[English] 日本語
Yorodumi
- PDB-1euf: BOVINE DUODENASE(NEW SERINE PROTEASE), CRYSTAL STRUCTURE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1euf
TitleBOVINE DUODENASE(NEW SERINE PROTEASE), CRYSTAL STRUCTURE
ComponentsDUODENASE
KeywordsHYDROLASE / bovine duodenase / serine protease / dual specificity
Function / homology
Function and homology information


granzyme-mediated apoptotic signaling pathway / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity / cytoplasm
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Duodenase-1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsPletnev, V.Z. / Zamolodchikova, T.S. / Pangborn, W.A. / Duax, W.L.
CitationJournal: Proteins / Year: 2000
Title: Crystal structure of bovine duodenase, a serine protease, with dual trypsin and chymotrypsin-like specificities.
Authors: Pletnev, V.Z. / Zamolodchikova, T.S. / Pangborn, W.A. / Duax, W.L.
History
DepositionApr 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DUODENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4733
Polymers25,1571
Non-polymers3162
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.117, 100.117, 39.753
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11A-368-

HOH

-
Components

#1: Protein DUODENASE


Mass: 25156.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: BRUNNER'S GLAND
References: UniProt: P80219, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.28 Å3/Da / Density % sol: 46.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: PEG 3350, K/Na phosphate, NaN3, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Details: Zamolodchikova, T.S., (1997) Eur. J. Biochem., 249, 612.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
210 %PEG33501drop
350 mMK/Na phosphate1drop
41 mM1dropNaN3
514 %satPEG33501reservoir

-
Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 4, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→99 Å / Num. all: 9001 / Num. obs: 8780 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 14.3
Reflection shellResolution: 2.4→2.51 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.247 / Num. unique all: 1150 / % possible all: 97.3
Reflection
*PLUS
Num. measured all: 87183
Reflection shell
*PLUS
% possible obs: 97.3 %

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementResolution: 2.4→99 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Cross-validated maximum likelihood simulated annealing refinement (CNS package)
RfactorNum. reflection% reflectionSelection details
Rfree0.223 928 -Random
Rwork0.179 ---
all-9001 --
obs-8780 97.5 %-
Refinement stepCycle: LAST / Resolution: 2.4→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1728 0 19 69 1816
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_torsion_deg24.67
X-RAY DIFFRACTIONc_torsion_impr_deg0.83
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.67

+
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