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

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Basic information

Entry
Database: PDB / ID: 6xpg
TitleCrystal Structure of Sialate O-acetylesterase from Bacteroides vulgatus by Serial Crystallography
ComponentsLysophospholipase L1
KeywordsHYDROLASE / Sialate O-acetylesterase / alpha-beta fold / Serial Crystallography / Structural Genomics / Midwest Center for Structural Genomics / PSI-Biology / MCSG
Function / homologySGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / lysophospholipase activity / SGNH hydrolase superfamily / 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: 1.9 Å
AuthorsKim, Y. / Sherrell, D.A. / Owen, R. / Axford, D. / Ebrahim, A. / Johnson, J. / Welk, L. / 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 by Serial Crystallography
Authors: Kim, Y. / Sherrell, D.A. / Owen, R. / Axford, D. / Ebrahim, A. / Johnson, J. / Welk, L. / 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
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysophospholipase L1


Theoretical massNumber of molelcules
Total (without water)23,1581
Polymers23,1581
Non-polymers00
Water1,04558
1
A: Lysophospholipase L1

A: Lysophospholipase L1


Theoretical massNumber of molelcules
Total (without water)46,3162
Polymers46,3162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Buried area2720 Å2
ΔGint-16 kcal/mol
Surface area15930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.533, 102.533, 103.042
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

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Components

#1: Protein Lysophospholipase L1 / Sialate O-acetylesterase


Mass: 23158.023 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: batch mode / 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: Y
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 17, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.9→45.91 Å / Num. obs: 25754 / % possible obs: 100 % / Redundancy: 97.3 % / Biso Wilson estimate: 15.29 Å2 / CC1/2: 0.982 / Net I/σ(I): 2.22
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 6.85 % / Mean I/σ(I) obs: 0.45 / Num. unique obs: 1256 / CC1/2: 0.288 / % possible all: 99.3
Serial crystallography sample deliveryDescription: Silicon nitride chips / Method: fixed target
Serial crystallography sample delivery fixed targetDescription: Silicon nitride chips / Motion control: GeoBrick / SmarAct / Sample dehydration prevention: 6um Mylar / Sample holding: Diamond/Hamburg holder
Serial crystallography data reductionCrystal hits: 10846 / Frame hits: 10846 / Frames indexed: 10846 / Frames total: 51200 / Lattices indexed: 10608

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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: 1.9→45.9 Å / SU ML: 0.2563 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.3666
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2423 1319 5.12 %
Rwork0.2056 24425 -
obs0.2076 25744 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.42 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1587 0 0 58 1645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00591620
X-RAY DIFFRACTIONf_angle_d0.73572189
X-RAY DIFFRACTIONf_chiral_restr0.0495244
X-RAY DIFFRACTIONf_plane_restr0.0039276
X-RAY DIFFRACTIONf_dihedral_angle_d14.3207610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.980.35061350.33642648X-RAY DIFFRACTION99.29
1.98-2.070.32941300.30552667X-RAY DIFFRACTION100
2.07-2.170.32581250.27762678X-RAY DIFFRACTION100
2.17-2.310.30151510.24322675X-RAY DIFFRACTION100
2.31-2.490.30831520.22912673X-RAY DIFFRACTION100
2.49-2.740.25981450.22662709X-RAY DIFFRACTION100
2.74-3.140.25991540.20822697X-RAY DIFFRACTION99.96
3.14-3.950.19971630.15072764X-RAY DIFFRACTION100
3.95-45.90.1491640.12742914X-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)
11.09375116958-0.962776257331-0.5601251038212.63437591144-0.8930444610922.69330166947-0.0133042093179-0.0204972665809-0.130708397127-0.04878158200690.03267999019860.1111813028690.146208573419-0.120039506544-0.07587224427630.0693512125411-0.00615423757398-0.02445220805920.05080618207420.04259900231020.08031518163933.12021344657.71872758743-4.37020845991
20.253057554016-0.03341812453130.109737166050.260618036613-0.03523647972750.163400057321-0.02635928617410.04950025570860.04989216653850.0329191282876-0.00817815327415-0.115619365304-0.07131764215510.0804425883171-0.03933086838890.109260140404-0.0783101942059-0.07371994816730.07821075956560.03539791357050.11950607234436.97660052219.98190881060.0519513160639
32.061533895560.304509483274-0.1205282109820.58775720260.2655278411860.5516921477530.0744573312294-0.034337117762-0.1254334576960.103192040591-0.0266278556589-0.107488018770.0288438777710.0519882052393-0.06102009206040.161810990819-0.051987301115-0.08109385790240.08765892352650.02129852235250.10646159235133.215154328816.40670325767.41910174099
45.230258114810.351540672158-0.5268521252640.673224580027-0.5328321649941.06740547082-0.0523748428594-0.329823538023-0.1882604513280.155848932116-0.0314763406818-0.101324322290.04621929027010.08430335642980.02827828582630.264044406844-0.0164444957173-0.0515080310920.08331383681790.02011531637370.080432744927733.179243096814.220040975416.1695708678
50.876411997579-0.08934566352020.3580462838460.370898766756-0.09814755282950.898186457741-0.0721537681678-0.1431099072650.02918586732180.250435744180.013961282408-0.0650297144858-0.0962373438896-0.1042421129030.02917014171380.248179735940.0155356207906-0.05204827722110.136259306288-0.01854641754820.097956275158624.47435297524.822674508410.0833812038
67.247513610532.36518830605-2.057080053471.18673978294-1.555445936295.104405094970.00300278412764-0.2870964802250.5512089063780.194685173279-0.03581221137790.160091394289-0.47208781563-0.1403661279120.01210291305370.3112893579030.09222032174980.03047260330280.226257288249-0.04775677893290.19334007710714.679468503633.20257953145.44881503185
70.6370656531660.3284801535760.329137915260.1779931513260.1915894524520.22491760877-0.0216855498846-0.006596667588870.08506203227340.0435281815726-0.0104693500086-0.0700004130661-0.09792814693290.04338244645040.0003254164555750.128423382919-0.0223189877393-0.06241069745850.03692287831460.01366724787120.11364269044327.592421988331.5057455059-1.01241480856
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 84 )
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 110 )
4X-RAY DIFFRACTION4chain 'A' and (resid 111 through 128 )
5X-RAY DIFFRACTION5chain 'A' and (resid 129 through 184 )
6X-RAY DIFFRACTION6chain 'A' and (resid 185 through 193 )
7X-RAY DIFFRACTION7chain 'A' and (resid 194 through 220 )

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