[English] 日本語
Yorodumi
- PDB-6yon: Crystal structure of Endoglucanase S127C/A165C from Penicillium v... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6yon
TitleCrystal structure of Endoglucanase S127C/A165C from Penicillium verruculosum
ComponentsEndoglucanase
KeywordsHYDROLASE / ENDOHYDROLYSIS / CELLULOSE
Function / homologyglucan catabolic process / cellulase / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / hydrolase activity, hydrolyzing O-glycosyl compounds / Glycoside hydrolase superfamily / cellulase
Function and homology information
Biological speciesTalaromyces verruculosus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsNemashkalov, V. / Kravchenko, O. / Gabdulkhakov, A. / Tischenko, S. / Rozhkova, A. / Sinitsyn, A.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation Russian Federation
CitationJournal: To Be Published
Title: Crystal structure of Endoglucanase S127C/A165C from Penicillium verruculosum
Authors: Nemashkalov, V. / Kravchenko, O. / Gabdulkhakov, A. / Tischenko, S. / Rozhkova, A. / Sinitsyn, A.
History
DepositionApr 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endoglucanase
B: Endoglucanase
C: Endoglucanase
D: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,85812
Polymers138,7764
Non-polymers2,0828
Water25214
1
A: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2143
Polymers34,6941
Non-polymers5202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2143
Polymers34,6941
Non-polymers5202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2143
Polymers34,6941
Non-polymers5202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2143
Polymers34,6941
Non-polymers5202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.500, 85.690, 91.150
Angle α, β, γ (deg.)90.00, 89.99, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Endoglucanase


Mass: 34693.934 Da / Num. of mol.: 4 / Mutation: S127C/A165C
Source method: isolated from a genetically manipulated source
Details: ANSKEVKKRASSFEWFGSNESGAEFGSGNIPGVEGTDYTFPNTTAIQILIDAGMNIFRVPFLMERMIPTEMTGSLDTAYF EGYSEVINYITGKGAHAVVDPHNFGRYYGTPISSTSDFQTFWSTLASQFKSNDLVIFDTNNEYHDMDESVVVALNQAAID ...Details: ANSKEVKKRASSFEWFGSNESGAEFGSGNIPGVEGTDYTFPNTTAIQILIDAGMNIFRVPFLMERMIPTEMTGSLDTAYF EGYSEVINYITGKGAHAVVDPHNFGRYYGTPISSTSDFQTFWSTLASQFKSNDLVIFDTNNEYHDMDESVVVALNQAAID GIRDAGATTQYIFVEGNAYSGAWTWTTYNTAMVNLTDPSDLIVYEMHQYLDSAGSGTSDQCVSSTVGQERVVDATTWLQS NGKLGILGEFAGGANSVCEEAVEGMLDYLAENSDVWLGASWWSAGPWWQDYIYSMEPPNGIAYESYLSILETYF
Source: (gene. exp.) Talaromyces verruculosus (fungus) / Production host: Penicillium canescens (fungus) / References: UniProt: A0A1U7Q1U3
#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpN]{[(2+1)][ethyl]{}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / Details: PEG 6000,Bis-Tris-Propane, MPD, tert-butanol

-
Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.978565037251 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565037251 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.384
11-h,-k,l20.616
ReflectionResolution: 2.4→49.34 Å / Num. obs: 48284 / % possible obs: 99.24 % / Redundancy: 4.08 % / CC1/2: 0.994 / Net I/σ(I): 5.15
Reflection shellResolution: 2.4→2.46 Å / Num. unique obs: 3354 / CC1/2: 0.683

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I6S

5i6s


Resolution: 2.6→49.34 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.893 / SU B: 12.569 / SU ML: 0.276 / Cross valid method: THROUGHOUT / ESU R Free: 0.085 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29197 1911 5 %RANDOM
Rwork0.23639 ---
obs0.23923 36235 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.506 Å2
Baniso -1Baniso -2Baniso -3
1--35.43 Å2-0 Å2-5.97 Å2
2--81.56 Å20 Å2
3----46.14 Å2
Refinement stepCycle: 1 / Resolution: 2.6→49.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9488 0 131 14 9633
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0139942
X-RAY DIFFRACTIONr_bond_other_d0.0020.0188250
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.65113614
X-RAY DIFFRACTIONr_angle_other_deg1.2591.57919216
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0551220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.75524.652503
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.659151388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5671520
X-RAY DIFFRACTIONr_chiral_restr0.0660.21319
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211419
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022160
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_it3.4764.6634889
X-RAY DIFFRACTIONr_mcbond_other3.4724.6624888
X-RAY DIFFRACTIONr_mcangle_it5.3136.9896106
X-RAY DIFFRACTIONr_mcangle_other5.3146.996107
X-RAY DIFFRACTIONr_scbond_it3.0844.6735053
X-RAY DIFFRACTIONr_scbond_other3.0834.6765038
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6516.9987485
X-RAY DIFFRACTIONr_long_range_B_refined7.14954.03411646
X-RAY DIFFRACTIONr_long_range_B_other7.14454.03411646
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å
RfactorNum. reflection% reflection
Rfree0.34 139 -
Rwork0.338 2619 -
obs--98.68 %

+
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