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- PDB-7pzg: Phocaeicola vulgatus sialic acid esterase at 1.44 Angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 7pzg
TitlePhocaeicola vulgatus sialic acid esterase at 1.44 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 A1 activity / Hydrolases; Acting on ester bonds / metal ion binding / MALONIC ACID / SGNH/GDSL hydrolase family protein
Function and homology information
Biological speciesPhocaeicola vulgatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,67316
Polymers100,9124
Non-polymers76212
Water12,538696
1
AAA: Lysophospholipase L1
DDD: Lysophospholipase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8378
Polymers50,4562
Non-polymers3816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-37 kcal/mol
Surface area16080 Å2
MethodPISA
2
BBB: Lysophospholipase L1
CCC: Lysophospholipase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8378
Polymers50,4562
Non-polymers3816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-34 kcal/mol
Surface area16090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.269, 90.150, 76.579
Angle α, β, γ (deg.)90.000, 99.289, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Lysophospholipase L1 / Sialate O-acetylesterase


Mass: 25227.924 Da / Num. of mol.: 4
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.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H4O4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 696 / 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: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 18 % (w/v) PEG 3350, 200 mM sodium malonate pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.44→70.434 Å / Num. obs: 168248 / % possible obs: 97.7 % / Redundancy: 6.8 % / CC1/2: 1 / Net I/σ(I): 18.3
Reflection shellResolution: 1.44→1.46 Å / Num. unique obs: 7900 / CC1/2: 0.712

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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: 1.44→70.434 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.202 / WRfactor Rwork: 0.172 / SU B: 1.156 / SU ML: 0.044 / Average fsc free: 0.9248 / Average fsc work: 0.9304 / Cross valid method: FREE R-VALUE / ESU R: 0.061 / ESU R Free: 0.063
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.203 8262 4.913 %
Rwork0.177 159915 -
all0.178 --
obs-168177 97.573 %
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: 22.426 Å2
Baniso -1Baniso -2Baniso -3
1--0.072 Å2-0 Å20.685 Å2
2---0.424 Å2-0 Å2
3---0.258 Å2
Refinement stepCycle: LAST / Resolution: 1.44→70.434 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6350 0 48 696 7094
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0136597
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176239
X-RAY DIFFRACTIONr_angle_refined_deg1.8351.6448920
X-RAY DIFFRACTIONr_angle_other_deg1.5291.58214505
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3925809
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.92523.259316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.062151201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9821530
X-RAY DIFFRACTIONr_chiral_restr0.10.2849
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027276
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021326
X-RAY DIFFRACTIONr_nbd_refined0.2290.21355
X-RAY DIFFRACTIONr_symmetry_nbd_other0.170.26029
X-RAY DIFFRACTIONr_nbtor_refined0.1760.23284
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.22803
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2480
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0920.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2760.213
X-RAY DIFFRACTIONr_nbd_other0.1640.235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1750.225
X-RAY DIFFRACTIONr_mcbond_it1.8532.1573224
X-RAY DIFFRACTIONr_mcbond_other1.8482.1563223
X-RAY DIFFRACTIONr_mcangle_it2.5263.2334037
X-RAY DIFFRACTIONr_mcangle_other2.5253.2344038
X-RAY DIFFRACTIONr_scbond_it2.9562.4583373
X-RAY DIFFRACTIONr_scbond_other2.9552.4583374
X-RAY DIFFRACTIONr_scangle_it4.373.5574883
X-RAY DIFFRACTIONr_scangle_other4.373.5584884
X-RAY DIFFRACTIONr_lrange_it7.14326.5727737
X-RAY DIFFRACTIONr_lrange_other7.14126.577737
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.4770.2695680.27111313X-RAY DIFFRACTION93.0821
1.477-1.5180.2585450.2511315X-RAY DIFFRACTION95.7224
1.518-1.5620.2685500.23811046X-RAY DIFFRACTION96.7381
1.562-1.610.2495760.21110781X-RAY DIFFRACTION96.8449
1.61-1.6630.2275400.20610500X-RAY DIFFRACTION97.0976
1.663-1.7210.2215310.19510102X-RAY DIFFRACTION97.4253
1.721-1.7860.2254890.1869860X-RAY DIFFRACTION97.5401
1.786-1.8590.2144820.1819498X-RAY DIFFRACTION97.8144
1.859-1.9410.2134910.1829100X-RAY DIFFRACTION97.9773
1.941-2.0360.2064560.1798754X-RAY DIFFRACTION98.2505
2.036-2.1460.1984510.1778284X-RAY DIFFRACTION98.4669
2.146-2.2760.2023860.1737937X-RAY DIFFRACTION98.7424
2.276-2.4330.1993790.1667459X-RAY DIFFRACTION98.8399
2.433-2.6280.213910.1666939X-RAY DIFFRACTION99.0005
2.628-2.8790.1913390.1666375X-RAY DIFFRACTION99.2608
2.879-3.2180.2083170.1725823X-RAY DIFFRACTION99.4493
3.218-3.7150.192810.1755137X-RAY DIFFRACTION99.5956
3.715-4.5480.1532070.1514404X-RAY DIFFRACTION99.762
4.548-6.4240.2121950.1863378X-RAY DIFFRACTION99.8603
6.424-70.4340.2880.161910X-RAY DIFFRACTION98.9109

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