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- PDB-5n71: CRYSTAL STRUCTURE OF MATURE CATHEPSIN D FROM THE TICK IXODES RICI... -

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Basic information

Entry
Database: PDB / ID: 5n71
TitleCRYSTAL STRUCTURE OF MATURE CATHEPSIN D FROM THE TICK IXODES RICINUS (IRCD1)
ComponentsPutative 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
DI(HYDROXYETHYL)ETHER / Putative cathepsin d
Similarity search - Component
Biological speciesIxodes ricinus (castor bean tick)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.88 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 13, 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

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Assembly

Deposited unit
A: Putative cathepsin d
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8173
Polymers37,6151
Non-polymers2022
Water2,198122
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint-8 kcal/mol
Surface area14630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.156, 98.156, 90.795
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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 (E. coli) / Strain (production host): BL21 / References: UniProt: V5HCK7
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.99 Å3/Da / Density % sol: 58.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: CRYSTALLIZATION CONDITIONS: 1:1 PROTEIN (6 MG/ML IN 2 MM BIS-TRIS, PH 6.5, 20 MM SODIUM CHLORIDE) TO RESERVOIR (0.2 M AMMONIUM SULFATE, 0.1 M SODIUM ACETATE, PH 4.6, 30% PEG2000 MME), ...Details: CRYSTALLIZATION CONDITIONS: 1:1 PROTEIN (6 MG/ML IN 2 MM BIS-TRIS, PH 6.5, 20 MM SODIUM CHLORIDE) TO RESERVOIR (0.2 M AMMONIUM SULFATE, 0.1 M SODIUM ACETATE, PH 4.6, 30% PEG2000 MME), CRYOCOOLED IN MOTHER LIQUOR, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 15, 2015
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.88→49.08 Å / Num. obs: 36745 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 7.98 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 16.16
Reflection shellResolution: 1.88→1.99 Å / Rmerge(I) obs: 0.948 / Mean I/σ(I) obs: 2.33 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.88→49.08 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.131 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.119 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22441 1838 5 %RANDOM
Rwork0.19799 ---
obs0.19933 34906 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.146 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å2-0 Å2-0 Å2
2--0.07 Å20 Å2
3----0.14 Å2
Refinement stepCycle: 1 / Resolution: 1.88→49.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2551 0 12 122 2685
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192648
X-RAY DIFFRACTIONr_bond_other_d0.0020.022434
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.9733607
X-RAY DIFFRACTIONr_angle_other_deg1.00535638
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.895344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.33625110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.96115409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.664157
X-RAY DIFFRACTIONr_chiral_restr0.1030.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213032
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02579
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_it2.5393.151355
X-RAY DIFFRACTIONr_mcbond_other2.5293.1481354
X-RAY DIFFRACTIONr_mcangle_it3.8074.7061694
X-RAY DIFFRACTIONr_mcangle_other3.8114.7071695
X-RAY DIFFRACTIONr_scbond_it2.9573.2911293
X-RAY DIFFRACTIONr_scbond_other2.9573.2911293
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5484.8251910
X-RAY DIFFRACTIONr_long_range_B_refined5.83623.7012710
X-RAY DIFFRACTIONr_long_range_B_other5.83523.682700
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.877→1.925 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 129 -
Rwork0.281 2452 -
obs--95.98 %

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