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- PDB-3edy: Crystal Structure of the Precursor Form of Human Tripeptidyl-Pept... -

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Basic information

Entry
Database: PDB / ID: 3edy
TitleCrystal Structure of the Precursor Form of Human Tripeptidyl-Peptidase 1
ComponentsTripeptidyl-peptidase 1
KeywordsHYDROLASE / protease / TPP1 / sedolisin / Batten disease / LINCL / zymogen / prodomain / exopeptidase / endopeptidase / S53 family / cln2 / catalytic triad / oxyanion hole / Disease mutation / Epilepsy / Glycoprotein / Lysosome / Neuronal ceroid lipofuscinosis / Serine protease
Function / homology
Function and homology information


tripeptidyl-peptidase I / sulfatide binding / lysophosphatidic acid binding / lysosomal protein catabolic process / tripeptidyl-peptidase activity / XBP1(S) activates chaperone genes / protein localization to chromosome, telomeric region / peptide catabolic process / lysosome organization / neuromuscular process controlling balance ...tripeptidyl-peptidase I / sulfatide binding / lysophosphatidic acid binding / lysosomal protein catabolic process / tripeptidyl-peptidase activity / XBP1(S) activates chaperone genes / protein localization to chromosome, telomeric region / peptide catabolic process / lysosome organization / neuromuscular process controlling balance / bone resorption / epithelial cell differentiation / serine-type peptidase activity / lysosomal lumen / central nervous system development / peptide binding / protein catabolic process / lipid metabolic process / recycling endosome / melanosome / peptidase activity / nervous system development / endopeptidase activity / lysosome / membrane raft / serine-type endopeptidase activity / Golgi apparatus / proteolysis / extracellular exosome / metal ion binding
Similarity search - Function
Peptidase S53, activation domain / Sedolisin domain / : / Pro-kumamolisin, activation domain / Sedolisin domain profile. / Pro-kumamolisin, activation domain / Peptidase S8/S53 domain / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain ...Peptidase S53, activation domain / Sedolisin domain / : / Pro-kumamolisin, activation domain / Sedolisin domain profile. / Pro-kumamolisin, activation domain / Peptidase S8/S53 domain / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Tripeptidyl-peptidase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.85 Å
AuthorsGuhaniyogi, J. / Sohar, I. / Das, K. / Lobel, P. / Stock, A.M.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Crystal Structure and Autoactivation Pathway of the Precursor Form of Human Tripeptidyl-peptidase 1, the Enzyme Deficient in Late Infantile Ceroid Lipofuscinosis
Authors: Guhaniyogi, J. / Sohar, I. / Das, K. / Stock, A.M. / Lobel, P.
History
DepositionSep 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _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: Tripeptidyl-peptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,54210
Polymers59,3691
Non-polymers1,1739
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.807, 93.173, 102.479
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tripeptidyl-peptidase 1 / Tripeptidyl-peptidase I / TPP-1 / TPP-I / Tripeptidyl aminopeptidase / Lysosomal pepstatin- ...Tripeptidyl-peptidase I / TPP-1 / TPP-I / Tripeptidyl aminopeptidase / Lysosomal pepstatin- insensitive protease / LPIC / Cell growth-inhibiting gene 1 protein


Mass: 59369.121 Da / Num. of mol.: 1 / Fragment: residues 20-563
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TPP1, CLN2 / Cell (production host): OVARY CELLS / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: O14773, tripeptidyl-peptidase I
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.4 Å3/Da / Density % sol: 48.85 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 6000, citrate, pH 5.0, vapor diffusion, hanging drop, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97908 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 2, 2007 / Details: mirrors
RadiationMonochromator: horizontally deflecting and focusing crystal preceded by a vertically focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. all: 48561 / Num. obs: 50890 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.079 / Χ2: 1.043
Reflection shellResolution: 1.83→1.9 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 2.3 / Num. unique all: 4675 / Χ2: 0.644 / % possible all: 93.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
SOLVEphasing
RefinementResolution: 1.85→29.72 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.214 / WRfactor Rwork: 0.187 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.871 / SU B: 5.22 / SU ML: 0.082 / SU R Cruickshank DPI: 0.141 / SU Rfree: 0.125 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.134 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1231 2.6 %RANDOM
Rwork0.179 ---
obs0.179 48127 97.01 %-
all-48561 --
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 max: 63.13 Å2 / Biso mean: 26.882 Å2 / Biso min: 13.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.13 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4195 0 73 235 4503
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0214428
X-RAY DIFFRACTIONr_bond_other_d0.0010.022987
X-RAY DIFFRACTIONr_angle_refined_deg1.2631.9666046
X-RAY DIFFRACTIONr_angle_other_deg1.0383.0027204
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3285543
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.40523.3200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89415638
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0691530
X-RAY DIFFRACTIONr_chiral_restr0.0880.2656
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024948
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02912
X-RAY DIFFRACTIONr_nbd_refined0.2260.2910
X-RAY DIFFRACTIONr_nbd_other0.2270.23163
X-RAY DIFFRACTIONr_nbtor_refined0.1910.22189
X-RAY DIFFRACTIONr_nbtor_other0.1060.22223
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2234
X-RAY DIFFRACTIONr_metal_ion_refined0.1350.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2910.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1090.212
X-RAY DIFFRACTIONr_mcbond_it1.4661.52788
X-RAY DIFFRACTIONr_mcbond_other0.4621.51093
X-RAY DIFFRACTIONr_mcangle_it2.16524395
X-RAY DIFFRACTIONr_scbond_it3.35131870
X-RAY DIFFRACTIONr_scangle_it4.8714.51651
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 48 -
Rwork0.193 2319 -
all-2367 -
obs--65.7 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5650.13730.37020.4290.34892.4410.02940.0164-0.10740.0235-0.0523-0.03710.3268-0.00870.02290.1090.00460.023-0.01840.04180.06966.2738-13.05382.152
26.3336-0.66180.42166.8069-6.44096.1013-0.0083-0.23370.5861.3167-0.3865-0.3336-0.95410.69320.39470.1573-0.0775-0.02030.09080.03630.168162.617831.8842-3.9333
31.40370.1583-0.13151.6964-0.32951.58270.01230.0931-0.0044-0.0877-0.0353-0.13220.00290.10540.0230.048-0.00170.00540.08690.03420.099378.241615.35925.4954
41.5278-0.10390.16471.1679-0.04151.03630.0340.02590.034-0.0423-0.0643-0.020.01-0.02060.03030.07620.00040.02020.06830.04320.057663.3732.67068.356
50.89050.10130.07950.5261-0.08480.35470.0297-0.16730.05120.0851-0.03160.0229-0.0269-0.06710.00190.06820.00860.02730.09890.01710.053460.13612.702416.863
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA20 - 1831 - 164
2X-RAY DIFFRACTION2AA184 - 197165 - 178
3X-RAY DIFFRACTION3AA198 - 292179 - 273
4X-RAY DIFFRACTION4AA293 - 401274 - 382
5X-RAY DIFFRACTION5AA402 - 563383 - 544

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