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- PDB-7lbv: Crystal structure of the Propionibacterium acnes surface sialidas... -

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Basic information

Entry
Database: PDB / ID: 7lbv
TitleCrystal structure of the Propionibacterium acnes surface sialidase in complex with Neu5Ac2en
ComponentsExo-alpha-sialidase
KeywordsHYDROLASE / acne
Function / homology2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / PHOSPHATE ION / :
Function and homology information
Biological speciesCutibacterium acnes (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsYu, A.C.Y. / Volkers, G. / Strynadka, N.C.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Glycobiology / Year: 2022
Title: Crystal structure of the Propionibacterium acnes surface sialidase, a drug target for P. acnes-associated diseases.
Authors: Yu, A.C.Y. / Volkers, G. / Jongkees, S.A.K. / Worrall, L.J. / Withers, S.G. / Strynadka, N.C.J.
History
DepositionJan 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Exo-alpha-sialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1763
Polymers48,7891
Non-polymers3862
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.978, 46.650, 49.659
Angle α, β, γ (deg.)116.930, 99.100, 91.730
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Exo-alpha-sialidase / Sialidase


Mass: 48789.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cutibacterium acnes (bacteria) / Gene: B1B09_09755, FD518_10685 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2B7IY20
#2: Sugar ChemComp-DAN / 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / Neu5Ac2en


Type: D-saccharide / Mass: 291.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17NO8 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.01 Å3/Da / Density % sol: 38.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.8
Details: 18% (w/v) polyethylene glycol monomethylether 2000, 100 mM HEPES, pH 6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 12, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 33635 / % possible obs: 93.2 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.17
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 4.43 / Num. unique obs: 1000 / % possible all: 88.2

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EUR

1eur


Resolution: 1.7→43.44 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.543 / SU ML: 0.062 / SU R Cruickshank DPI: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1816 1796 5.1 %RANDOM
Rwork0.1517 ---
obs0.1532 33635 92.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 77.15 Å2 / Biso mean: 29.48 Å2 / Biso min: 20.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20.29 Å20.05 Å2
2--1.07 Å20.56 Å2
3----0.04 Å2
Refinement stepCycle: final / Resolution: 1.7→43.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2895 0 25 302 3222
Biso mean--30.64 34.8 -
Num. residues----380
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0193042
X-RAY DIFFRACTIONr_angle_refined_deg2.0471.9484165
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4835395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.07122.606142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.42115458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1271534
X-RAY DIFFRACTIONr_chiral_restr0.1540.2461
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212391
LS refinement shellResolution: 1.7→1.741 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.256 104 -
Rwork0.179 2237 -
obs--82.26 %
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)
10.8498-0.20740.50920.49540.03190.4040.08990.0099-0.2140.0206-0.01470.05350.11210.0009-0.07520.11820.0174-0.04020.0079-0.02620.1977-19.322-17.8646.348
20.0176-0.04010.04490.2248-0.1860.17070.0101-0.0088-0.02990.05740.02710.0084-0.0128-0.0193-0.03710.1220.0078-0.00590.0264-0.01090.1452-20.456-6.7722.8
30.4404-0.16690.53722.70391.2151.4180.0668-0.0203-0.05230.0887-0.03830.08620.1306-0.051-0.02850.1421-0.00150.00190.0022-0.00520.147-16.967-14.37523.001
40.11-0.1677-0.2250.40310.40890.7549-0.0031-0.0184-0.04320.02310.0396-0.0547-0.03310.0726-0.03650.13550.0119-0.01450.0248-0.02630.1482-9.430.73720.983
50.31830.12470.13290.38950.47660.6067-0.0261-0.0123-0.00460.00030.0431-0.0345-0.03880.0664-0.01710.15060.0088-0.02320.0314-0.02660.1397-10.1046.32818.918
60.2971-0.05480.12570.29510.01130.1674-0.01580.0060.01760.07190.004-0.1127-0.03150.05290.01190.12150.002-0.01370.0343-0.02050.1513-4.7827.33916.789
70.2139-0.10930.01760.50570.14070.11840.0130.02780.01110.0007-0.0029-0.0232-0.01340.0162-0.010.11230.0080.00180.0236-0.02640.1347-10.3035.9274.584
80.2919-0.09-0.19830.40110.23760.22440.0080.0193-0.0181-0.01590.00520.0091-0.0236-0.0048-0.01320.1210.02490.00050.0308-0.02870.1291-21.8167.0852.759
90.4249-0.0748-0.08830.29120.08080.32520.03070.05370.014-0.023-0.00740.0436-0.0149-0.0247-0.02330.10080.0229-0.00990.0347-0.02220.1264-23.6124.2680.28
104.0759-1.2291-1.1813.85752.90622.20730.02060.4101-0.0622-0.1304-0.11740.1353-0.0936-0.10870.09680.15320.0564-0.02980.0737-0.04680.0892-20.733-10.231-10.552
110.60420.0534-0.21310.0231-0.04930.47090.0085-0.0031-0.0665-0.0323-0.00650.0264-0.0384-0.0592-0.0020.11230.0206-0.01910.0258-0.02880.1433-32.949-1.8185.024
120.85420.11280.09740.025-0.03980.4120.0572-0.0289-0.1308-0.00630.00730.01070.0218-0.0026-0.06450.11980.0083-0.03410.009-0.01250.1854-28.076-10.6149.47
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A81 - 101
2X-RAY DIFFRACTION2A102 - 162
3X-RAY DIFFRACTION3A163 - 171
4X-RAY DIFFRACTION4A172 - 195
5X-RAY DIFFRACTION5A196 - 211
6X-RAY DIFFRACTION6A212 - 254
7X-RAY DIFFRACTION7A255 - 308
8X-RAY DIFFRACTION8A309 - 334
9X-RAY DIFFRACTION9A335 - 374
10X-RAY DIFFRACTION10A375 - 382
11X-RAY DIFFRACTION11A383 - 420
12X-RAY DIFFRACTION12A421 - 460

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