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- PDB-1xkg: Crystal structure of the major house dust mite allergen Der p 1 i... -

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Basic information

Entry
Database: PDB / ID: 1xkg
TitleCrystal structure of the major house dust mite allergen Der p 1 in its pro form at 1.61 A resolution
ComponentsMajor mite fecal allergen Der p 1
KeywordsHYDROLASE / Major allergen / cysteine protease / house dust mite / Dermatophagoides pteronyssinus / inactive mutant / pro peptide
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
YTTRIUM (III) ION / Peptidase 1
Similarity search - Component
Biological speciesDermatophagoides pteronyssinus (European house dust mite)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsMeno, K. / Thorsted, P.B. / Gajhede, M.
CitationJournal: J.Immunol. / Year: 2005
Title: The crystal structure of recombinant proDer p 1, a major house dust mite proteolytic allergen.
Authors: Meno, K. / Thorsted, P.B. / Ipsen, H. / Kristensen, O. / Larsen, J.N. / Spangfort, M.D. / Gajhede, M. / Lund, K.
History
DepositionSep 29, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8896
Polymers35,4241
Non-polymers4655
Water5,621312
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.659, 66.557, 73.388
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 35424.148 Da / Num. of mol.: 1 / Fragment: residues 19-320 / Mutation: C114A, N132D, V204A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dermatophagoides pteronyssinus (European house dust mite)
Gene: DERP1 / Plasmid: pGAPZalphaA / Production host: Pichia pastoris (fungus) / Strain (production host): X33
References: UniProt: P08176, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-YT3 / YTTRIUM (III) ION


Mass: 88.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Y
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: PEG-4000, ammonium sulfate, sodium acetate, glycerol, yttrium chloride, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 16, 2004
RadiationMonochromator: Osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.61→40 Å / Num. all: 41503 / Num. obs: 41444 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rsym value: 0.055 / Net I/σ(I): 18.2
Reflection shellResolution: 1.61→1.67 Å / Num. unique all: 3978 / Rsym value: 0.403 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4(MOLREP)phasing
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YAL

1yal


Resolution: 1.61→40 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.447 / SU ML: 0.051 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The close contact between S194 OG and L302 O could not be improved by model building, as the data enforced the reported conformations. No ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The close contact between S194 OG and L302 O could not be improved by model building, as the data enforced the reported conformations. No interpretable electron density was observed for residues 1-3, 77-81 and 307-312.
RfactorNum. reflection% reflectionSelection details
Rfree0.186 2083 5 %RANDOM
Rwork0.153 ---
all0.154 41444 --
obs0.154 41444 99.6 %-
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: 24.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20 Å20 Å2
2---0.7 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.61→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2375 0 23 312 2710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212472
X-RAY DIFFRACTIONr_bond_other_d0.0010.022100
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.923347
X-RAY DIFFRACTIONr_angle_other_deg0.80934885
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6545298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.54624.348138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.49415394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.41517
X-RAY DIFFRACTIONr_chiral_restr0.090.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022819
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02534
X-RAY DIFFRACTIONr_nbd_refined0.2170.2521
X-RAY DIFFRACTIONr_nbd_other0.1850.22211
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21266
X-RAY DIFFRACTIONr_nbtor_other0.0830.21333
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2236
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2460.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.3531.51922
X-RAY DIFFRACTIONr_mcbond_other0.2751.5614
X-RAY DIFFRACTIONr_mcangle_it1.46622370
X-RAY DIFFRACTIONr_scbond_it2.72531188
X-RAY DIFFRACTIONr_scangle_it3.7984.5977
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.611→1.653 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 148 -
Rwork0.271 2753 -
obs-2901 95.3 %

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