[English] 日本語
Yorodumi
- PDB-3n0k: Proteinase inhibitor from Coprinopsis cinerea -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3n0k
TitleProteinase inhibitor from Coprinopsis cinerea
ComponentsSerine protease inhibitor 1
KeywordsHydrolase Inhibitor / Proteinase inhibitor
Function / homologyPeptidase inhibitor I66 / Peptidase inhibitor I66 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / serine-type endopeptidase inhibitor activity / Mainly Beta / Serine protease inhibitor 1
Function and homology information
Biological speciesCoprinopsis cinerea (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRenko, M. / Sabotic, J. / Bleuler-Martinez, S. / Kallert, S. / Avanzo, P. / Kos, J. / Aebi, M. / Kuenzler, M. / Turk, D.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural Basis of Trypsin Inhibition and Entomotoxicity of Cospin, Serine Protease Inhibitor Involved in Defense of Coprinopsis cinerea Fruiting Bodies.
Authors: Sabotic, J. / Bleuler-Martinez, S. / Renko, M. / Avanzo Caglic, P. / Kallert, S. / Strukelj, B. / Turk, D. / Aebi, M. / Kos, J. / Kunzler, M.
History
DepositionMay 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 7, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software
Revision 1.4Feb 21, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine protease inhibitor 1


Theoretical massNumber of molelcules
Total (without water)16,7311
Polymers16,7311
Non-polymers00
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.631, 38.192, 55.078
Angle α, β, γ (deg.)90.000, 96.870, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-237-

HOH

-
Components

#1: Protein Serine protease inhibitor 1


Mass: 16730.748 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coprinopsis cinerea (fungus) / Plasmid: pet24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D0EWJ0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.45 Å3/Da / Density % sol: 49.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M MES buffer, 20% MPD, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 10, 2009 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→16.87 Å / Num. all: 15292 / Num. obs: 14500 / % possible obs: 95 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.1 % / Rmerge(I) obs: 0.034 / Χ2: 2.396 / Net I/σ(I): 51.3
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.115 / Num. unique all: 621 / Χ2: 3.508 / % possible all: 83.4

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
AMoREphasing
MAINrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→16.87 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.215 / WRfactor Rwork: 0.185 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.88 / SU B: 2.207 / SU ML: 0.071 / SU R Cruickshank DPI: 0.133 / SU Rfree: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.194 727 5 %RANDOM
Rwork0.168 ---
obs0.169 14500 94.84 %-
all-15292 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 66.86 Å2 / Biso mean: 23.282 Å2 / Biso min: 8.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å2-0 Å2-0.59 Å2
2---0.07 Å2-0 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.8→16.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1180 0 0 251 1431
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221203
X-RAY DIFFRACTIONr_angle_refined_deg1.7611.9631645
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0985148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.80725.08857
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55815190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.102156
X-RAY DIFFRACTIONr_chiral_restr0.1430.2181
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022940
X-RAY DIFFRACTIONr_mcbond_it1.2011.5749
X-RAY DIFFRACTIONr_mcangle_it2.04921221
X-RAY DIFFRACTIONr_scbond_it2.9673454
X-RAY DIFFRACTIONr_scangle_it4.8724.5424
LS refinement shellResolution: 1.8→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 41 -
Rwork0.285 914 -
all-955 -
obs--86.11 %

+
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://pdbjlvh1.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