[English] 日本語
Yorodumi
- PDB-6ycc: Structure the ananain protease from Ananas comosus covalently bou... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ycc
TitleStructure the ananain protease from Ananas comosus covalently bound to the E64 inhibitor
ComponentsAnanain
KeywordsHYDROLASE / cysteine protease / stem bromelain protein
Function / homology
Function and homology information


ananain / cysteine-type peptidase activity / proteolysis
Similarity search - Function
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesAnanas comosus (pineapple)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsAzarkan, M. / Charlier, P. / Herman, R. / Delbrassine, F. / Sauvage, E. / M Rabet, N. / Calvo Esposito, R. / Kerff, F.
CitationJournal: Sci Rep / Year: 2020
Title: Structures of the free and inhibitors-bound forms of bromelain and ananain from Ananas comosus stem and in vitro study of their cytotoxicity.
Authors: Azarkan, M. / Maquoi, E. / Delbrassine, F. / Herman, R. / M'Rabet, N. / Calvo Esposito, R. / Charlier, P. / Kerff, F.
History
DepositionMar 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ananain
B: Ananain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,28711
Polymers46,9052
Non-polymers1,3819
Water8,053447
1
A: Ananain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0975
Polymers23,4531
Non-polymers6454
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ananain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1896
Polymers23,4531
Non-polymers7375
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.324, 59.486, 119.061
Angle α, β, γ (deg.)90.000, 92.860, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Ananain


Mass: 23452.572 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ananas comosus (pineapple) / References: UniProt: P80884, ananain
#2: Chemical ChemComp-E64 / N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE


Mass: 360.429 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H30N5O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 447 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 0.5 M Li2SO4, 0.1 M citrate buffer at pH 5.6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.3→118.913 Å / Num. all: 114958 / Num. obs: 114958 / % possible obs: 97.7 % / Redundancy: 6.2 % / Rpim(I) all: 0.044 / Rrim(I) all: 0.115 / Rsym value: 0.106 / Net I/av σ(I): 3.3 / Net I/σ(I): 8.3 / Num. measured all: 714869
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.3-1.375.10.5831.380007156490.2710.6460.5832.191.3
1.37-1.455.60.421.887352155490.1890.4630.423.196.2
1.45-1.5560.2892.589734149570.1260.3160.2894.698.2
1.55-1.686.40.223.189767139910.0930.240.226.498.9
1.68-1.846.60.1733.885773129620.0720.1870.1738.599.3
1.84-2.066.70.1374.678931118030.0570.1490.13711.399.6
2.06-2.376.80.1175.170637104580.0480.1270.1171499.9
2.37-2.916.80.1045.76015688590.0430.1120.10415.5100
2.91-4.116.80.0826.44691168710.0340.0880.08217.8100
4.11-39.6386.60.07172560138590.030.0770.07117.199.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
SCALA3.3.16data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Y6L

6y6l


Resolution: 1.3→34.281 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 16.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1685 5763 5.02 %
Rwork0.1441 109087 -
obs0.1453 114850 97.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.68 Å2 / Biso mean: 19.0257 Å2 / Biso min: 7.93 Å2
Refinement stepCycle: final / Resolution: 1.3→34.281 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3284 0 168 447 3899
Biso mean--26.25 29.48 -
Num. residues----430
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3-1.31480.28371620.263309383
1.3148-1.33030.25811810.2232338092
1.3303-1.34650.24581890.2066350894
1.3465-1.36350.23681670.1904347394
1.3635-1.38150.23111640.1832351694
1.3815-1.40040.21491860.1754355896
1.4004-1.42040.20432040.1664357896
1.4204-1.44160.20442010.1546357797
1.4416-1.46410.19891950.1551360598
1.4641-1.48810.20591990.1483362097
1.4881-1.51380.17772370.1464356799
1.5138-1.54130.16451860.1451364598
1.5413-1.5710.18822100.1377364798
1.571-1.6030.17481900.1359368799
1.603-1.63790.16932090.1364370199
1.6379-1.6760.16792110.1284363199
1.676-1.71790.17931850.1279374199
1.7179-1.76430.14281850.1291361499
1.7643-1.81630.15872070.1289374399
1.8163-1.87490.17431900.13123659100
1.8749-1.94190.13961800.12553727100
1.9419-2.01960.15811930.12643789100
2.0196-2.11150.1671960.1283665100
2.1115-2.22280.15951890.12773726100
2.2228-2.36210.15611820.12973740100
2.3621-2.54440.17611760.14013764100
2.5444-2.80030.16391850.14433752100
2.8003-3.20530.16442130.14723743100
3.2053-4.03730.13761720.13663816100
4.0373-34.2810.17172190.17033822100

+
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