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- PDB-2as8: Crystal structure of mature and fully active Der p 1 allergen -

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Basic information

Entry
Database: PDB / ID: 2as8
TitleCrystal structure of mature and fully active Der p 1 allergen
ComponentsMajor mite fecal allergen Der p 1
KeywordsHYDROLASE / cysteine proteinase fold
Function / homology
Function and homology information


peptidase 1 (mite) / proteolysis involved in protein catabolic process / lysosome / cysteine-type endopeptidase activity / extracellular space
Similarity search - Function
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesDermatophagoides pteronyssinus (European house dust mite)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
Authorsde Halleux, S. / Stura, E. / VanderElst, L. / Carlier, V. / Jacquemin, M. / Saint-Remy, J.-M.
CitationJournal: J.Allergy Clin.Immunol. / Year: 2006
Title: Three-dimensional structure and IgE-binding properties of mature fully active Der p 1, a clinically relevant major allergen
Authors: de Halleux, S. / Stura, E. / VanderElst, L. / Carlier, V. / Jacquemin, M. / Saint-Remy, J.-M.
History
DepositionAug 23, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.value / _struct_conn.pdbx_dist_value / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major mite fecal allergen Der p 1
B: Major mite fecal allergen Der p 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1064
Polymers50,0582
Non-polymers492
Water14,250791
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.120, 78.430, 83.774
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-2282-

HOH

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Components

#1: Protein Major mite fecal allergen Der p 1 / Der p I


Mass: 25028.832 Da / Num. of mol.: 2 / Mutation: N52Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dermatophagoides pteronyssinus (European house dust mite)
Plasmid: pPICZ C / Production host: Pichia pastoris (fungus) / Strain (production host): X-33
References: UniProt: P08176, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 791 / 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: 2.46 Å3/Da / Density % sol: 50.08 %
Crystal growTemperature: 277 K / Method: low salt / pH: 4.5
Details: 25mM sodium acetate, pH 4.5, Low salt, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.006768 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 6, 2004
Details: channel-cut silicon monochromator, toroidally bent cylindrical grazing incidence mirror. Two monochromator crystals Si(311) cut and a lower resolution Si(111) cut.
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.006768 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 36029 / Num. obs: 42045 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 34 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.117 / Rsym value: 0.1 / Χ2: 1.434
Reflection shellResolution: 1.85→1.89 Å / % possible obs: 95.2 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 3 / Num. measured obs: 2476 / Num. unique all: 2476 / Rsym value: 0.429 / Χ2: 1.206 / % possible all: 95.2

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å28.63 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT1.7data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 7PCK

7pck


Resolution: 1.95→28.6 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.068 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25171 1832 5.1 %RANDOM
Rwork0.18492 ---
all0.191 36177 --
obs0.18819 34344 98.42 %-
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 mean: 21.39 Å2
Baniso -1Baniso -2Baniso -3
1--2.31 Å20 Å20 Å2
2--3.73 Å20 Å2
3----1.42 Å2
Refinement stepCycle: LAST / Resolution: 1.95→28.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3520 0 2 791 4313
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0213610
X-RAY DIFFRACTIONr_bond_other_d0.0070.023086
X-RAY DIFFRACTIONr_angle_refined_deg1.9991.9174916
X-RAY DIFFRACTIONr_angle_other_deg1.19237140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2835442
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.223.838198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.97515544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.991530
X-RAY DIFFRACTIONr_chiral_restr0.4910.2508
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024172
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02786
X-RAY DIFFRACTIONr_nbd_refined0.2320.2869
X-RAY DIFFRACTIONr_nbd_other0.2280.23517
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21787
X-RAY DIFFRACTIONr_nbtor_other0.0950.22000
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.2621
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5190.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.4240.281
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3840.265
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5191.52811
X-RAY DIFFRACTIONr_mcbond_other0.1691.5912
X-RAY DIFFRACTIONr_mcangle_it1.39923528
X-RAY DIFFRACTIONr_scbond_it2.98231687
X-RAY DIFFRACTIONr_scangle_it3.9274.51388
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 142 -
Rwork0.25 2439 -
all-2587 -
obs--97.54 %

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