[English] 日本語
Yorodumi
- PDB-1fn8: FUSARIUM OXYSPORUM TRYPSIN AT ATOMIC RESOLUTION -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fn8
TitleFUSARIUM OXYSPORUM TRYPSIN AT ATOMIC RESOLUTION
Components
  • GLY-ALA-ARG
  • TRYPSIN
KeywordsHYDROLASE/HYDROLASE SUBSTRATE / beta barrel / HYDROLASE / HYDROLASE-HYDROLASE SUBSTRATE COMPLEX
Function / homology
Function and homology information


trypsin / serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin ...: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / 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
Biological speciesFusarium oxysporum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 0.81 Å
AuthorsRypniewski, W.R. / Oestergaard, P. / Noerregaard-Madsen, M. / Dauter, M. / Wilson, K.S.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Fusarium oxysporum trypsin at atomic resolution at 100 and 283 K: a study of ligand binding.
Authors: Rypniewski, W.R. / Ostergaard, P.R. / Norregaard-Madsen, M. / Dauter, M. / Wilson, K.S.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Structure of inhibited trypsin from Fusarium oxysporum at 1.55A
Authors: Rypniewski, W.R. / Dambmann, C. / von der Osten, C. / Dauter, M. / Wilson, K.S.
History
DepositionAug 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Oct 30, 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 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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: TRYPSIN
B: GLY-ALA-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9687
Polymers22,5042
Non-polymers4645
Water7,224401
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.146, 36.696, 39.556
Angle α, β, γ (deg.)102.09, 104.75, 103.01
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein TRYPSIN


Mass: 22200.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Fusarium oxysporum (fungus) / References: UniProt: P35049, trypsin
#2: Protein/peptide GLY-ALA-ARG


Mass: 303.339 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 1.93 Å3/Da / Density % sol: 36.31 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6
Details: sodium sulphate, sodium citrate, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal grow
*PLUS
pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125 Mprotein1drop
210 mM3,3-dimethyl glutaric acid1drop
32 mM1dropCaCl2
4100 mM1dropNaCl
51.4 M1reservoirNa2SO4
60.1 Msodium citrate1reservoir
70-5 %2-propanol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8468
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8468 Å / Relative weight: 1
ReflectionResolution: 0.81→20 Å / Num. all: 990347 / Num. obs: 990347 / % possible obs: 92.6 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 7 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 21
Reflection shellResolution: 0.81→0.82 Å / Redundancy: 2 % / Rmerge(I) obs: 0.38 / Num. unique all: 7036 / % possible all: 83
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 158550 / Num. measured all: 990347
Reflection shell
*PLUS
% possible obs: 82.5 %

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementResolution: 0.81→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: least-squares refinement against I's. Full-matrix least-squares at the end to obtain error estimates
RfactorNum. reflection% reflectionSelection details
Rwork0.1085 ---
all0.1085 158550 --
obs0.1085 158550 92.6 %-
Rfree---not used
Refinement stepCycle: LAST / Resolution: 0.81→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1577 0 29 401 2007
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.015
X-RAY DIFFRACTIONs_bond_d0.035
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_chiral_restr0.095
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.035

+
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