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- PDB-4mws: Crystal structure of human PPCA (trigonal crystal form 1) -

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Basic information

Entry
Database: PDB / ID: 4mws
TitleCrystal structure of human PPCA (trigonal crystal form 1)
ComponentsLysosomal protective protein
KeywordsHYDROLASE / cathepsin A / glycoprotein / serine protease / carboxypeptidase / protective protein / N-linked glycosylation / proteolytically activated form / lysosomal enzyme
Function / homology
Function and homology information


carboxypeptidase C / Defective NEU1 causes sialidosis / serine-type carboxypeptidase activity / Sialic acid metabolism / regulation of chaperone-mediated autophagy / 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 / Sialic acid metabolism / regulation of chaperone-mediated autophagy / 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
Lysosomal protective protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsKolli, N. / Garman, S.C.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Proteolytic activation of human cathepsin A.
Authors: Kolli, N. / Garman, S.C.
History
DepositionSep 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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 / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysosomal protective protein
B: Lysosomal protective protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,5658
Polymers97,3112
Non-polymers2,2546
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6240 Å2
ΔGint20 kcal/mol
Surface area33220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.889, 134.889, 99.805
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: _ / Auth seq-ID: 1 - 452 / Label seq-ID: 1 - 422

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#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: 48655.582 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Selected with blasticidin / Source: (gene. exp.) Homo sapiens (human) / Gene: CTSA, PPGB / Plasmid: pIB/V5-His-TOPO TA / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): HI-FIVE / References: UniProt: P10619, carboxypeptidase C

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Sugars , 3 types, 4 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-1-3-4/a3-b1_a4-c1_c4-d1_d3-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5]/1-2-1-3/a3-b1_a4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: 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.: 2
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 , 2 types, 6 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAN UNIDENTIFIED PROTEASE CONVERTED THE ZYMOGEN INTO ACTIVE ENZYME. PUTATIVE TERMINI ASSUME ...AN UNIDENTIFIED PROTEASE CONVERTED THE ZYMOGEN INTO ACTIVE ENZYME. PUTATIVE TERMINI ASSUME PROTEOLYTIC REMOVAL OF 263-292, CONSISTENT WITH MASS SPECTROMETRY AND N-TERMINAL SEQUENCING DATA.

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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: 2.69 Å3/Da / Density % sol: 54.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10% PEG 3350, 0.1M sodium formate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: PILATUS CBF / Detector: PIXEL / Date: Aug 12, 2012 / Details: FOCUSING MIRRORS
RadiationMonochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.53
11-h,-k,l20.47
ReflectionResolution: 2.8→50 Å / Num. all: 26252 / Num. obs: 25989 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 75.7 Å2 / Rmerge(I) obs: 0.149 / Χ2: 1.52 / Net I/σ(I): 5.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.8-2.855.20.88412571.079198
2.85-2.95.80.71912901.034199.5
2.9-2.965.70.60712850.967199.3
2.96-3.025.60.53313010.983199.9
3.02-3.085.60.48412751.097199.5
3.08-3.155.60.41912851.05199.5
3.15-3.235.50.35413101.164199.6
3.23-3.325.40.31112821.1721100
3.32-3.425.20.25812951.234199.5
3.42-3.535.10.22312601.341196.3
3.53-3.655.70.1913361.442199.8
3.65-3.85.60.16612871.596199.8
3.8-3.975.70.15112961.581199.8
3.97-4.185.50.13213141.752199.7
4.18-4.445.30.11712942.112199.7
4.44-4.795.30.1112962.245197
4.79-5.275.60.10913182.173199.7
5.27-6.035.50.10613311.881199.7
6.03-7.595.20.09613051.848197
7.59-505.20.08513722.669196.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IVY

1ivy


Resolution: 2.8→45.89 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 1 / SU B: 19.907 / SU ML: 0.186 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1951 1258 4.9 %RANDOM
Rwork0.1465 ---
obs0.1489 25868 98.85 %-
all-26169 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 143.32 Å2 / Biso mean: 67.8703 Å2 / Biso min: 34.94 Å2
Baniso -1Baniso -2Baniso -3
1--19.15 Å20 Å20 Å2
2---19.15 Å20 Å2
3---38.29 Å2
Refinement stepCycle: LAST / Resolution: 2.8→45.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6596 0 149 4 6749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.026950
X-RAY DIFFRACTIONr_bond_other_d0.0030.026309
X-RAY DIFFRACTIONr_angle_refined_deg1.1641.9789466
X-RAY DIFFRACTIONr_angle_other_deg0.7853.00214475
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1865822
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.42924.824340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.27151076
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9161526
X-RAY DIFFRACTIONr_chiral_restr0.0630.21017
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217916
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021670
Refine LS restraints NCS

Ens-ID: 1 / Number: 25478 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.04 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 98 -
Rwork0.245 1781 -
all-1879 -
obs--98.38 %
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)
10.2639-0.0568-0.10891.0286-0.03440.3084-0.0010.0322-0.0077-0.03650.0185-0.031-0.0376-0.0617-0.01750.1246-0.0033-0.0040.20690.01390.004516.956-26.593-6.488
20.9145-0.6097-0.41710.92120.15810.3251-0.1472-0.1046-0.04560.04480.0782-0.03830.15460.09310.0690.18340.04280.03850.18150.02270.02138.721-62.887-10.282
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 182
2X-RAY DIFFRACTION1A183 - 303
3X-RAY DIFFRACTION1A304 - 452
4X-RAY DIFFRACTION2B1 - 182
5X-RAY DIFFRACTION2B183 - 303
6X-RAY DIFFRACTION2B304 - 452

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