0.3965-1.60824.2662-0.54525.8088-0.6481-1.6790.35081.40120.3503-0.3048-1.44830.09070.16681.03710.252-0.15371.07280.00350.5171-18.5221-45.069345.3868
133.95980.4131-0.2463.0282-1.21281.5754-0.1175-0.9999-0.46250.92230.1274-0.0363-0.26450.2251-0.01540.64760.1527-0.00380.85160.22820.5093-17.8055-52.793241.4927
144.42450.10521.15972.41610.32110.7732-0.3687-0.5118-0.55910.4088-0.0534-0.30990.06160.93080.34130.39450.15790.01380.88070.23840.6111-11.9887-56.778933.9915
156.4678-1.01312.24193.8101-1.07865.40760.0882-0.0159-0.8428-0.1257-0.1143-0.19780.4270.62680.05150.35710.11020.06150.56020.07810.4797-19.8549-57.718325.2987
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 22 )
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 41 )
3X-RAY DIFFRACTION3chain 'A' and (resid 42 through 70 )
4X-RAY DIFFRACTION4chain 'A' and (resid 71 through 91 )
5X-RAY DIFFRACTION5chain 'A' and (resid 92 through 107 )
6X-RAY DIFFRACTION6chain 'A' and (resid 108 through 134 )
7X-RAY DIFFRACTION7chain 'A' and (resid 135 through 269 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 22 )
9X-RAY DIFFRACTION9chain 'B' and (resid 23 through 36 )
10X-RAY DIFFRACTION10chain 'B' and (resid 37 through 70 )
11X-RAY DIFFRACTION11chain 'B' and (resid 71 through 107 )
12X-RAY DIFFRACTION12chain 'B' and (resid 108 through 159 )
13X-RAY DIFFRACTION13chain 'B' and (resid 160 through 178 )
14X-RAY DIFFRACTION14chain 'B' and (resid 179 through 211 )
15X-RAY DIFFRACTION15chain 'B' and (resid 212 through 269 )

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