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- PDB-8gn6: Crystallization of Sialidase from Porphyromonas gingivalis -

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Basic information

Entry
Database: PDB / ID: 8gn6
TitleCrystallization of Sialidase from Porphyromonas gingivalis
Components(Sialidase) x 2
KeywordsCARBOHYDRATE / sialidase
Function / homology
Function and homology information


exo-alpha-sialidase activity
Similarity search - Function
BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
Unknown ligand / Sialidase
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDong, W.B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2023
Title: Structural and enzymatic characterization of the sialidase SiaPG from Porphyromonas gingivalis.
Authors: Dong, W.B. / Jiang, Y.L. / Zhu, Z.L. / Zhu, J. / Li, Y. / Xia, R. / Zhou, K.
History
DepositionAug 23, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sialidase
B: Sialidase
C: Sialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,3836
Polymers175,0733
Non-polymers3093
Water15,349852
1
A: Sialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5562
Polymers58,4531
Non-polymers1031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5562
Polymers58,4531
Non-polymers1031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2712
Polymers58,1681
Non-polymers1031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.160, 131.160, 181.173
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11C-1020-

HOH

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Components

#1: Protein Sialidase


Mass: 58452.863 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Gene: PGIN_13-1_00174
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A1R4DV85
#2: Protein Sialidase


Mass: 58167.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Gene: PGIN_13-1_00174
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A1R4DV85
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Mass: 103.120 Da / Num. of mol.: 3 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 852 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.73 Å3/Da / Density % sol: 54.92 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop / Details: 1.4M Ammonium tartrate dibasic,0.1M Tris PH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.1→56.86 Å / Num. obs: 101168 / % possible obs: 95.8 % / Redundancy: 15.3 % / CC1/2: 0.999 / Net I/σ(I): 48.4
Reflection shellResolution: 2.1→2.2381 Å / Num. unique obs: 101168 / CC1/2: 1

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
MLPHAREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MYV

6myv


Resolution: 2.1→56.86 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.969 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21597 5017 5 %RANDOM
Rwork0.17335 ---
obs0.17548 96101 95.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.539 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.1→56.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11631 0 0 852 12483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01211877
X-RAY DIFFRACTIONr_bond_other_d0.0020.01610620
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.64816084
X-RAY DIFFRACTIONr_angle_other_deg0.4821.56224749
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.71551480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.6825130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.086101955
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0650.21726
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213973
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022479
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9053.6225929
X-RAY DIFFRACTIONr_mcbond_other2.9033.6225929
X-RAY DIFFRACTIONr_mcangle_it4.1125.4247406
X-RAY DIFFRACTIONr_mcangle_other4.1125.4257407
X-RAY DIFFRACTIONr_scbond_it3.383.9475948
X-RAY DIFFRACTIONr_scbond_other3.383.9475949
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9795.7938679
X-RAY DIFFRACTIONr_long_range_B_refined6.91545.75212895
X-RAY DIFFRACTIONr_long_range_B_other6.85544.87412693
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 360 -
Rwork0.263 7216 -
obs--97.54 %

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