[English] 日本語
Yorodumi
- PDB-5n7n: CRYSTAL STRUCTURE OF CATHEPSIN D ZYMOGEN FROM THE TICK IXODES RIC... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5n7n
TitleCRYSTAL STRUCTURE OF CATHEPSIN D ZYMOGEN FROM THE TICK IXODES RICINUS (IRCD1)
ComponentsPutative cathepsin d
KeywordsHYDROLASE
Function / homology
Function and homology information


aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
AMMONIUM ION / Putative cathepsin d
Similarity search - Component
Biological speciesIxodes ricinus (castor bean tick)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsBrynda, J. / Hanova, I. / Hobizalova, R. / Mares, M.
CitationJournal: Cell Chem Biol / Year: 2018
Title: Novel Structural Mechanism of Allosteric Regulation of Aspartic Peptidases via an Evolutionarily Conserved Exosite.
Authors: Hanova, I. / Brynda, J. / Houstecka, R. / Alam, N. / Sojka, D. / Kopacek, P. / Maresova, L. / Vondrasek, J. / Horn, M. / Schueler-Furman, O. / Mares, M.
History
DepositionFeb 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Advisory / Database references
Category: citation / citation_author / pdbx_database_PDB_obs_spr
Revision 1.2Mar 28, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative cathepsin d
B: Putative cathepsin d
C: Putative cathepsin d
D: Putative cathepsin d
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,70226
Polymers160,9014
Non-polymers1,80122
Water2,648147
1
A: Putative cathepsin d
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5315
Polymers40,2251
Non-polymers3064
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative cathepsin d
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8208
Polymers40,2251
Non-polymers5947
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative cathepsin d
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7247
Polymers40,2251
Non-polymers4986
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Putative cathepsin d
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6276
Polymers40,2251
Non-polymers4025
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.322, 94.981, 106.170
Angle α, β, γ (deg.)90.00, 99.28, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Putative cathepsin d


Mass: 40225.188 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ixodes ricinus (castor bean tick) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: V5HCK7
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H4N
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.95 Å3/Da / Density % sol: 58.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1:1 PROTEIN (10 MG/ML IN 2 MM BIS- TRIS, PH 6.5, 20 MM SODIUM CHLORIDE) TO RESERVOIR (0.085 M TRIS-HCL, PH 8.0, 1.7 M AMMONIUM SULFATE, 1 MM DTT), CRYOCOOLED IN MOTHER LIQUOR, VAPOR ...Details: 1:1 PROTEIN (10 MG/ML IN 2 MM BIS- TRIS, PH 6.5, 20 MM SODIUM CHLORIDE) TO RESERVOIR (0.085 M TRIS-HCL, PH 8.0, 1.7 M AMMONIUM SULFATE, 1 MM DTT), CRYOCOOLED IN MOTHER LIQUOR, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1.07161 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 30, 2013
RadiationMonochromator: CHANNEL CUT SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07161 Å / Relative weight: 1
ReflectionResolution: 2.3→45.87 Å / Num. obs: 82782 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 14.81
Reflection shellResolution: 2.3→2.44 Å / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2.79 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.3→45.87 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.906 / SU B: 7.849 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.297 / ESU R Free: 0.23 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25999 4145 5 %RANDOM
Rwork0.22017 ---
obs0.22218 78636 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.185 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0 Å2-0.04 Å2
2--0.13 Å20 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 2.3→45.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10963 0 94 147 11204
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01911325
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210348
X-RAY DIFFRACTIONr_angle_refined_deg1.451.97515423
X-RAY DIFFRACTIONr_angle_other_deg0.97323900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.28851441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.82424.557474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.359151729
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1411539
X-RAY DIFFRACTIONr_chiral_restr0.0870.21705
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02112889
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022510
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0964.0035770
X-RAY DIFFRACTIONr_mcbond_other2.0964.0035769
X-RAY DIFFRACTIONr_mcangle_it3.3865.9957206
X-RAY DIFFRACTIONr_mcangle_other3.3865.9967207
X-RAY DIFFRACTIONr_scbond_it2.2354.2065555
X-RAY DIFFRACTIONr_scbond_other2.2274.1945531
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6096.2038180
X-RAY DIFFRACTIONr_long_range_B_refined5.4530.90811619
X-RAY DIFFRACTIONr_long_range_B_other5.4530.91111619
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.301→2.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 287 -
Rwork0.296 5732 -
obs--98.69 %

+
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