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- PDB-6xpm: Crystal Structure of Sialate O-acetylesterase from Bacteroides vu... -

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Basic information

Entry
Database: PDB / ID: 6xpm
TitleCrystal Structure of Sialate O-acetylesterase from Bacteroides vulgatus with microfluidics crystals at room temperature
ComponentsLysophospholipase L1
KeywordsHYDROLASE / Sialate O-acetylesterase / alpha-beta fold / microfluidics / Structural Genomics / Midwest Center for Structural Genomics / PSI-Biology / MCSG
Function / homology: / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / phosphatidylcholine lysophospholipase activity / Hydrolases; Acting on ester bonds / metal ion binding / SGNH/GDSL hydrolase family protein / Sialate O-acetylesterase
Function and homology information
Biological speciesBacteroides vulgatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKim, Y. / Johnson, J. / Welk, L. / Endres, M. / Levens, A. / Sherrell, D.A. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Crystal Structure of Sialate O-acetylesterase from Bacteroides vulgatus with microfluidics crystals at room temperature
Authors: Kim, Y. / Johnson, J. / Welk, L. / Endres, M. / Levens, A. / Sherrell, D.A. / Babnigg, G. / Joachimiak, A.
History
DepositionJul 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Oct 18, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysophospholipase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9932
Polymers22,9701
Non-polymers231
Water52229
1
A: Lysophospholipase L1
hetero molecules

A: Lysophospholipase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9874
Polymers45,9412
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Buried area2740 Å2
ΔGint-35 kcal/mol
Surface area16130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.627, 102.627, 102.834
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-412-

HOH

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Components

#1: Protein Lysophospholipase L1 / Sialate O-acetylesterase


Mass: 22970.443 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides vulgatus (bacteria)
Gene: DW857_02595, DW869_04095, DWX04_04065, DWZ06_04430, DXA04_10705, EAJ12_11850, ERS852457_01148, ERS852509_00617, ERS852556_01195, SAMN04487923_100221
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold
References: UniProt: A0A174J845, UniProt: A6L7S9*PLUS, Hydrolases
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.4 Å3/Da / Density % sol: 63.85 %
Crystal growTemperature: 295 K / Method: microfluidic / pH: 4.5
Details: 0.2 M lithium sulfate, 0.1 M acetate, pH 4.5, 2.5 M sodium chloride

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Data collection

DiffractionMean temperature: 295 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97922 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Nov 4, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 14414 / % possible obs: 97.8 % / Redundancy: 22.4 % / Biso Wilson estimate: 54.72 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.158 / Net I/σ(I): 29.3
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.966 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 620 / CC1/2: 0.461 / % possible all: 84.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6NJC

6njc


Resolution: 2.3→33.59 Å / SU ML: 0.1833 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.8964
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1843 693 4.83 %
Rwork0.1488 13650 -
obs0.1505 14343 97.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.19 Å2
Refinement stepCycle: LAST / Resolution: 2.3→33.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1576 0 1 29 1606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311609
X-RAY DIFFRACTIONf_angle_d0.54282175
X-RAY DIFFRACTIONf_chiral_restr0.0447243
X-RAY DIFFRACTIONf_plane_restr0.0037274
X-RAY DIFFRACTIONf_dihedral_angle_d15.1695604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.480.2981240.24792409X-RAY DIFFRACTION88.85
2.48-2.730.2521420.20492716X-RAY DIFFRACTION99.31
2.73-3.120.21561540.18192757X-RAY DIFFRACTION100
3.12-3.930.19511310.14482808X-RAY DIFFRACTION99.97
3.94-33.590.14571420.1242960X-RAY DIFFRACTION99.61
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)
16.00081234542.713260203082.365075859632.173097074280.006692296553652.30154702677-0.000451744461627-0.2806644331350.1850432240210.279523267667-0.191866489142-2.09987920213E-5-0.467347233981-0.02384893843840.1277243235870.490289545615-0.03963522476750.05578216552890.369646015003-0.03752903140180.469174889461-33.901826134-8.23879302359-4.22757873249
22.30962871922-0.72649905247-0.7359159034653.22871572892-0.3828569958243.62232178194-0.008152764607110.191533566421-0.2329023843460.356889938486-0.1410157712320.3404903569050.175171953362-0.3935149636490.1004762168490.413059532741-0.06620229330120.1185691081260.370627698099-0.01712700651140.476181536928-37.1190897196-20.1241015843-0.0550176124417
36.5127087219-0.3906376137010.3653102435394.111174721380.1601374168362.86740494552-0.150466143958-0.3582440982340.2061017531080.9400456478960.0117896778820.410673925195-0.00517963399575-0.2837427194840.1564406148910.667470999942-0.04044046433220.1408258474570.401140835344-0.02470916306940.3729882802-34.6457009468-17.005361527611.348989703
43.87056928546-0.824225004176-1.83161704533.779010067180.9288610048355.17838623734-0.193580256403-0.623714871536-0.1912641311720.8953896289390.0944316300337-0.361506059120.4604146440610.7964989371660.09122064247660.5782273213260.053797013553-0.04475057375510.4585639479060.04168603987340.415620257186-20.0680971714-26.71612483757.17220991146
54.790345175122.13233788555-3.946154506024.70228358581-1.897730469763.28193636427-0.144208512102-0.00179017725518-0.5267652598690.524316401813-0.111541678294-0.02742385011460.842401092262-0.2966069199350.3738562344840.709699638779-0.09128526856040.07443899395510.375389782624-0.02991685704540.523044341677-32.9829450346-33.81751482150.823541164764
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 84 )
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 137 )
4X-RAY DIFFRACTION4chain 'A' and (resid 138 through 204 )
5X-RAY DIFFRACTION5chain 'A' and (resid 205 through 220 )

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