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- PDB-5n7n: CRYSTAL STRUCTURE OF CATHEPSIN D ZYMOGEN FROM THE TICK IXODES RIC... -

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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 / 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
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
Revision 1.3Oct 23, 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
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

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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
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: 2.95 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

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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

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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 %

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