[English] 日本語
Yorodumi
- PDB-3dgt: The 1.5 A crystal structure of endo-1,3-beta-glucanase from Strep... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3dgt
TitleThe 1.5 A crystal structure of endo-1,3-beta-glucanase from Streptomyces sioyaensis
ComponentsEndo-1,3-beta-glucanase
KeywordsHYDROLASE / GHF16 / 1 / 3-beta-glucanase
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process / metal ion binding
Similarity search - Function
: / Cellulose binding, type IV / Cellulose Binding Domain Type IV / Glycosyl hydrolases family 16 / Carbohydrate binding module (family 6) / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Twin arginine translocation (Tat) signal profile. ...: / Cellulose binding, type IV / Cellulose Binding Domain Type IV / Glycosyl hydrolases family 16 / Carbohydrate binding module (family 6) / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Jelly Rolls - #200 / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Endo-1,3-beta-glucanase
Similarity search - Component
Biological speciesStreptomyces sioyaensis (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.5 Å
AuthorsLi, T.H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: The 1.5 A structure of endo-1,3-beta-glucanase from Streptomyces sioyaensis: evolution of the active-site structure for 1,3-beta-glucan-binding specificity and hydrolysis
Authors: Hong, T.-Y. / Hsiao, Y.-Y. / Meng, M. / Li, T.T.
History
DepositionJun 16, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endo-1,3-beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4062
Polymers29,3821
Non-polymers241
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.509, 75.967, 79.663
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Endo-1,3-beta-glucanase


Mass: 29382.033 Da / Num. of mol.: 1 / Fragment: catalytic domain, UNP residues 49-321
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sioyaensis (bacteria) / Plasmid: PUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner(DE3)
References: UniProt: Q9L816, glucan endo-1,3-beta-D-glucosidase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHERE ARE CONFLICTS BETWEEN THE GIVEN SEQUENCE AND THE DATABASE REFERENCE SEQUENCE. THESE RESIDUES ...THERE ARE CONFLICTS BETWEEN THE GIVEN SEQUENCE AND THE DATABASE REFERENCE SEQUENCE. THESE RESIDUES IDENTIFIED IN THE STRUCTURE DETERMINTION WORK SOULD BE THE CORRECT SEQUENCE OF THE PROTEIN. THE DEPOSITORS ALSO DID THE SEQUENCING OF THE PLASMID AND CONFIRMED THESE RESIDUE SEQUENCES ARE CONSISTENT WITH THE X-RAY STRUCTURE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.54 %
Crystal growTemperature: 278 K / Method: microseeding method / pH: 7.5
Details: 25% PEG MME 2000, 100mM Hepes pH 7.5, 10mM MgCl2, 0.01% NaN3, microseeding method, temperature 278K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE
RadiationMonochromator: MSC blue-optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 38840 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 10.246 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 34.8
Reflection shellResolution: 1.5→1.57 Å / Redundancy: 3.39 % / Rmerge(I) obs: 0.098 / Mean I/σ(I) obs: 14.4 / Num. unique all: 4632 / % possible all: 96.3

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.5→19.75 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.939 / SU B: 1.016 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19832 1949 5 %RANDOM
Rwork0.18284 ---
obs0.18361 36838 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.559 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2053 0 1 150 2204
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212117
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2441.9162901
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8825277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.26824.62493
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.49115274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.983159
X-RAY DIFFRACTIONr_chiral_restr0.0820.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021701
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.21005
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21459
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.080.2128
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0640.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4761.51393
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.81122196
X-RAY DIFFRACTIONr_scbond_it1.2493849
X-RAY DIFFRACTIONr_scangle_it1.6424.5705
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.184 153 -
Rwork0.158 2559 -
obs--95.19 %

+
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