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- PDB-6nkc: Crystal Structure of the Lipase Lip_vut1 from Goat Rumen metagenome. -

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Basic information

Entry
Database: PDB / ID: 6nkc
TitleCrystal Structure of the Lipase Lip_vut1 from Goat Rumen metagenome.
ComponentsLipase, Lip_vut1
KeywordsHYDROLASE / Lipase / goat rumen metagenomics
Function / homology
Function and homology information


lipase activity / triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process
Similarity search - Function
Lipase EstA/Esterase EstB / Lipase (class 2) / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
AZIDE ION / Lipase / Lipase
Similarity search - Component
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.631 Å
AuthorsKim, Y. / Welk, L. / Mukendi, G. / Nkhi, G. / Motloi, T. / Jedrzejczak, R. / Feto, N. / Joachimiak, A.
CitationJournal: To Be Published
Title: Crystal Structure of the Lipase Lip_vut1 from Goat Rumen metagenome.
Authors: Kim, Y. / Welk, L. / Jedrzejczak, R. / Feto, A. / Joachimiak, A.
History
DepositionJan 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Nov 20, 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, Lip_vut1
B: Lipase, Lip_vut1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4607
Polymers39,2232
Non-polymers2375
Water6,954386
1
A: Lipase, Lip_vut1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7514
Polymers19,6121
Non-polymers1403
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lipase, Lip_vut1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7093
Polymers19,6121
Non-polymers982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.870, 49.870, 141.625
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Lipase, Lip_vut1


Mass: 19611.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1D8GR37, UniProt: Q65HR4*PLUS, triacylglycerol lipase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 2.26 Å3/Da / Density % sol: 45.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1 % Tryptone, 0.05 M HEPES sodium pH 7.0, 12% w/v Polyethylene glycol 3,350, 0.001 M Sodium azide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. obs: 42897 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 18.48 Å2 / Rmerge(I) obs: 0.172 / Net I/σ(I): 16.9
Reflection shellResolution: 1.63→1.66 Å / Redundancy: 5 % / Rmerge(I) obs: 0.819 / Mean I/σ(I) obs: 1.67 / Num. unique obs: 2156 / CC1/2: 0.732 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T2N

1t2n


Resolution: 1.631→35.263 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.08
RfactorNum. reflection% reflection
Rfree0.1885 2017 4.71 %
Rwork0.1573 --
obs0.1587 42819 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.2 Å2
Refinement stepCycle: LAST / Resolution: 1.631→35.263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2575 0 13 387 2975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012634
X-RAY DIFFRACTIONf_angle_d1.0183572
X-RAY DIFFRACTIONf_dihedral_angle_d13.751927
X-RAY DIFFRACTIONf_chiral_restr0.069418
X-RAY DIFFRACTIONf_plane_restr0.006458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6308-1.67160.24431560.24082868X-RAY DIFFRACTION98
1.6716-1.71680.28831380.21652935X-RAY DIFFRACTION100
1.7168-1.76730.2141360.20272893X-RAY DIFFRACTION100
1.7673-1.82440.22381540.18982880X-RAY DIFFRACTION100
1.8244-1.88960.22031270.17592947X-RAY DIFFRACTION100
1.8896-1.96520.20031300.16242912X-RAY DIFFRACTION100
1.9652-2.05470.18321320.15672925X-RAY DIFFRACTION100
2.0547-2.1630.19711860.15362900X-RAY DIFFRACTION100
2.163-2.29850.17191560.14672863X-RAY DIFFRACTION100
2.2985-2.47590.18471330.15452949X-RAY DIFFRACTION100
2.4759-2.7250.23681450.15742932X-RAY DIFFRACTION100
2.725-3.11910.19641380.16092937X-RAY DIFFRACTION100
3.1191-3.92890.17161630.14422892X-RAY DIFFRACTION100
3.9289-35.27160.14311230.14022969X-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)
13.9135-0.16211.8911.68310.11335.89780.430.0169-0.32730.1363-0.1187-0.20030.7186-0.2558-0.29550.1862-0.0164-0.00210.17740.01870.176228.540210.3005139.1534
22.56010.2893-0.01412.3736-0.72392.7180.04990.0879-0.037-0.1028-0.0876-0.24530.02650.24230.03090.14460.02430.00190.1956-0.00260.169331.37077.2126140.9123
31.7886-0.1606-1.1871.4902-0.76782.86420.11270.11990.1831-0.0125-0.0804-0.0901-0.21020.0345-0.02750.16250.0050.00240.18010.02520.194129.999616.8001134.4855
41.44050.5386-0.53642.4806-0.7162.87770.11410.20450.2402-0.0303-0.00250.0558-0.2928-0.1428-0.10440.19420.02860.01650.18720.02650.215522.689519.8299136.1891
52.44-0.2578-0.71575.02291.00532.9792-0.04260.13910.1711-0.2467-0.06830.4589-0.7756-0.71550.14220.21230.07140.00720.22940.02180.235215.693321.7141140.1986
61.62840.0616-0.120.98530.24952.48590.0621-0.11620.07380.0208-0.04590.0998-0.0436-0.2597-0.00890.136-0.0020.00940.1694-0.00890.167817.650712.9186151.0706
74.0816-0.16740.66765.8534-1.25677.9320.2078-0.1602-0.1577-0.19260.00530.54690.5059-0.8439-0.21790.1619-0.0627-0.00010.181-0.02560.221717.0333.394142.2082
84.23570.27180.97541.79710.17745.16930.39250.0367-0.471-0.0933-0.06180.18330.70010.4238-0.2990.19470.0204-0.00640.1746-0.02090.1755-3.2028-15.2265134.5851
92.5164-0.4641-0.06982.17080.58062.5370.0357-0.0824-0.06980.0711-0.07030.23940.017-0.22440.03410.1549-0.034-0.00440.19580.0010.184-6.4382-17.7217132.3161
101.67610.2443-1.24541.31260.59232.66790.1502-0.11390.1502-0.0214-0.10360.1048-0.183-0.0072-0.03960.1536-0.00110.00780.1696-0.02620.1913-5.0637-8.14138.7422
111.399-0.5187-0.49732.20260.76882.87980.0955-0.22880.25980.10310.0083-0.0805-0.30280.1284-0.09810.1795-0.03810.01310.1809-0.02720.21252.2489-5.1001137.0487
122.02620.54-0.85264.7301-1.13994.1544-0.0279-0.16010.25080.3515-0.1027-0.3668-0.76630.8070.16330.2418-0.07140.01250.2451-0.02850.24859.6885-3.4504133.5483
131.87510.0491-0.05491.0642-0.29492.51880.05860.16630.0841-0.0256-0.0199-0.1247-0.09320.2509-0.03110.14530.00080.01160.17010.00450.18047.2747-12.0201122.1405
144.59380.46181.26736.55061.96371.94870.33420.0691-0.34480.14590.0811-0.5290.45260.7498-0.42710.17480.0446-0.01240.19940.0190.21057.8836-21.5316131.0051
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 15 )
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 47 )
3X-RAY DIFFRACTION3chain 'A' and (resid 48 through 79 )
4X-RAY DIFFRACTION4chain 'A' and (resid 80 through 102 )
5X-RAY DIFFRACTION5chain 'A' and (resid 103 through 119 )
6X-RAY DIFFRACTION6chain 'A' and (resid 120 through 158 )
7X-RAY DIFFRACTION7chain 'A' and (resid 159 through 172 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 15 )
9X-RAY DIFFRACTION9chain 'B' and (resid 16 through 47 )
10X-RAY DIFFRACTION10chain 'B' and (resid 48 through 79 )
11X-RAY DIFFRACTION11chain 'B' and (resid 80 through 102 )
12X-RAY DIFFRACTION12chain 'B' and (resid 103 through 119 )
13X-RAY DIFFRACTION13chain 'B' and (resid 120 through 158 )
14X-RAY DIFFRACTION14chain 'B' and (resid 159 through 172 )

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