[English] 日本語
Yorodumi
- PDB-3h6r: Clitocypin, a beta-trefoil cysteine protease inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3h6r
TitleClitocypin, a beta-trefoil cysteine protease inhibitor
Components(Clitocypin analog) x 2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Clitocypin / cysteine proteinase inhibitor / Kunitz inhibitor / beta trefoil / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homologyProteinase inhibitor I48, clitocypin / Peptidase inhibitor clitocypin / cysteine-type endopeptidase inhibitor activity / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta / Clitocypin-2
Function and homology information
Biological speciesClitocybe nebularis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.948 Å
AuthorsRenko, M. / Sabotic, J. / Brzin, J. / Turk, D.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Versatile loops in mycocypins inhibit three protease families.
Authors: Renko, M. / Sabotic, J. / Mihelic, M. / Brzin, J. / Kos, J. / Turk, D.
History
DepositionApr 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Revision 1.3Feb 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_atoms / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Clitocypin analog
B: Clitocypin analog


Theoretical massNumber of molelcules
Total (without water)33,7202
Polymers33,7202
Non-polymers00
Water5,008278
1
A: Clitocypin analog


Theoretical massNumber of molelcules
Total (without water)16,8111
Polymers16,8111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Clitocypin analog


Theoretical massNumber of molelcules
Total (without water)16,9101
Polymers16,9101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Clitocypin analog

B: Clitocypin analog


Theoretical massNumber of molelcules
Total (without water)33,7202
Polymers33,7202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y+1/2,-z1
Buried area1540 Å2
ΔGint-9 kcal/mol
Surface area13990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.540, 58.000, 58.260
Angle α, β, γ (deg.)90.000, 111.200, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Clitocypin analog


Mass: 16810.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Isolated from fruit bodies / Source: (natural) Clitocybe nebularis (fungus) / References: UniProt: Q3Y9I4
#2: Protein Clitocypin analog


Mass: 16909.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Clitocybe nebularis (fungus) / References: UniProt: Q3Y9I4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.17 Å3/Da / Density % sol: 43.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.76
Details: 50 mM monopotassium dihydrogen phosphate, 20%(w/v) polyethylene glycol 8000, pH 3.76, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.95 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 13, 2005
RadiationMonochromator: Double Crystal Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. all: 21569 / Num. obs: 21089 / % possible obs: 97.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Rmerge(I) obs: 0.026 / Χ2: 0.761 / Net I/σ(I): 63.126
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.098 / Mean I/σ(I) obs: 16.8 / Num. unique all: 1828 / Χ2: 0.727 / % possible all: 85

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.5.0044refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
AMoREphasing
MAINrefinement
RefinementResolution: 1.948→30 Å / Occupancy max: 1 / Occupancy min: 0 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1040 -random
Rwork0.186 ---
all0.196 21074 --
obs0.189 21074 100 %-
Displacement parametersBiso max: 95.89 Å2 / Biso mean: 28.465 Å2 / Biso min: 6.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.265 Å20 Å20.008 Å2
2--0.289 Å20 Å2
3----0.548 Å2
Refinement stepCycle: LAST / Resolution: 1.948→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2388 0 0 278 2666
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.025
X-RAY DIFFRACTIONr_angle_refined_deg2.21
LS refinement shellResolution: 1.948→2.02 Å
RfactorNum. reflection
Rfree0.317 115
Rwork0.23 -
obs-2064

+
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