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- PDB-6nkd: Crystal Structure of the Lipase Lip_vut3 from Goat Rumen metagenome. -

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Basic information

Entry
Database: PDB / ID: 6nkd
TitleCrystal Structure of the Lipase Lip_vut3 from Goat Rumen metagenome.
ComponentsLip_vut3, C2L
KeywordsHYDROLASE / Lipase / goat rumen metagenomics
Function / homology: / Hydrolases / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / sporulation resulting in formation of a cellular spore / hydrolase activity / FORMIC ACID / Spore germination lipase LipC
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 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_vut3 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 1.1Nov 13, 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: Lip_vut3, C2L
B: Lip_vut3, C2L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,31313
Polymers50,5302
Non-polymers78311
Water36020
1
A: Lip_vut3, C2L
B: Lip_vut3, C2L
hetero molecules

A: Lip_vut3, C2L
B: Lip_vut3, C2L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,62626
Polymers101,0594
Non-polymers1,56722
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/31
Buried area13650 Å2
ΔGint-218 kcal/mol
Surface area32250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.120, 93.120, 196.898
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-408-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Lip_vut3, C2L


Mass: 25264.869 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: Q65NA4

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Non-polymers , 5 types, 31 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.47 Å3/Da / Density % sol: 50.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 2.40 M Ammonium Sulfate, 150 mM Formate pH 4.0, 3.0 % (v/v) 2-Butanol

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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: Oct 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 13353 / % possible obs: 100 % / Redundancy: 29.2 % / Biso Wilson estimate: 66.15 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.173 / Net I/σ(I): 32.9
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 30.6 % / Rmerge(I) obs: 0.879 / Num. unique obs: 654 / CC1/2: 0.945 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→42.09 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.4
RfactorNum. reflection% reflection
Rfree0.2565 701 5.27 %
Rwork0.2198 --
obs0.2218 13298 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 79.4 Å2
Refinement stepCycle: LAST / Resolution: 2.8→42.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3366 0 42 20 3428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023457
X-RAY DIFFRACTIONf_angle_d0.4694643
X-RAY DIFFRACTIONf_dihedral_angle_d18.4982103
X-RAY DIFFRACTIONf_chiral_restr0.04504
X-RAY DIFFRACTIONf_plane_restr0.002592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7857-3.00080.35531300.30052442X-RAY DIFFRACTION99
3.0008-3.30270.32771490.26882438X-RAY DIFFRACTION100
3.3027-3.78030.27511410.24152471X-RAY DIFFRACTION100
3.7803-4.76170.22841440.20482530X-RAY DIFFRACTION100
4.7617-42.0950.22851370.19422716X-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)
14.07722.2937-0.79982.9556-1.18644.3505-0.3343-0.4191-0.22520.3129-0.14160.02871.07820.00680.49710.84550.04820.03010.4346-0.03970.638325.9617.142334.0168
26.00812.13343.44415.16111.92545.69180.1110.3527-0.4519-1.05350.1292-0.55621.10681.88140.04120.75990.24510.17850.9286-0.17770.631337.340312.813619.872
35.0875-2.26712.43528.47311.67443.4020.6936-0.2012-0.48430.6102-0.574-0.38312.27820.50620.09971.1940.1974-0.07990.5467-0.04060.766631.64796.70527.6617
43.45370.8770.58618.0054-4.6838.5924-0.16130.5136-1.1295-0.59990.4699-0.4372-0.01860.5914-0.43480.5453-0.05970.14310.9551-0.05750.568134.207828.49775.3879
56.36723.4692-1.45363.4172-1.81991.022-0.36610.83110.2444-0.14960.84160.21111.88910.341-0.28591.68120.13770.12410.2971-0.26990.655329.663310.027512.5926
63.4691-0.7742-0.62464.9143-1.40443.4150.25660.507-0.26110.3082-0.12010.91411.2143-0.4119-0.03860.8903-0.1519-0.10350.5341-0.07410.560120.909916.093116.0047
74.619-2.24480.43521.5408-0.02253.1615-0.04110.11320.07980.02610.12870.3030.5084-0.3712-0.12730.4892-0.0649-0.0070.3165-0.00860.484620.11825.698825.3385
84.61250.1533-0.1941.7522-0.84932.86450.04770.4411-0.06510.0653-0.0409-0.50381.18160.9444-0.10751.17170.4149-0.04390.69-0.1090.452439.948510.959341.3613
94.2096-0.71860.11872.1621-0.694.7164-0.02270.35170.1293-0.32350.230.00680.51830.3072-0.18530.6820.2095-0.06750.47020.06150.556335.260822.062745.3532
103.27680.99640.56525.3216-0.69787.67740.0533-0.97670.5470.23820.0956-0.3676-0.50891.2529-0.12670.7960.1477-0.00521.0276-0.08470.793961.403131.992543.6368
119.44924.63891.1842.470.62084.603-0.1188-0.07480.54621.16130.270.1644-0.0889-0.0454-0.18240.81420.2066-0.01990.5503-0.03830.750939.983627.503354.7179
125.16170.1412-0.55122.3580.52833.3354-0.1891-0.3759-0.27660.41790.1554-0.53980.99770.8782-0.15890.85920.3354-0.05390.7781-0.0180.611150.008119.087353.8306
134.3935-0.06010.09692.8965-0.05353.7054-0.53840.1348-0.33280.51330.5934-0.58671.19621.1219-0.06580.97970.4677-0.07520.918-0.12060.619851.30629.617944.6033
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 47 )
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 61 )
3X-RAY DIFFRACTION3chain 'A' and (resid 62 through 80 )
4X-RAY DIFFRACTION4chain 'A' and (resid 81 through 97 )
5X-RAY DIFFRACTION5chain 'A' and (resid 98 through 122 )
6X-RAY DIFFRACTION6chain 'A' and (resid 123 through 170 )
7X-RAY DIFFRACTION7chain 'A' and (resid 171 through 211 )
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 37 )
9X-RAY DIFFRACTION9chain 'B' and (resid 38 through 80 )
10X-RAY DIFFRACTION10chain 'B' and (resid 81 through 105 )
11X-RAY DIFFRACTION11chain 'B' and (resid 106 through 122 )
12X-RAY DIFFRACTION12chain 'B' and (resid 123 through 170 )
13X-RAY DIFFRACTION13chain 'B' and (resid 171 through 211 )

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