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- PDB-3ee6: Crystal Structure Analysis of Tripeptidyl peptidase -I -

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Basic information

Entry
Database: PDB / ID: 3ee6
TitleCrystal Structure Analysis of Tripeptidyl peptidase -I
ComponentsTripeptidyl-peptidase 1
KeywordsHYDROLASE / tripepetidyl peptidase -I / Disease mutation / Epilepsy / Glycoprotein / Lysosome / Neuronal ceroid lipofuscinosis / Protease / Serine protease / Zymogen
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 / lysosome organization / peptide catabolic process / 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 / lysosome organization / peptide catabolic process / 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 / nervous system development / peptidase activity / 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 / Rossmann fold ...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 / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsPal, A. / Kraetzner, R. / Grapp, M. / Gruene, T. / Schreiber, K. / Granborg, M. / Urlaub, H. / Asif, A.R. / Becker, S. / Gartner, J. ...Pal, A. / Kraetzner, R. / Grapp, M. / Gruene, T. / Schreiber, K. / Granborg, M. / Urlaub, H. / Asif, A.R. / Becker, S. / Gartner, J. / Sheldrick, G.M. / Steinfeld, R.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structure of tripeptidyl-peptidase I provides insight into the molecular basis of late infantile neuronal ceroid lipofuscinosis
Authors: Pal, A. / Kraetzner, R. / Gruene, T. / Grapp, M. / Schreiber, K. / Gronborg, M. / Urlaub, H. / Becker, S. / Asif, A.R. / Gartner, J. / Sheldrick, G.M. / Steinfeld, R.
History
DepositionSep 4, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 20, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_ref_seq_dif / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tripeptidyl-peptidase 1
B: Tripeptidyl-peptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,39024
Polymers124,7542
Non-polymers2,63622
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-228 kcal/mol
Surface area39900 Å2
MethodPISA
2
A: Tripeptidyl-peptidase 1
B: Tripeptidyl-peptidase 1
hetero molecules

A: Tripeptidyl-peptidase 1
B: Tripeptidyl-peptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,77948
Polymers249,5074
Non-polymers5,27244
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area11980 Å2
ΔGint-765 kcal/mol
Surface area77040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.450, 128.930, 100.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12B
22A

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERGLUAA392 - 402392 - 402
21SERGLUBB392 - 402392 - 402
12ASPGLNBB215 - 225215 - 225
22ASPGLNAA215 - 225215 - 225

NCS ensembles :
ID
1
2

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Components

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Protein / Sugars , 2 types, 10 molecules AB

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


Mass: 62376.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLN2 / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / References: UniProt: O14773, tripeptidyl-peptidase I
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
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

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Non-polymers , 5 types, 87 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O

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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: 58.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.9
Details: 7% PEG 4000, 0.02M zinc sulfate, 0.1M sodium acetate, 0.1M ammonium sulfate, pH 4.9, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→39.21 Å / Num. all: 62056 / Num. obs: 61321 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 7.18 % / Biso Wilson estimate: 42.1 Å2 / Rmerge(I) obs: 0.0343 / Rsym value: 0.0591 / Net I/σ(I): 17.2
Reflection shellResolution: 2.35→2.45 Å / Redundancy: 6.11 % / Rmerge(I) obs: 0.3121 / Mean I/σ(I) obs: 3.15 / Num. unique all: 7206 / Rsym value: 0.4155 / % possible all: 97.2

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0069refinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
HKL-2000data reduction
SADABSdata scaling
SHELXDphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→39.21 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 19.702 / SU ML: 0.217 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.303 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.262 3150 5.1 %RANDOM
Rwork0.218 ---
all0.221 61829 --
obs0.221 61321 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 117.35 Å2 / Biso mean: 68.4 Å2 / Biso min: 40.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2--5.46 Å20 Å2
3----5.26 Å2
Refinement stepCycle: LAST / Resolution: 2.35→39.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8162 0 126 73 8361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0218580
X-RAY DIFFRACTIONr_bond_other_d0.0010.025768
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.95911702
X-RAY DIFFRACTIONr_angle_other_deg1.4153.00213922
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.4951056
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.20223.299388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.457151224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6321556
X-RAY DIFFRACTIONr_chiral_restr0.0740.21262
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219630
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021790
X-RAY DIFFRACTIONr_mcbond_it0.4541.55292
X-RAY DIFFRACTIONr_mcbond_other0.0761.52134
X-RAY DIFFRACTIONr_mcangle_it0.84728530
X-RAY DIFFRACTIONr_scbond_it1.18733288
X-RAY DIFFRACTIONr_scangle_it1.8444.53172
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A157TIGHT POSITIONAL0.040.05
1B157TIGHT THERMAL0.060.5
2B115TIGHT POSITIONAL0.020.05
2A115TIGHT THERMAL0.040.5
LS refinement shellResolution: 2.35→2.45 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 232 -
Rwork0.311 4118 -
all-4350 -
obs-7005 95.9 %
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)
12.5873-0.7541-0.26392.27941.11144.24680.1749-0.3348-0.13180.0411-0.06690.0635-0.0126-0.3867-0.108-0.30460.08490.005-0.30390.0698-0.303394.015225.501364.1675
22.90471.0245-1.00422.224-1.1184.6535-0.0287-0.0197-0.1576-0.0390.0135-0.09820.40180.47020.0152-0.2598-0.1246-0.0054-0.1372-0.0386-0.3324137.599521.033886.9148
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA20 - 56220 - 562
2X-RAY DIFFRACTION2BB20 - 56220 - 562

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