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- PDB-5n70: CRYSTAL STRUCTURE OF MATURE CATHEPSIN D FROM THE TICK IXODES RICI... -

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Basic information

Entry
Database: PDB / ID: 5n70
TitleCRYSTAL STRUCTURE OF MATURE CATHEPSIN D FROM THE TICK IXODES RICINUS (IRCD1) IN COMPLEX WITH THE N-TERMINAL OCTAPEPTIDE OF THE PROPEPTID
Components
  • ALA-PHE-ARG-ILE-PRO-LEU-THR-ARG
  • Putative cathepsin d
KeywordsHYDROLASE
Function / homology
Function and homology information


aspartic-type endopeptidase activity / lysosome / 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
Cathepsin D-like aspartic protease / Putative cathepsin d
Similarity search - Component
Biological speciesIxodes ricinus (castor bean tick)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.81 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 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation / citation_author
Revision 1.2Mar 28, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative cathepsin d
B: ALA-PHE-ARG-ILE-PRO-LEU-THR-ARG


Theoretical massNumber of molelcules
Total (without water)38,5902
Polymers38,5902
Non-polymers00
Water1,67593
1
A: Putative cathepsin d


Theoretical massNumber of molelcules
Total (without water)37,6151
Polymers37,6151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ALA-PHE-ARG-ILE-PRO-LEU-THR-ARG


Theoretical massNumber of molelcules
Total (without water)9751
Polymers9751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.925, 63.925, 80.496
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Putative cathepsin d


Mass: 37615.113 Da / Num. of mol.: 1
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: Protein/peptide ALA-PHE-ARG-ILE-PRO-LEU-THR-ARG


Mass: 975.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Ixodes ricinus (castor bean tick) / References: UniProt: A4GTA5*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: CRYSTALLIZATION CONDITIONS: 1:1 PROTEIN (5 MG/ML IN 5 MM TRIS-HCL, REMARK 280 PH 7.0, 10% DMSO) TO RESERVOIR (0.2 M SODIUM ACETATE, 0.1 M SODIUM CACODYLATE, PH 6.5, 30% PEG8000), CRYOCOOLED ...Details: CRYSTALLIZATION CONDITIONS: 1:1 PROTEIN (5 MG/ML IN 5 MM TRIS-HCL, REMARK 280 PH 7.0, 10% DMSO) TO RESERVOIR (0.2 M SODIUM ACETATE, 0.1 M SODIUM CACODYLATE, PH 6.5, 30% PEG8000), CRYOCOOLED AFTER A QUICK SOAK IN RESERVOIR BUFFER + 25% GLYCEROL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.979402 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2013
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979402 Å / Relative weight: 1
ReflectionResolution: 1.8→45.2 Å / Num. obs: 30080 / % possible obs: 99.4 % / Redundancy: 6 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 16.18
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.43 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.81→45.2 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.294 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.133 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23094 1479 5 %RANDOM
Rwork0.18312 ---
obs0.18554 28087 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.517 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å2-0 Å20 Å2
2--0.18 Å20 Å2
3----0.37 Å2
Refinement stepCycle: 1 / Resolution: 1.81→45.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2632 0 0 93 2725
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192729
X-RAY DIFFRACTIONr_bond_other_d0.0020.022518
X-RAY DIFFRACTIONr_angle_refined_deg1.6581.9723722
X-RAY DIFFRACTIONr_angle_other_deg1.0135828
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1985353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.06924.649114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5215423
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.969159
X-RAY DIFFRACTIONr_chiral_restr0.10.2411
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213130
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02601
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_it3.1633.8331396
X-RAY DIFFRACTIONr_mcbond_other3.163.8321395
X-RAY DIFFRACTIONr_mcangle_it4.5335.7381744
X-RAY DIFFRACTIONr_mcangle_other4.5335.7391745
X-RAY DIFFRACTIONr_scbond_it3.6364.0821333
X-RAY DIFFRACTIONr_scbond_other3.6364.0831333
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5525.9921973
X-RAY DIFFRACTIONr_long_range_B_refined7.36430.3152909
X-RAY DIFFRACTIONr_long_range_B_other7.36430.332910
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.806→1.852 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 101 -
Rwork0.246 1905 -
obs--92.23 %

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