[English] 日本語
Yorodumi
- PDB-6rzd: Crystal structure of an inverting family GH156 exosialidase from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rzd
TitleCrystal structure of an inverting family GH156 exosialidase from uncultured bacterium pG7
Componentsexosialidase from uncultured bacterium pG7
KeywordsHYDROLASE / (beta/alpha )8 barrel / sialidase / inverting / homodimer
Function / homologyACETATE ION
Function and homology information
Biological speciesuncultured bacterium pG7 (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBule, P. / Blagova, E. / Chuzel, L. / Taron, C.H. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Royal Society United Kingdom
CitationJournal: Nat Commun / Year: 2019
Title: Inverting family GH156 sialidases define an unusual catalytic motif for glycosidase action.
Authors: Bule, P. / Chuzel, L. / Blagova, E. / Wu, L. / Gray, M.A. / Henrissat, B. / Rapp, E. / Bertozzi, C.R. / Taron, C.H. / Davies, G.J.
History
DepositionJun 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id / _refine_hist.d_res_low

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: exosialidase from uncultured bacterium pG7
B: exosialidase from uncultured bacterium pG7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,20921
Polymers117,5732
Non-polymers1,63619
Water7,566420
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SEC-MALLS confirmed the dimeric assembly in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8130 Å2
ΔGint-65 kcal/mol
Surface area34240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.112, 79.273, 112.214
Angle α, β, γ (deg.)90.000, 94.720, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein exosialidase from uncultured bacterium pG7


Mass: 58786.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium pG7 (environmental samples)
Plasmid: pET29a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: exo-alpha-sialidase

-
Non-polymers , 5 types, 439 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.11 % / Mosaicity: 0 °
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.8 M sodium formate, 15% PEG 4000, 0.1 M sodium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→64.67 Å / Num. obs: 75801 / % possible obs: 100 % / Redundancy: 5.4 % / CC1/2: 0.985 / Rmerge(I) obs: 0.198 / Rpim(I) all: 0.094 / Rrim(I) all: 0.219 / Net I/σ(I): 5.8 / Num. measured all: 412825 / Scaling rejects: 1502
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.045.60.8092479944470.5930.3770.8941.899.7
10-64.675.10.08433346510.9930.0390.09314.199.6

-
Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
Aimlessdata scaling
PHASERphasing
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Unpublished SeMet derivative

Resolution: 2→64.67 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.883 / SU B: 13.536 / SU ML: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.201
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2856 3839 5.1 %RANDOM
Rwork0.2337 ---
obs0.2363 71915 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 58.04 Å2 / Biso mean: 23.225 Å2 / Biso min: 7.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å2-0 Å2-0.89 Å2
2---0.09 Å2-0 Å2
3----0.14 Å2
Refinement stepCycle: final / Resolution: 2→64.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8020 0 106 420 8546
Biso mean--35.89 24.02 -
Num. residues----992
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0138405
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177731
X-RAY DIFFRACTIONr_angle_refined_deg1.8551.65211417
X-RAY DIFFRACTIONr_angle_other_deg1.3121.57217783
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.75651002
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.41719.49529
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.723151316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.07815106
X-RAY DIFFRACTIONr_chiral_restr0.0820.21017
X-RAY DIFFRACTIONr_gen_planes_refined0.010.029494
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022044
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 316 -
Rwork0.305 5211 -
all-5527 -
obs--99.87 %
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)
10.28290.1353-0.16940.8126-0.17821.65470.0234-0.02320.07110.091-0.02820.0364-0.104-0.17630.00480.15840.01420.04860.0268-0.00940.033411.951326.034944.211
20.2677-0.11060.12220.7475-0.14551.58060.03180.0029-0.05-0.0786-0.0260.02880.1319-0.1138-0.00580.1799-0.01190.02290.0104-0.00330.014615.1558.06898.9739
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 1301
2X-RAY DIFFRACTION2B6 - 1601

+
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