[English] 日本語
Yorodumi
- PDB-4dfs: Structure of the catalytic domain of an endo-1,3-beta-glucanase (... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4dfs
TitleStructure of the catalytic domain of an endo-1,3-beta-glucanase (laminarinase) from Thermotoga petrophila RKU-1
ComponentsGlycoside hydrolase, family 16
KeywordsHYDROLASE / GH16 / laminarinase / Thermotoga petrophila RKU-1 / beta-jelly roll / glycosyl hydrolase family 16 / sugar / Secreted
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Jelly Rolls - #200 / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Glycoside hydrolase, family 16
Similarity search - Component
Biological speciesThermotoga petrophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.754 Å
AuthorsMeza, A.N. / Ruller, R. / Prade, R.A. / Squina, F.M. / Santos, C.R. / Murakami, M.T.
CitationJournal: To be Published
Title: Structural studies of an endo-1,3-beta-glucanase from Thermotoga petrophila RKU-1
Authors: Meza, A.N. / Ruller, R. / Prade, R.A. / Squina, F.M. / Santos, C.R. / Murakami, M.T.
History
DepositionJan 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_label_asym_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: Glycoside hydrolase, family 16
B: Glycoside hydrolase, family 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5267
Polymers61,1572
Non-polymers3685
Water25214
1
A: Glycoside hydrolase, family 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8114
Polymers30,5791
Non-polymers2323
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycoside hydrolase, family 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7153
Polymers30,5791
Non-polymers1362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)130.036, 130.036, 141.466
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Glycoside hydrolase, family 16 /


Mass: 30578.641 Da / Num. of mol.: 2 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga petrophila (bacteria) / Strain: RKU-1 / ATCC BAA-488 / DSM 13995 / Gene: Tpet_0899 / Production host: Escherichia coli (E. coli) / References: UniProt: A5IL44
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 5.65 Å3/Da / Density % sol: 78.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 200 mM Hepes, 1.8 M ammonium sulphate, 100 mM sodium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.458 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 1, 2011
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.458 Å / Relative weight: 1
ReflectionResolution: 3.75→38.2 Å / Num. obs: 14073 / % possible obs: 95.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0
Reflection shellResolution: 3.75→3.88 Å / % possible all: 98

-
Processing

Software
NameVersionClassification
NatXraysoftwaredata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1AZX

1azx


Resolution: 3.754→36.152 Å / SU ML: 0.26 / σ(F): 0 / Phase error: 21.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2403 706 5.02 %RANDOM
Rwork0.202 ---
obs0.2038 14073 96.86 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 86.499 Å2 / ksol: 0.339 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.337 Å2-0 Å20 Å2
2--0.337 Å20 Å2
3----0.6739 Å2
Refinement stepCycle: LAST / Resolution: 3.754→36.152 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4082 0 17 14 4113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034235
X-RAY DIFFRACTIONf_angle_d0.6355771
X-RAY DIFFRACTIONf_dihedral_angle_d11.1021478
X-RAY DIFFRACTIONf_chiral_restr0.044566
X-RAY DIFFRACTIONf_plane_restr0.003752
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.754-4.04330.28971810.24472671X-RAY DIFFRACTION100
4.0433-4.44960.17671420.14812711X-RAY DIFFRACTION100
4.4496-5.09190.21021440.15122685X-RAY DIFFRACTION98
5.0919-6.40940.25551280.22262698X-RAY DIFFRACTION97
6.4094-36.15380.26521110.23182602X-RAY DIFFRACTION90

+
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