[English] 日本語
Yorodumi
- PDB-7lbu: Crystal structure of the Propionibacterium acnes surface sialidase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7lbu
TitleCrystal structure of the Propionibacterium acnes surface sialidase
ComponentsExo-alpha-sialidaseNeuraminidase
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

#1: Protein Exo-alpha-sialidase / Neuraminidase / 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 / Phosphate


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


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


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more