[English] 日本語
Yorodumi
- PDB-5m60: Chaetomium thermophilum beta-1-3-glucanase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5m60
TitleChaetomium thermophilum beta-1-3-glucanase
ComponentsBeta-1,3-glucanase
KeywordsTRANSFERASE / cellulose / glucanase / fungus / thermostability / glucans
Function / homology
Function and homology information


polygalacturonase activity
Similarity search - Function
Polygalacturonase QRT3-like / Pectate lyase superfamily protein / Pectate lyase superfamily protein / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
beta-D-glucopyranose / Beta-1,3-glucanase / Exo-beta-1,3-glucanase-like protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å
AuthorsPapageorgiou, A.C. / Chen, J. / Li, D.
Citation
Journal: Biochim. Biophys. Acta / Year: 2017
Title: Crystal structure and biological implications of a glycoside hydrolase family 55 beta-1,3-glucanase from Chaetomium thermophilum.
Authors: Papageorgiou, A.C. / Chen, J. / Li, D.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Expression, purification and crystallization of a family 55 beta-1,3-glucanase from Chaetomium thermophilum.
Authors: Papageorgiou, A.C. / Li, D.
History
DepositionOct 23, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Mar 11, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Polymer sequence
Category: atom_site / chem_comp ...atom_site / chem_comp / entity_poly / pdbx_nonpoly_scheme / pdbx_validate_close_contact
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_validate_close_contact.auth_seq_id_2
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-1,3-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2055
Polymers82,1531
Non-polymers1,0524
Water12,502694
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint7 kcal/mol
Surface area23210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.661, 83.535, 65.171
Angle α, β, γ (deg.)90.00, 93.10, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Beta-1,3-glucanase


Mass: 82152.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Pyroglutamic acid as first residue in the structure owing to post-translational modification of glutamine at the N-terminal
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: gluN / Production host: Komagataella pastoris (fungus) / References: UniProt: D8UU87, UniProt: G0S3N2*PLUS
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Mass: 424.401 Da / Num. of mol.: 2
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-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-BGC / beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 694 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.6 % / Description: Rods
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 1.8 M Na/K phosphate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.5→44.3 Å / Num. obs: 106298 / % possible obs: 99.8 % / Redundancy: 4.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.009 / Net I/σ(I): 10.3
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.765 / Mean I/σ(I) obs: 1.8 / CC1/2: 0.582 / % possible all: 96.4

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.5→44.291 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.91
RfactorNum. reflection% reflectionSelection details
Rfree0.1816 5337 5.02 %Random
Rwork0.157 ---
obs0.1582 106263 97.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→44.291 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5777 0 69 694 6540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066137
X-RAY DIFFRACTIONf_angle_d0.8658424
X-RAY DIFFRACTIONf_dihedral_angle_d12.1983615
X-RAY DIFFRACTIONf_chiral_restr0.059931
X-RAY DIFFRACTIONf_plane_restr0.0061124
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.51710.29351800.27153337X-RAY DIFFRACTION96
1.5171-1.53490.29941520.26383279X-RAY DIFFRACTION97
1.5349-1.55360.27361810.24793316X-RAY DIFFRACTION96
1.5536-1.57330.27041540.24073305X-RAY DIFFRACTION97
1.5733-1.5940.26431710.22983314X-RAY DIFFRACTION96
1.594-1.61580.24761610.22773349X-RAY DIFFRACTION97
1.6158-1.63890.25311800.22213315X-RAY DIFFRACTION96
1.6389-1.66340.27221690.22223318X-RAY DIFFRACTION97
1.6634-1.68940.23681810.22173276X-RAY DIFFRACTION96
1.6894-1.71710.25571570.19773383X-RAY DIFFRACTION97
1.7171-1.74670.22331900.19713296X-RAY DIFFRACTION98
1.7467-1.77840.22371910.19313325X-RAY DIFFRACTION97
1.7784-1.81270.2151920.17933386X-RAY DIFFRACTION97
1.8127-1.84970.20761750.17223343X-RAY DIFFRACTION98
1.8497-1.88990.2061900.16673312X-RAY DIFFRACTION97
1.8899-1.93380.18091690.16323371X-RAY DIFFRACTION97
1.9338-1.98220.19581650.15713375X-RAY DIFFRACTION98
1.9822-2.03580.16591870.15163382X-RAY DIFFRACTION98
2.0358-2.09570.18111830.1493328X-RAY DIFFRACTION98
2.0957-2.16330.1531910.14053374X-RAY DIFFRACTION98
2.1633-2.24070.16531840.13923373X-RAY DIFFRACTION98
2.2407-2.33040.18441530.14313448X-RAY DIFFRACTION99
2.3304-2.43640.1791700.1463383X-RAY DIFFRACTION99
2.4364-2.56480.1821780.14763398X-RAY DIFFRACTION98
2.5648-2.72550.16731970.14473400X-RAY DIFFRACTION99
2.7255-2.93590.15521850.14283423X-RAY DIFFRACTION99
2.9359-3.23130.17161930.13823427X-RAY DIFFRACTION99
3.2313-3.69870.14621910.12193435X-RAY DIFFRACTION99
3.6987-4.65910.12431850.11113450X-RAY DIFFRACTION99
4.6591-44.31070.17041820.16113505X-RAY DIFFRACTION99

+
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://pdbjlc1.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