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- PDB-7lbu: Crystal structure of the Propionibacterium acnes surface sialidase -

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Basic information

Entry
Database: PDB / ID: 7lbu
TitleCrystal structure of the Propionibacterium acnes surface sialidase
ComponentsExo-alpha-sialidase
KeywordsHYDROLASE / acne
Function / homologyACETATE ION / PHOSPHATE ION / :
Function and homology information
Biological speciesCutibacterium acnes (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.11 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 8, 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 1.3Oct 16, 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

Downloads & links

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Assembly

Deposited unit
A: Exo-alpha-sialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9433
Polymers48,7891
Non-polymers1542
Water2,972165
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)43.973, 46.847, 49.600
Angle α, β, γ (deg.)116.510, 98.940, 91.690
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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.06 Å3/Da / Density % sol: 40.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 20% (w/v) polyethylene glycol monomethylether 2000, 100 mM HEPES, pH 7.5

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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: 2.1→50 Å / Num. obs: 17676 / % possible obs: 91.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 29.05 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.26
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.235 / Num. unique obs: 1000 / % possible all: 77.4

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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: 2.11→43.6 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.928 / SU B: 11.696 / SU ML: 0.159 / SU R Cruickshank DPI: 0.2873 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.287 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2328 967 5.2 %RANDOM
Rwork0.1726 ---
obs0.1759 17676 92.98 %-
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: 90.08 Å2 / Biso mean: 39.361 Å2 / Biso min: 27.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20.34 Å20.22 Å2
2--0.37 Å2-0.07 Å2
3----0.23 Å2
Refinement stepCycle: final / Resolution: 2.11→43.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2895 0 9 165 3069
Biso mean--57.03 38.54 -
Num. residues----380
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192979
X-RAY DIFFRACTIONr_angle_refined_deg1.9131.9424068
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4975381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.50522.701137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.6815445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7391532
X-RAY DIFFRACTIONr_chiral_restr0.1250.2449
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212335
LS refinement shellResolution: 2.11→2.163 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.349 82 -
Rwork0.228 1247 -
obs--90.35 %
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)
12.5798-0.36920.79162.1663-0.04711.01460.0859-0.0443-0.1931-0.1368-0.0780.18060.2918-0.1851-0.00790.16770.0281-0.04770.21180.03550.2774-19.496-17.2185.849
20.9993-0.1004-0.29940.9977-0.19780.8883-0.0024-0.1405-0.15820.20440.02810.04620.04480.0272-0.02570.08630.0690.00350.1830.09680.1866-17.487-4.78621.736
31.69350.89810.19543.43620.41710.8494-0.0356-0.11660.01660.2550.0914-0.2824-0.07020.096-0.05580.08620.0697-0.01890.19040.07350.1471-8.33110.68919.024
41.2211-1.04580.35675.6946-0.95870.5233-0.0663-0.12210.0428-0.00550.0238-0.1954-0.02980.16270.04250.07830.03410.00270.19060.07290.1588-5.0624.76514.809
52.4342-1.1153-0.48711.8913-0.08440.167-0.00260.2048-0.00640.0251-0.00190.0317-0.0077-0.0680.00450.07990.051-0.01380.22030.07440.2101-13.4433.2485.207
61.1007-0.10050.23520.65330.42360.53660.03740.0115-0.0354-0.0398-0.0161-0.0043-0.10880.06-0.02140.09280.03930.00220.18770.07180.1681-14.1727.9062.672
72.9402-0.5226-0.80570.9168-0.39931.86360.20830.29680.1072-0.0474-0.08240.085-0.1492-0.0796-0.1260.08310.059-0.0140.20980.06810.1463-25.2688.1940.641
88.9234-0.58272.35220.3424-2.437117.77160.12710.41-0.3489-0.0217-0.11340.01230.1070.6878-0.01370.06940.0762-0.00510.1627-0.01490.1933-19.985-10.595-7.439
94.3666-2.581-1.88111.88070.8571.440.0346-0.0514-0.6012-0.1099-0.11690.4392-0.153-0.06480.08230.14590.0812-0.01440.19630.04720.267-31.22-0.3243.226
102.89050.40730.53980.7007-0.4740.5714-0.02910.0975-0.2799-0.02450.1104-0.00580.0136-0.0582-0.08140.07650.0702-0.02970.25330.05360.2656-32.808-0.8834.47
111.9298-0.5120.70081.3868-0.57721.74710.1229-0.0369-0.229-0.0552-0.10290.08740.0935-0.2015-0.020.04730.0412-0.0120.16250.08080.2063-29.909-5.5138.014
123.13370.24942.40991.95951.54695.87540.24770.2068-0.5038-0.01810.10670.23460.4937-0.0178-0.35430.0610.0135-0.03240.19230.07460.3574-30.912-11.8685.524
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 49
2X-RAY DIFFRACTION2A50 - 142
3X-RAY DIFFRACTION3A143 - 168
4X-RAY DIFFRACTION4A169 - 200
5X-RAY DIFFRACTION5A201 - 217
6X-RAY DIFFRACTION6A218 - 279
7X-RAY DIFFRACTION7A280 - 315
8X-RAY DIFFRACTION8A316 - 328
9X-RAY DIFFRACTION9A329 - 340
10X-RAY DIFFRACTION10A341 - 353
11X-RAY DIFFRACTION11A354 - 386
12X-RAY DIFFRACTION12A387 - 408

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