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- PDB-1ivy: PHYSIOLOGICAL DIMER HPP PRECURSOR -

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Basic information

Entry
Database: PDB / ID: 1ivy
TitlePHYSIOLOGICAL DIMER HPP PRECURSOR
ComponentsHUMAN PROTECTIVE PROTEIN
KeywordsCARBOXYPEPTIDASE / SERINE CARBOXYPEPTIDASE / PROTECTIVE PROTEIN / GLYCOPROTEIN / ZYMOGEN
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 / MHC class II antigen presentation / lysosomal lumen ...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 / MHC class II antigen presentation / lysosomal lumen / enzyme activator activity / 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, TWO-FOLD AVERAGING / Resolution: 2.2 Å
AuthorsRudenko, G. / Bonten, E. / D'Azzo, A. / Hol, W.G.J.
Citation
Journal: Structure / Year: 1995
Title: Three-dimensional structure of the human 'protective protein': structure of the precursor form suggests a complex activation mechanism.
Authors: Rudenko, G. / Bonten, E. / d'Azzo, A. / Hol, W.G.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Structure Determination of the Human Protective Protein: Twofold Averaging Reveals the Three-Dimensional Structure of a Domain which Was Entirely Absent in the Initial Model
Authors: Rudenko, G. / Bonten, E. / D'Azzo, A. / Hol, W.G.J.
#2: Journal: Cell(Cambridge,Mass.) / Year: 1988
Title: Expression of Cdna Encoding the Human 'Protective Protein' Associated with Lysosomal Beta-Galactosidase and Neuraminidase: Homology to Yeast Proteases
Authors: Galjart, N.J. / Gillemans, N. / Harris, A. / Van Der Horst, G.T. / Verheijen, F.W. / Galjaard, H. / D'Azzo, A.
History
DepositionJun 12, 1996Processing site: BNL
Revision 1.0Apr 21, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description / 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 / software / struct_asym / struct_conn / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _software.name / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Apr 3, 2024Group: 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
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HUMAN PROTECTIVE PROTEIN
B: HUMAN PROTECTIVE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,2636
Polymers102,9722
Non-polymers1,2914
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint3 kcal/mol
Surface area34600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.040, 148.110, 80.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein HUMAN PROTECTIVE PROTEIN / PROTECTIVE PROTEIN/CATHEPSIN A / CARBOXYPEPTIDASE L


Mass: 51486.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: BACULOVIRUS MEDIATED OVER-EXPRESSION. SEE BONTEN ET AL. 1995, J.B.C. 270, P. 26441-26445
Cell line: SF21 / Gene: HUPP54 / Gene (production host): HUPP54 / Production host: SF21 INSECT CELLS / References: UniProt: P10619, carboxypeptidase C
#2: Polysaccharide 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAca1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5_2*NCC/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: 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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 3.2 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 285 K / pH: 8.3
Details: PEG 8000, PH 8.0 - 8.3 AT 4 - 12 DEGREES CELSIUS, temperature 285K
Crystal grow
*PLUS
Method: unknown / PH range low: 8.3 / PH range high: 8
Components of the solutions
*PLUS
Common name: PEG8000

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 24, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.2→32.3 Å / Num. obs: 67740 / % possible obs: 95.7 % / Redundancy: 6 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 9.8
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 6 % / Mean I/σ(I) obs: 5.7 / Rsym value: 0.13 / % possible all: 87
Reflection
*PLUS
Num. measured all: 436709
Reflection shell
*PLUS
% possible obs: 87 % / Rmerge(I) obs: 0.13

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Processing

Software
NameVersionClassification
MOSFLM5.2data reduction
ROTAVATAdata reduction
Agrovatadata reduction
TRUNCATEdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
TRUNCATEdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, TWO-FOLD AVERAGING
Starting model: SERINE CARBOXYPEPTIDASE FROM WHEAT

Resolution: 2.2→8 Å
Details: RESIDUES ASN B 216 AND LEU B 217 ARE IN AN AREA OF POOR ELECTRON DENSITY. THE EXACT GEOMETRY OF THESE RESIDUES IS NOT CLEAR FROM THE ELECTRON DENSITY MAP, BUT THEIR GENERAL POSITION IS. IN ...Details: RESIDUES ASN B 216 AND LEU B 217 ARE IN AN AREA OF POOR ELECTRON DENSITY. THE EXACT GEOMETRY OF THESE RESIDUES IS NOT CLEAR FROM THE ELECTRON DENSITY MAP, BUT THEIR GENERAL POSITION IS. IN ADDITION, THE RESTRAINING DISULFIDE CYS 213 - CYS 218 SUPPORTS THE DEPOSITORS' MODEL IN THIS AREA.
RfactorNum. reflection% reflection
Rfree0.268 -5 %
Rwork0.213 --
obs0.213 57704 82.9 %
Refine analyzeLuzzati sigma a obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7172 0 84 296 7552
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.72
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.2→2.3 Å /
Rfactor% reflection
Rwork0.24 -
obs-56.9 %
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Total num. of bins used: 8 / Rfactor obs: 0.24

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