[English] 日本語
Yorodumi
- PDB-6ibu: Apo Crh5 transglycosylase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ibu
TitleApo Crh5 transglycosylase
ComponentsProbable glycosidase crf1
KeywordsHYDROLASE / cross-link / transglycosylase / GH16 / cell wall assembly
Function / homology
Function and homology information


Transferases; Glycosyltransferases / fungal-type cell wall / IgE binding / chitinase / hydrolase activity, hydrolyzing O-glycosyl compounds / side of membrane / cell wall organization / carbohydrate metabolic process / extracellular region / plasma membrane
Similarity search - Function
Glycoside hydrolase, family 16, CRH1, predicted / : / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsBartual, S.G. / Fang, W. / van Aalten, D.M.F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)M004139 United Kingdom
CitationJournal: Nat Commun / Year: 2019
Title: Mechanisms of redundancy and specificity of the Aspergillus fumigatus Crh transglycosylases.
Authors: Fang, W. / Sanz, A.B. / Bartual, S.G. / Wang, B. / Ferenbach, A.T. / Farkas, V. / Hurtado-Guerrero, R. / Arroyo, J. / van Aalten, D.M.F.
History
DepositionNov 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable glycosidase crf1
B: Probable glycosidase crf1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8399
Polymers53,1942
Non-polymers6457
Water4,143230
1
A: Probable glycosidase crf1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6892
Polymers26,5971
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable glycosidase crf1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1507
Polymers26,5971
Non-polymers5536
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.400, 74.171, 116.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 25 - 266 / Label seq-ID: 4 - 245

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Probable glycosidase crf1 / Crh-like protein 1


Mass: 26597.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold)
Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: crf1, AFUA_1G16190
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8J0P4, Hydrolases; Glycosylases
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium acetate trihydrate pH 4.0, 1,6M ammonium sulphate, 21mM ZnCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.885601 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.885601 Å / Relative weight: 1
ReflectionResolution: 2.25→62.62 Å / Num. obs: 23428 / % possible obs: 99.01 % / Redundancy: 4.1 % / CC1/2: 0.807 / Net I/σ(I): 7.99
Reflection shellResolution: 2.25→2.331 Å / Redundancy: 4.2 % / Num. unique obs: 2317 / % possible all: 99.44

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NDL

5ndl
PDB Unreleased entry


Resolution: 2.25→62.62 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.925 / SU B: 7.582 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.346 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23101 1160 5 %RANDOM
Rwork0.19206 ---
obs0.19404 22150 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.229 Å2
Baniso -1Baniso -2Baniso -3
1--1.51 Å20 Å20 Å2
2--0.49 Å20 Å2
3---1.02 Å2
Refinement stepCycle: 1 / Resolution: 2.25→62.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3664 0 42 230 3936
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133802
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173281
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.6565195
X-RAY DIFFRACTIONr_angle_other_deg1.4011.5777635
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6055480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.36423.864176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.14915524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2121512
X-RAY DIFFRACTIONr_chiral_restr0.0720.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024314
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02794
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3132.6711929
X-RAY DIFFRACTIONr_mcbond_other2.312.671928
X-RAY DIFFRACTIONr_mcangle_it3.8643.992406
X-RAY DIFFRACTIONr_mcangle_other3.8633.9922407
X-RAY DIFFRACTIONr_scbond_it2.8132.9821873
X-RAY DIFFRACTIONr_scbond_other2.8122.9841874
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5624.3322790
X-RAY DIFFRACTIONr_long_range_B_refined8.48549.74116597
X-RAY DIFFRACTIONr_long_range_B_other8.46449.59616432
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 7413 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 85 -
Rwork0.28 1634 -
obs--99.54 %

+
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