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- PDB-5n7q: CRYSTAL STRUCTURE OF MATURE CATHEPSIN D FROM THE TICK IXODES RICI... -

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Basic information

Entry
Database: PDB / ID: 5n7q
TitleCRYSTAL STRUCTURE OF MATURE CATHEPSIN D FROM THE TICK IXODES RICINUS (IRCD1) IN COMPLEX WITH THE INHIBITOR PEPSTATIN A
Components
  • PEPSTATIN A
  • 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
Pepstatin / DI(HYDROXYETHYL)ETHER / Putative cathepsin d
Similarity search - Component
Biological speciesIxodes ricinus (castor bean tick)
Actinobacteria (actinobacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.45 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: 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 1.3Jun 13, 2018Group: Data collection / Structure summary / Category: pdbx_molecule_features
Revision 1.4Nov 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: Putative cathepsin d
I: PEPSTATIN A
J: PEPSTATIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1446
Polymers74,9464
Non-polymers1982
Water23,5641308
1
A: Putative cathepsin d
I: PEPSTATIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5793
Polymers37,4732
Non-polymers1061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-12 kcal/mol
Surface area14230 Å2
MethodPISA
2
B: Putative cathepsin d
J: PEPSTATIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5653
Polymers37,4732
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-9 kcal/mol
Surface area14270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.140, 82.820, 61.390
Angle α, β, γ (deg.)90.00, 91.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative cathepsin d


Mass: 36787.234 Da / Num. of mol.: 2
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: Protein/peptide PEPSTATIN A


Type: Oligopeptide / Class: Enzyme inhibitor / Mass: 685.891 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Actinobacteria (actinobacteria) / References: Pepstatin
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1308 / 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: 2.07 Å3/Da / Density % sol: 40.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1:1 PROTEIN (5 MG/ML IN 2.5 MM SODIUM FORMATE, 20 MM SODIUM CHLORIDE) TO RESERVOIR (0.14 M SODIUM CHLORIDE, 0.07 M BIS-TRIS, PH 5.5, 17.5% PEG3350, 1 MM DTT), CRYOCOOLED AFTER A QUICK SOAK ...Details: 1:1 PROTEIN (5 MG/ML IN 2.5 MM SODIUM FORMATE, 20 MM SODIUM CHLORIDE) TO RESERVOIR (0.14 M SODIUM CHLORIDE, 0.07 M BIS-TRIS, PH 5.5, 17.5% PEG3350, 1 MM DTT), CRYOCOOLED AFTER A QUICK SOAK IN RESERVOIR BUFFER + 30% PEG3350, 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: Jul 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.455→61.378 Å / Num. obs: 104842 / % possible obs: 98 % / Redundancy: 3 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 7.2
Reflection shellResolution: 1.455→1.53 Å / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.227 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.45→61.38 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.135 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16646 5335 5 %RANDOM
Rwork0.14522 ---
obs0.14629 101593 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.814 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20.02 Å2
2---0.12 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.45→61.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5219 0 13 1308 6540
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195482
X-RAY DIFFRACTIONr_bond_other_d0.0070.025127
X-RAY DIFFRACTIONr_angle_refined_deg1.51.9837461
X-RAY DIFFRACTIONr_angle_other_deg0.983311885
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7615.028714
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.0925.089224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.0815852
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2461514
X-RAY DIFFRACTIONr_chiral_restr0.0880.2838
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216212
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021182
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_it0.8771.1422788
X-RAY DIFFRACTIONr_mcbond_other0.8731.1422788
X-RAY DIFFRACTIONr_mcangle_it1.381.7113466
X-RAY DIFFRACTIONr_mcangle_other1.3811.7123467
X-RAY DIFFRACTIONr_scbond_it1.2691.2592694
X-RAY DIFFRACTIONr_scbond_other1.2691.262695
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0011.8353980
X-RAY DIFFRACTIONr_long_range_B_refined4.84211.0426496
X-RAY DIFFRACTIONr_long_range_B_other4.84111.0446497
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.455→1.493 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 413 -
Rwork0.205 7425 -
obs--99.59 %

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