[English] 日本語
Yorodumi
- PDB-5b6t: Catalytic domain of Coprinopsis cinerea GH62 alpha-L-arabinofuran... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5b6t
TitleCatalytic domain of Coprinopsis cinerea GH62 alpha-L-arabinofuranosidase complexed with Pb
ComponentsGlycosyl hydrolase family 62 protein
KeywordsHYDROLASE / Coprinopsis cinerea / alpha-L-arabinofuranosidase / arabinoxylan / GH62 / hemicellulose
Function / homology
Function and homology information


L-arabinose metabolic process / non-reducing end alpha-L-arabinofuranosidase / alpha-L-arabinofuranosidase activity / cellulose binding / xylan catabolic process / extracellular region / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 62, arabinosidase / Glycosyl hydrolase family 62 / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / Glycosyl hydrolase domain; family 43 / 5 Propeller ...Glycoside hydrolase, family 62, arabinosidase / Glycosyl hydrolase family 62 / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Mainly Beta
Similarity search - Domain/homology
LEAD (II) ION / Alpha-L-arabinofuranosidase
Similarity search - Component
Biological speciesCoprinopsis cinerea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsTonozuka, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science16K07687 Japan
CitationJournal: Appl. Biochem. Biotechnol. / Year: 2017
Title: Structure of the Catalytic Domain of alpha-L-Arabinofuranosidase from Coprinopsis cinerea, CcAbf62A, Provides Insights into Structure-Function Relationships in Glycoside Hydrolase Family 62
Authors: Tonozuka, T. / Tanaka, Y. / Okuyama, S. / Miyazaki, T. / Nishikawa, A. / Yoshida, M.
History
DepositionJun 1, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Feb 15, 2017Group: Database references
Revision 1.3Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycosyl hydrolase family 62 protein
B: Glycosyl hydrolase family 62 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,12111
Polymers73,2812
Non-polymers8409
Water11,151619
1
A: Glycosyl hydrolase family 62 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2567
Polymers36,6401
Non-polymers6166
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-0 kcal/mol
Surface area12230 Å2
MethodPISA
2
B: Glycosyl hydrolase family 62 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8654
Polymers36,6401
Non-polymers2243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.854, 77.765, 74.458
Angle α, β, γ (deg.)90.00, 93.01, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Glycosyl hydrolase family 62 protein / alpha-L-arabinofuranosidase


Mass: 36640.316 Da / Num. of mol.: 2 / Fragment: UNP residues 82-397
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coprinopsis cinerea (strain Okayama-7 / 130 / ATCC MYA-4618 / FGSC 9003) (fungus)
Strain: Okayama-7 / 130 / ATCC MYA-4618 / FGSC 9003 / Gene: CC1G_01577 / Plasmid: pET21a / Production host: Escherichia coli (E. coli)
References: UniProt: A8NI40, non-reducing end alpha-L-arabinofuranosidase
#2: Chemical ChemComp-PB / LEAD (II) ION


Mass: 207.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pb
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 619 / 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: 1.89 Å3/Da / Density % sol: 34.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: MES buffer, NaBr, PEG 20000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.95064 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95064 Å / Relative weight: 1
ReflectionResolution: 1.48→27.63 Å / Num. obs: 321802 / % possible obs: 99.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 24.5
Reflection shellResolution: 1.48→1.53 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 3.8 / % possible all: 97.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N4B

4n4b


Resolution: 1.48→27.63 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.281 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.069 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17434 4455 5 %RANDOM
Rwork0.1504 ---
obs0.15162 84386 97.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 11.522 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.48→27.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5014 0 39 619 5672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195230
X-RAY DIFFRACTIONr_bond_other_d0.0010.024625
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.927138
X-RAY DIFFRACTIONr_angle_other_deg0.804310593
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5815640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.12723.308266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.2515735
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6821539
X-RAY DIFFRACTIONr_chiral_restr0.0940.2726
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216137
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021382
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_it0.7561.0482542
X-RAY DIFFRACTIONr_mcbond_other0.7551.0482541
X-RAY DIFFRACTIONr_mcangle_it1.2321.5713176
X-RAY DIFFRACTIONr_mcangle_other1.2321.5713177
X-RAY DIFFRACTIONr_scbond_it1.1941.1262688
X-RAY DIFFRACTIONr_scbond_other1.1941.1262688
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8361.6493959
X-RAY DIFFRACTIONr_long_range_B_refined3.6889.3746439
X-RAY DIFFRACTIONr_long_range_B_other3.4938.946168
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.48→1.518 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 294 -
Rwork0.243 5758 -
obs--90.67 %

+
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