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- PDB-6wia: CRYSTAL STRUCTURE OF HUMAN PROTECTIVE PROTEIN/CATHEPSIN A, DFP-IN... -

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Basic information

Entry
Database: PDB / ID: 6wia
TitleCRYSTAL STRUCTURE OF HUMAN PROTECTIVE PROTEIN/CATHEPSIN A, DFP-INHIBITED (AGED)
ComponentsLysosomal protective protein
KeywordsHYDROLASE / Lysosomal / Cathepsin A / CatA / CTSA / organophosphate / renin-angiotensin system (RAS)
Function / homology
Function and homology information


carboxypeptidase C / Defective NEU1 causes sialidosis / serine-type carboxypeptidase activity / regulation of chaperone-mediated autophagy / Sialic acid metabolism / Glycosphingolipid catabolism / negative regulation of chaperone-mediated autophagy / carboxypeptidase activity / enzyme activator activity / MHC class II antigen presentation ...carboxypeptidase C / Defective NEU1 causes sialidosis / serine-type carboxypeptidase activity / regulation of chaperone-mediated autophagy / Sialic acid metabolism / Glycosphingolipid catabolism / negative regulation of chaperone-mediated autophagy / carboxypeptidase activity / enzyme activator activity / MHC class II antigen presentation / lysosomal lumen / intracellular protein transport / regulation of protein stability / azurophil granule lumen / lysosome / intracellular membrane-bounded organelle / Neutrophil degranulation / endoplasmic reticulum / proteolysis / extracellular exosome / extracellular region / membrane
Similarity search - Function
Serine carboxypeptidase, serine active site / Serine carboxypeptidases, serine active site. / Peptidase S10, serine carboxypeptidase / Serine carboxypeptidases, histidine active site / Serine carboxypeptidase / Serine carboxypeptidases, histidine active site. / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / : / Lysosomal protective protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsCompton, J.R. / Legler, P.M.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)#GW150096 United States
CitationJournal: Biochem. Pharmacol. / Year: 2020
Title: Structural and kinetic evidence of aging after organophosphate inhibition of human Cathepsin A.
Authors: Bouknight, K.D. / Jurkouich, K.M. / Compton, J.R. / Khavrutskii, I.V. / Guelta, M.A. / Harvey, S.P. / Legler, P.M.
History
DepositionApr 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 18, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Lysosomal protective protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,31715
Polymers52,4071
Non-polymers1,91114
Water3,117173
1
A: Lysosomal protective protein
hetero molecules

A: Lysosomal protective protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,63530
Polymers104,8142
Non-polymers3,82128
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area9420 Å2
ΔGint-65 kcal/mol
Surface area32760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.273, 101.999, 48.114
Angle α, β, γ (deg.)90.000, 101.610, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-690-

HOH

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Components

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Protein / Sugars , 2 types, 3 molecules A

#1: Protein Lysosomal protective protein / Carboxypeptidase C / Carboxypeptidase L / Cathepsin A / Protective protein cathepsin A / PPCA / ...Carboxypeptidase C / Carboxypeptidase L / Cathepsin A / Protective protein cathepsin A / PPCA / Protective protein for beta-galactosidase


Mass: 52406.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: cell line / Source: (gene. exp.) Homo sapiens (human) / Gene: CTSA, PPGB / Plasmid: pcDNA3.4 / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: P10619, carboxypeptidase C
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 185 molecules

#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.09 Å3/Da / Density % sol: 41.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Crystallized in Crystal Screen Cryo II condition #12 (0.095 M cadmium chloride hydrate, 0.095 M sodium acetate trihydrate pH 4.6, 28.5% v/v PEG 400, 5% glycerol). Mounted in 30% glycerol and ...Details: Crystallized in Crystal Screen Cryo II condition #12 (0.095 M cadmium chloride hydrate, 0.095 M sodium acetate trihydrate pH 4.6, 28.5% v/v PEG 400, 5% glycerol). Mounted in 30% glycerol and 70% CS Cryo II condition #12. Protein was inhibited with DFP in 25 mM Tris pH 8, 300 mM NaCl at R.T.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Nov 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.21→41.7 Å / Num. obs: 21594 / % possible obs: 99.8 % / Redundancy: 5.12 % / Rmerge(I) obs: 0.0836 / Net I/σ(I): 11.55
Reflection shellResolution: 2.21→2.31 Å / Redundancy: 5.05 % / Rmerge(I) obs: 0.3905 / Mean I/σ(I) obs: 3.36 / Num. unique obs: 2654 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
APEXdata reduction
APEXdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4az3

4az3


Resolution: 2.21→41.7 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.33 / ESU R Free: 0.21
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2235 1075 5 %RANDOM
Rwork0.1947 ---
obs0.1962 20455 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 114.4 Å2 / Biso mean: 35.424 Å2 / Biso min: 4.71 Å2
Baniso -1Baniso -2Baniso -3
1--2.41 Å20 Å2-2.25 Å2
2---0.85 Å2-0 Å2
3---3.86 Å2
Refinement stepCycle: final / Resolution: 2.21→41.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3281 0 88 173 3542
Biso mean--69.02 38.54 -
Num. residues----411
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133474
X-RAY DIFFRACTIONr_bond_other_d0.0350.0173027
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.6644701
X-RAY DIFFRACTIONr_angle_other_deg2.6391.597056
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9285411
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.07923.944180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.31415536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.81512
X-RAY DIFFRACTIONr_chiral_restr0.0750.2425
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023876
X-RAY DIFFRACTIONr_gen_planes_other0.0350.02723
LS refinement shellResolution: 2.21→2.267 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 80 -
Rwork0.29 1483 -
all-1563 -
obs--99.49 %

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