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- PDB-8oim: Crystal structure of the lipase SpL from Sphingomonas sp. HXN-200 -

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Basic information

Entry
Database: PDB / ID: 8oim
TitleCrystal structure of the lipase SpL from Sphingomonas sp. HXN-200
ComponentsLipase
KeywordsHYDROLASE / alpha-beta hydrolase / lipase / SpL
Function / homologyLipase, GDXG, putative serine active site / Lipolytic enzymes "G-D-X-G" family, putative serine active site. / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold / hydrolase activity / Lipase
Function and homology information
Biological speciesSphingomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.994 Å
AuthorsMokos, D. / Gruber, K. / Daniel, B.
Funding support Austria, 2items
OrganizationGrant numberCountry
Austrian Science Fund Austria
Austrian Research Promotion Agency Austria
CitationJournal: To Be Published
Title: Amide formation of (hetero)aromatic esters and primary amines in buffer catalyzed by serine hydrolases: An Asp next to Ser of the catalytic triad of serine hydrolases is crucial for activity
Authors: Zukic, E. / Mokos, D. / Daniel, B. / Weber, M. / Stix, N. / Ditrich, K. / Willrodt, C. / Gruber, K. / Kroutil, W.
History
DepositionMar 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipase
B: Lipase


Theoretical massNumber of molelcules
Total (without water)70,9762
Polymers70,9762
Non-polymers00
Water6,485360
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-3 kcal/mol
Surface area23450 Å2
Unit cell
Length a, b, c (Å)60.812, 88.966, 65.627
Angle α, β, γ (deg.)90.000, 96.411, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ALA / End label comp-ID: ALA / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 6 - 314 / Label seq-ID: 20 - 328

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Lipase /


Mass: 35488.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas sp. (bacteria) / Gene: LH19_08550 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0N7I173
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.49 Å3/Da / Density % sol: 50.63 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 5 mg/ml SPL, Index screen condition 78 (0.2 M Ammonium acetate, 0.1 M BIS-TRIS, 25% PEG 3350)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03321 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 1.99→42.05 Å / Num. obs: 44854 / % possible obs: 94.9 % / Redundancy: 3.4 % / CC1/2: 0.992 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.068 / Rrim(I) all: 0.099 / Net I/σ(I): 9.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.92-42.053.30.0535490.9880.0520.074
1.99-2.053.40.28131100.9250.2730.392

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.994→42.048 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.699 / SU ML: 0.102 / Cross valid method: FREE R-VALUE / ESU R: 0.162 / ESU R Free: 0.144
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2017 2309 5.153 %
Rwork0.1647 42496 -
all0.167 --
obs-44805 94.571 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 30.462 Å2
Baniso -1Baniso -2Baniso -3
1--1.029 Å2-0 Å20.507 Å2
2--1.902 Å2-0 Å2
3----0.962 Å2
Refinement stepCycle: LAST / Resolution: 1.994→42.048 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4674 0 0 360 5034
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0124798
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164476
X-RAY DIFFRACTIONr_angle_refined_deg2.0371.6586560
X-RAY DIFFRACTIONr_angle_other_deg0.6411.56810326
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9665616
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.198538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.41510704
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.94310206
X-RAY DIFFRACTIONr_chiral_restr0.1060.2722
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025716
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021036
X-RAY DIFFRACTIONr_nbd_refined0.2140.21006
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.24185
X-RAY DIFFRACTIONr_nbtor_refined0.1840.22369
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.22504
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2304
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0210.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0570.21
X-RAY DIFFRACTIONr_nbd_other0.1380.223
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1620.23
X-RAY DIFFRACTIONr_mcbond_it3.7762.9152470
X-RAY DIFFRACTIONr_mcbond_other3.762.9142470
X-RAY DIFFRACTIONr_mcangle_it4.7045.2143084
X-RAY DIFFRACTIONr_mcangle_other4.7055.2163085
X-RAY DIFFRACTIONr_scbond_it6.0513.5362328
X-RAY DIFFRACTIONr_scbond_other6.053.5382329
X-RAY DIFFRACTIONr_scangle_it8.6446.1653476
X-RAY DIFFRACTIONr_scangle_other8.6436.1663477
X-RAY DIFFRACTIONr_lrange_it9.5328.3945404
X-RAY DIFFRACTIONr_lrange_other9.49328.0065327
X-RAY DIFFRACTIONr_ncsr_local_group_10.0880.059813
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.087570.05008
12AX-RAY DIFFRACTIONLocal ncs0.087570.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.994-2.0460.2641570.21229410.21534740.9540.96889.17670.195
2.046-2.1020.2621390.19831390.233970.9580.97196.49690.181
2.102-2.1630.2461620.18530260.18833070.9580.97696.40160.169
2.163-2.2290.2381580.19729070.19932050.9640.97395.63180.178
2.229-2.3020.2671690.19428050.19831000.9490.97695.93550.183
2.302-2.3820.2261570.16726680.1729900.9690.98294.48160.156
2.382-2.4720.2471350.1725220.17429260.9660.98290.80660.161
2.472-2.5730.2391470.16525640.16928020.9620.98496.75230.159
2.573-2.6860.211130.15924820.16126940.9750.98496.32520.155
2.686-2.8170.1941350.16122980.16325420.9750.98495.7120.162
2.817-2.9690.2151250.16222200.16524550.9710.98495.51930.165
2.969-3.1480.2161190.1620880.16323340.9710.98494.55870.168
3.148-3.3640.198990.16419310.16621750.9790.98393.33330.177
3.364-3.6310.196980.15916820.16120210.980.98588.07520.174
3.631-3.9750.171090.14516920.14618680.9830.98796.41330.16
3.975-4.4390.143710.13515780.13617040.9880.98896.77230.156
4.439-5.1160.148680.14213920.14315120.9820.98896.56080.168
5.116-6.2430.192680.16411440.16512700.9820.98695.43310.187
6.243-8.7330.17510.1668640.16610040.980.98291.13550.196
8.733-42.0480.204290.2065530.2065910.9760.97198.47720.22

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