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- PDB-7pzh: Phocaeicola vulgatus sialic acid esterase at 2.06 Angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 7pzh
TitlePhocaeicola vulgatus sialic acid esterase at 2.06 Angstrom resolution
ComponentsLysophospholipase L1
KeywordsHYDROLASE / Serine hydrolase / Sialic acid acetyl esterase
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
Function and homology information
Biological speciesPhocaeicola vulgatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsScott, H. / Armstrong, Z. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R001162/1 United Kingdom
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: The structure of Phocaeicola vulgatus sialic acid acetylesterase.
Authors: Scott, H. / Davies, G.J. / Armstrong, Z.
History
DepositionOct 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Lysophospholipase L1
BBB: Lysophospholipase L1
CCC: Lysophospholipase L1
DDD: Lysophospholipase L1
EEE: Lysophospholipase L1
FFF: Lysophospholipase L1
HHH: Lysophospholipase L1
GGG: Lysophospholipase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,01816
Polymers201,8238
Non-polymers1948
Water4,666259
1
AAA: Lysophospholipase L1
BBB: Lysophospholipase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5044
Polymers50,4562
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-30 kcal/mol
Surface area16100 Å2
MethodPISA
2
CCC: Lysophospholipase L1
DDD: Lysophospholipase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5044
Polymers50,4562
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-31 kcal/mol
Surface area16120 Å2
MethodPISA
3
EEE: Lysophospholipase L1
FFF: Lysophospholipase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5044
Polymers50,4562
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-28 kcal/mol
Surface area15870 Å2
MethodPISA
4
HHH: Lysophospholipase L1
GGG: Lysophospholipase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5044
Polymers50,4562
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-25 kcal/mol
Surface area15990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.233, 93.233, 353.623
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
Lysophospholipase L1 / Sialate O-acetylesterase


Mass: 25227.924 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phocaeicola vulgatus (bacteria)
Gene: DW869_04095, DWX04_04065, DXA04_10705, ERS852457_01148, ERS852509_00617, ERS852556_01195, F9001_09225, F9Z94_13025, GAS37_03660, GAX98_11820, GAY79_04625, GAY98_11740, GAZ06_07335, GAZ09_07170, ...Gene: DW869_04095, DWX04_04065, DXA04_10705, ERS852457_01148, ERS852509_00617, ERS852556_01195, F9001_09225, F9Z94_13025, GAS37_03660, GAX98_11820, GAY79_04625, GAY98_11740, GAZ06_07335, GAZ09_07170, GAZ65_18905, GAZ76_12675, GAZ90_18550, HKQ51_19175, HUV05_02570, SAMN04487923_100221
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A174J845
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.2 Å3/Da / Density % sol: 44.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 12.5 % w/v PEG 1000, 12.5 % w/v PEG 3350, 12.5 % v/v MPD, sodium nitrate, 0.03 M sodium phosphate, 0.03 M ammonium sulphate, 0.1 M MOPS/HEPES-Na pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97624 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11h, k, l10.8473
pseudo-merohedral11-k, -h, -l20.1527
ReflectionResolution: 2.06→80.74 Å / Num. obs: 106903 / % possible obs: 100 % / Redundancy: 20.5 % / CC1/2: 0.998 / Net I/σ(I): 11.2
Reflection shellResolution: 2.06→2.1 Å / Num. unique obs: 5267 / CC1/2: 0.54

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6njc

6njc


Resolution: 2.06→80.742 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.225 / WRfactor Rwork: 0.185 / SU B: 3.793 / SU ML: 0.111 / Average fsc free: 0.9606 / Average fsc work: 0.9754 / Cross valid method: FREE R-VALUE / ESU R: 0.042 / ESU R Free: 0.036
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2258 5355 5.016 %
Rwork0.185 101414 -
all0.187 --
obs-106769 99.988 %
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: 37.958 Å2
Baniso -1Baniso -2Baniso -3
1--0.037 Å2-0 Å2-0 Å2
2---0.037 Å2-0 Å2
3---0.073 Å2
Refinement stepCycle: LAST / Resolution: 2.06→80.742 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12619 0 62 259 12940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01313081
X-RAY DIFFRACTIONr_bond_other_d0.0020.01712425
X-RAY DIFFRACTIONr_angle_refined_deg1.6461.6417695
X-RAY DIFFRACTIONr_angle_other_deg1.321.58328906
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.61451604
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.97723.333639
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.037152411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.721561
X-RAY DIFFRACTIONr_chiral_restr0.0820.21690
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214399
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022628
X-RAY DIFFRACTIONr_nbd_refined0.2180.22823
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.212227
X-RAY DIFFRACTIONr_nbtor_refined0.1690.26293
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.25301
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2421
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0990.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2080.214
X-RAY DIFFRACTIONr_nbd_other0.2090.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1980.210
X-RAY DIFFRACTIONr_mcbond_it3.5173.9386413
X-RAY DIFFRACTIONr_mcbond_other3.5173.9376412
X-RAY DIFFRACTIONr_mcangle_it4.5665.8928018
X-RAY DIFFRACTIONr_mcangle_other4.5665.8928019
X-RAY DIFFRACTIONr_scbond_it3.6064.2036668
X-RAY DIFFRACTIONr_scbond_other3.6024.2036666
X-RAY DIFFRACTIONr_scangle_it5.0546.1939677
X-RAY DIFFRACTIONr_scangle_other5.0516.1939677
X-RAY DIFFRACTIONr_lrange_it6.54645.95314743
X-RAY DIFFRACTIONr_lrange_other6.54645.95614744
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.1130.2983690.2387559X-RAY DIFFRACTION99.8866
2.113-2.1710.2833810.2277287X-RAY DIFFRACTION100
2.171-2.2340.2863750.2277086X-RAY DIFFRACTION99.9732
2.234-2.3030.2963800.2146895X-RAY DIFFRACTION100
2.303-2.3790.2573550.2066695X-RAY DIFFRACTION100
2.379-2.4620.2943200.2076482X-RAY DIFFRACTION100
2.462-2.5550.2773460.2196209X-RAY DIFFRACTION100
2.555-2.6590.2643140.2156025X-RAY DIFFRACTION100
2.659-2.7780.2553310.2045718X-RAY DIFFRACTION100
2.778-2.9130.2462970.1965538X-RAY DIFFRACTION100
2.913-3.0710.2582860.2075199X-RAY DIFFRACTION100
3.071-3.2570.2392360.2054984X-RAY DIFFRACTION100
3.257-3.4820.2362480.1994676X-RAY DIFFRACTION100
3.482-3.7610.2152450.1834320X-RAY DIFFRACTION100
3.761-4.120.1821950.1564001X-RAY DIFFRACTION100
4.12-4.6060.1771950.1413619X-RAY DIFFRACTION100
4.606-5.3180.1731850.1443161X-RAY DIFFRACTION100
5.318-6.5130.2151390.172707X-RAY DIFFRACTION100
6.513-9.2090.148980.1422103X-RAY DIFFRACTION100
9.209-80.740.169600.1581150X-RAY DIFFRACTION99.835

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