[English] 日本語
Yorodumi
- PDB-7qyp: The structure of T. forsythia NanH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qyp
TitleThe structure of T. forsythia NanH
ComponentsBNR/Asp-box repeat protein
KeywordsHYDROLASE / Sialidase
Function / homologySialidase, N-terminal / N-terminal domain of BNR-repeat neuraminidase / BNR repeat-like domain / exo-alpha-sialidase activity / Sialidase family / Sialidase / Sialidase superfamily / BNR/Asp-box repeat protein
Function and homology information
Biological speciesTannerella forsythia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.659 Å
AuthorsRafferty, J. / Stafford, G. / Satur, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Biochem.J. / Year: 2022
Title: Structural and functional characterisation of a stable, broad-specificity multimeric sialidase from the oral pathogen Tannerella forsythia.
Authors: Satur, M.J. / Urbanowicz, P.A. / Spencer, D.I.R. / Rafferty, J. / Stafford, G.P.
History
DepositionJan 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BNR/Asp-box repeat protein
B: BNR/Asp-box repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,41012
Polymers114,7892
Non-polymers62110
Water12,683704
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.895, 79.895, 349.328
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 34 - 552 / Label seq-ID: 1 - 519

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AA
22BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

-
Components

#1: Protein BNR/Asp-box repeat protein


Mass: 57394.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tannerella forsythia (bacteria)
Strain: ATCC 43037 / JCM 10827 / CCUG 33226 / KCTC 5666 / FDC 338
Gene: BFO_2207 / Production host: Escherichia coli (E. coli) / References: UniProt: G8UIQ1
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 704 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.34 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 7% PEG6000 0.1M HEPES

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.659→79.89 Å / Num. obs: 135097 / % possible obs: 100 % / Redundancy: 12.1 % / CC1/2: 0.992 / Rmerge(I) obs: 0.168 / Net I/σ(I): 6.9
Reflection shellResolution: 1.66→1.69 Å / Rmerge(I) obs: 0.851 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 6572 / CC1/2: 0.435 / % possible all: 99.21

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4bbw

4bbw


Resolution: 1.659→78.005 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.914 / SU B: 8.357 / SU ML: 0.131 / Cross valid method: FREE R-VALUE / ESU R: 0.117 / ESU R Free: 0.122
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2727 6556 4.917 %
Rwork0.2218 126770 -
all0.224 --
obs-133326 98.77 %
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 29.929 Å2
Baniso -1Baniso -2Baniso -3
1-0.764 Å20 Å20 Å2
2--0.764 Å20 Å2
3----1.529 Å2
Refinement stepCycle: LAST / Resolution: 1.659→78.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8046 0 40 704 8790
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0138268
X-RAY DIFFRACTIONr_bond_other_d0.0020.0147842
X-RAY DIFFRACTIONr_angle_refined_deg1.6811.64511214
X-RAY DIFFRACTIONr_angle_other_deg1.3571.5818012
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.16351044
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.12921.284436
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.289151404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7141572
X-RAY DIFFRACTIONr_chiral_restr0.0790.21118
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029388
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021920
X-RAY DIFFRACTIONr_nbd_refined0.1980.21447
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.27931
X-RAY DIFFRACTIONr_nbtor_refined0.1550.23918
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.24146
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2679
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1050.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1780.25
X-RAY DIFFRACTIONr_nbd_other0.1760.220
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1260.25
X-RAY DIFFRACTIONr_mcbond_it7.1061.7284170
X-RAY DIFFRACTIONr_mcbond_other7.1061.7284169
X-RAY DIFFRACTIONr_mcangle_it6.7472.5625216
X-RAY DIFFRACTIONr_mcangle_other6.7472.5625217
X-RAY DIFFRACTIONr_scbond_it10.582.0834098
X-RAY DIFFRACTIONr_scbond_other10.5792.0834099
X-RAY DIFFRACTIONr_scangle_it10.7252.9465998
X-RAY DIFFRACTIONr_scangle_other10.7252.9475999
X-RAY DIFFRACTIONr_lrange_it11.08221.8069115
X-RAY DIFFRACTIONr_lrange_other11.13121.2868950
X-RAY DIFFRACTIONr_ncsr_local_group_10.0890.0516907
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.08890.05009
12BX-RAY DIFFRACTIONLocal ncs0.08890.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.659-1.7020.4044730.3969300X-RAY DIFFRACTION99.3999
1.702-1.7490.3774650.3619076X-RAY DIFFRACTION99.979
1.749-1.80.3374610.3288870X-RAY DIFFRACTION99.8929
1.8-1.8550.3334500.318633X-RAY DIFFRACTION99.8571
1.855-1.9160.3694420.3058302X-RAY DIFFRACTION99.5333
1.916-1.9830.3183640.2788121X-RAY DIFFRACTION99.5425
1.983-2.0580.3044140.2467784X-RAY DIFFRACTION99.4541
2.058-2.1420.3033810.2397488X-RAY DIFFRACTION99.3937
2.142-2.2370.2883650.2387170X-RAY DIFFRACTION98.8586
2.237-2.3460.3193460.2376897X-RAY DIFFRACTION98.6785
2.346-2.4730.2813430.2146478X-RAY DIFFRACTION98.4413
2.473-2.6230.3083210.2146152X-RAY DIFFRACTION97.7499
2.623-2.8040.3033120.2265746X-RAY DIFFRACTION97.3329
2.804-3.0290.2622780.2165365X-RAY DIFFRACTION96.7759
3.029-3.3180.2572640.2094964X-RAY DIFFRACTION96.618
3.318-3.710.2732510.2164475X-RAY DIFFRACTION97.063
3.71-4.2840.2181870.1784074X-RAY DIFFRACTION97.5504
4.284-5.2460.1812030.1433473X-RAY DIFFRACTION98.0267
5.246-7.4180.1811430.1512752X-RAY DIFFRACTION97.5076
7.418-78.0050.266930.1871650X-RAY DIFFRACTION98.4746
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)
10.8082-0.13490.06140.96280.26730.5405-0.0217-0.09490.07570.11450.00280.0339-0.00680.02460.01890.0334-0.00480.00280.0977-0.02770.01340.854116.001734.2084
20.99010.1325-0.25890.91280.12250.57250.0091-0.0253-0.0966-0.0163-0.0137-0.12550.13980.08090.00460.09190.08110.00380.10090.02430.040519.0152-17.12113.3773
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA34 - 552
2X-RAY DIFFRACTION1ALLA601
3X-RAY DIFFRACTION1ALLA701
4X-RAY DIFFRACTION1ALLA801
5X-RAY DIFFRACTION1ALLA901
6X-RAY DIFFRACTION2ALLB34 - 552
7X-RAY DIFFRACTION2ALLB601
8X-RAY DIFFRACTION2ALLB701

+
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