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- PDB-6nkg: Crystal Structure of the Lipase Lip_vut5 from Goat Rumen metagenome. -

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Basic information

Entry
Database: PDB / ID: 6nkg
TitleCrystal Structure of the Lipase Lip_vut5 from Goat Rumen metagenome.
ComponentsLip_vut5, C4L
KeywordsHYDROLASE / Lipase / goat rumen metagenomics
Function / homology
Function and homology information


carboxylic ester hydrolase activity
Similarity search - Function
Esterase/lipase / Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Esterase/lipase/thioesterase
Similarity search - Component
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 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_vut5 from Goat Rumen metagenome.
Authors: Kim, Y. / Welk, L. / Jedrzejczak, R. / Feto, N. / Joachimiak, A.
History
DepositionJan 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lip_vut5, C4L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9274
Polymers29,7431
Non-polymers1843
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.110, 60.110, 169.898
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Lip_vut5, C4L


Mass: 29743.197 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli (E. coli) / References: UniProt: Q65EQ1
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

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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: 2.62 Å3/Da / Density % sol: 53.08 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.9 / Details: 0.2 M magnesium acetate, 20 % PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Nov 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.15→56.7 Å / Num. obs: 17833 / % possible obs: 100 % / Redundancy: 15.9 % / Biso Wilson estimate: 38.97 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.115 / Net I/σ(I): 13.5
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.981 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 849 / CC1/2: 0.943 / % 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: 2.15→56.668 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.58
RfactorNum. reflection% reflection
Rfree0.2351 935 5.28 %
Rwork0.1947 --
obs0.1967 17706 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 52 Å2
Refinement stepCycle: LAST / Resolution: 2.15→56.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1972 0 12 67 2051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022087
X-RAY DIFFRACTIONf_angle_d0.4042825
X-RAY DIFFRACTIONf_dihedral_angle_d14.9821248
X-RAY DIFFRACTIONf_chiral_restr0.037296
X-RAY DIFFRACTIONf_plane_restr0.004367
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1501-2.26340.29321150.26242321X-RAY DIFFRACTION99
2.2634-2.40520.26521310.24042369X-RAY DIFFRACTION99
2.4052-2.59090.30031320.22952308X-RAY DIFFRACTION100
2.5909-2.85170.23811380.22712375X-RAY DIFFRACTION100
2.8517-3.26430.25681280.23542385X-RAY DIFFRACTION100
3.2643-4.11250.26971550.18142409X-RAY DIFFRACTION100
4.1125-56.68750.17541360.16022604X-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)
11.00160.0239-0.39220.91480.61434.2242-0.02630.0320.04630.221-0.01710.00910.1050.2650.02650.34010.0141-0.01240.33440.060.3586-0.299428.129727.92
22.9351-1.14613.86692.7543-1.25585.1226-0.3916-0.2012-0.01230.89950.0404-0.2391-0.2808-0.2510.19820.6340.0713-0.04660.3522-0.00630.4215-11.03847.767742.4257
31.6012-0.5059-0.54940.72020.92915.1962-0.00040.17010.08860.0653-0.0228-0.167-0.15870.97260.02640.3226-0.0303-0.00720.49020.05330.39277.278830.550317.5612
41.61451.3590.68572.88040.93314.18580.1048-0.00850.1992-0.0188-0.25180.47020.0298-0.96210.20450.2412-0.004-0.00280.4498-0.00760.4213-9.275427.058919.4881
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 41 through 140 )
2X-RAY DIFFRACTION2chain 'A' and (resid 141 through 157 )
3X-RAY DIFFRACTION3chain 'A' and (resid 158 through 248 )
4X-RAY DIFFRACTION4chain 'A' and (resid 4 through 40 )

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