[English] 日本語
Yorodumi
- PDB-6k0n: Catalytic domain of GH87 alpha-1,3-glucanase in complex with nigerose -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6k0n
TitleCatalytic domain of GH87 alpha-1,3-glucanase in complex with nigerose
ComponentsAlpha-1,3-glucanase
KeywordsHYDROLASE / GH87 alpha-1 / 3-glucanase / catalytic domain
Function / homology
Function and homology information


carbohydrate binding / metal ion binding
Similarity search - Function
: / CBM6/CBM35/CBM36-like 1 / Alpha-1,3-glucanase catalytic domain D2 / Alpha-1,3-glucanase catalytic domain D1 / CARDB domain / CARDB / Carbohydrate binding module (family 35) / Parallel beta-helix repeat / Parallel beta-helix repeats / CBM6 (carbohydrate binding type-6) domain profile. ...: / CBM6/CBM35/CBM36-like 1 / Alpha-1,3-glucanase catalytic domain D2 / Alpha-1,3-glucanase catalytic domain D1 / CARDB domain / CARDB / Carbohydrate binding module (family 35) / Parallel beta-helix repeat / Parallel beta-helix repeats / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / Pectin lyase fold / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Pectin lyase fold/virulence factor / Galactose-binding-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
alpha-nigerose / ACETIC ACID / Alpha-1,3-glucanase
Similarity search - Component
Biological speciesPaenibacillus glycanilyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsItoh, T. / Intuy, R. / Suyotha, W. / Hayashi, J. / Yano, S. / Makabe, K. / Wakayama, M. / Hibi, T.
CitationJournal: Febs J. / Year: 2020
Title: Structural insights into substrate recognition and catalysis by glycoside hydrolase family 87 alpha-1,3-glucanase from Paenibacillus glycanilyticus FH11.
Authors: Itoh, T. / Intuy, R. / Suyotha, W. / Hayashi, J. / Yano, S. / Makabe, K. / Wakayama, M. / Hibi, T.
History
DepositionMay 7, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.journal_volume ..._chem_comp.type / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_conn_type / 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.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)63,64612
Polymers61,9791
Non-polymers1,66711
Water15,817878
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-32 kcal/mol
Surface area19090 Å2
Unit cell
Length a, b, c (Å)132.656, 132.656, 76.236
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2692-

HOH

21A-2718-

HOH

31A-2957-

HOH

-
Components

-
Protein / Sugars , 2 types, 4 molecules A

#1: Protein Alpha-1,3-glucanase


Mass: 61979.055 Da / Num. of mol.: 1 / Fragment: Catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus glycanilyticus (bacteria)
Gene: agl / Production host: Brevibacillus (bacteria) / References: UniProt: A0A068PS59
#2: Polysaccharide alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose / alpha-nigerose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-nigerose
DescriptorTypeProgram
DGlcpa1-3DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(3+1)][a-D-Glcp]{}}LINUCSPDB-CARE

-
Non-polymers , 4 types, 886 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 878 / 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: 2.77 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.5 M (NH4)2SO4, 25% (v/v) glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→46.82 Å / Num. obs: 89788 / % possible obs: 100 % / Redundancy: 14.3 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 32.5
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.905 / Num. unique obs: 4456

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6K0M

6k0m


Resolution: 1.6→46.82 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.57
RfactorNum. reflection% reflection
Rfree0.1723 4469 4.98 %
Rwork0.1485 --
obs0.1496 89707 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 58.25 Å2 / Biso mean: 16.2637 Å2 / Biso min: 5.13 Å2
Refinement stepCycle: final / Resolution: 1.6→46.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4282 0 103 878 5263
Biso mean--27.37 29.57 -
Num. residues----559
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5997-1.61790.24941400.19872775291598
1.6179-1.63690.20631200.196528062926100
1.6369-1.65690.22491340.187128572991100
1.6569-1.67790.22651410.179227842925100
1.6779-1.70.2021770.182327892966100
1.7-1.72330.19691690.180727672936100
1.7233-1.74790.21361530.176928002953100
1.7479-1.7740.17751440.165728332977100
1.774-1.80170.18041280.162828172945100
1.8017-1.83120.20681590.164427892948100
1.8312-1.86280.17091570.156828202977100
1.8628-1.89670.20031440.155128142958100
1.8967-1.93320.19771550.147428182973100
1.9332-1.97260.19021650.148127852950100
1.9726-2.01550.15231640.138328403004100
2.0155-2.06240.14861460.142528122958100
2.0624-2.1140.17791560.148328122968100
2.114-2.17110.16061490.140228292978100
2.1711-2.2350.17911360.138828392975100
2.235-2.30710.16381460.141228392985100
2.3071-2.38960.18391530.142528473000100
2.3896-2.48530.1831460.146128342980100
2.4853-2.59840.1661380.148728853023100
2.5984-2.73540.18731450.155728653010100
2.7354-2.90670.17041490.154128422991100
2.9067-3.13110.17931230.148229063029100
3.1311-3.44610.15071540.13728833037100
3.4461-3.94450.14641550.125929183073100
3.9445-4.96880.12891500.114129463096100
4.9688-46.83960.18621730.177630873260100

+
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