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- PDB-5vpk: CRYSTAL STRUCTURE OF MITE ALLERGEN DER F 1 -

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Basic information

Entry
Database: PDB / ID: 5vpk
TitleCRYSTAL STRUCTURE OF MITE ALLERGEN DER F 1
ComponentsDer f 1 variant
KeywordsHYDROLASE / ALLERGY / DUST MITES / ALLERGEN / GLYCOPROTEIN / PROTEASE / SECRETED / THIOL PROTEASE / ZYMOGEN
Function / homology
Function and homology information


peptidase 1 (mite) / cysteine-type peptidase activity / proteolysis / extracellular region
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
Der f 1 variant / Peptidase 1
Similarity search - Component
Biological speciesDermatophagoides farinae (American house dust mite)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChruszcz, M. / Chapman, M.D. / Vailes, L.D. / Pomes, A. / Minor, W.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal Structures Of Mite Allergens Der F 1 And Der P 1 Reveal Differences In Surface-Exposed Residues That May Influence Antibody Binding
Authors: Chruszcz, M. / Chapman, M.D. / Vailes, L.D. / Stura, E.A. / Saint-Remy, J.M. / Minor, W. / Pomes, A.
History
DepositionMay 5, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionMay 24, 2017ID: 3D6S
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Apr 13, 2022Group: Database references / Structure summary
Category: audit_author / chem_comp ...audit_author / chem_comp / citation_author / database_2
Item: _audit_author.identifier_ORCID / _chem_comp.pdbx_synonyms ..._audit_author.identifier_ORCID / _chem_comp.pdbx_synonyms / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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: Der f 1 variant
B: Der f 1 variant
C: Der f 1 variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,53211
Polymers75,5133
Non-polymers1,0198
Water5,206289
1
A: Der f 1 variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8727
Polymers25,1711
Non-polymers7026
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Der f 1 variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4883
Polymers25,1711
Non-polymers3172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Der f 1 variant


Theoretical massNumber of molelcules
Total (without water)25,1711
Polymers25,1711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.159, 91.159, 77.743
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: MET / End label comp-ID: MET / Refine code: 0 / Auth seq-ID: 1 - 223 / Label seq-ID: 1 - 223

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Der f 1 variant


Mass: 25170.975 Da / Num. of mol.: 3 / Fragment: SEQUENCE DATABASE RESIDUES 99-321 / Source method: isolated from a natural source
Source: (natural) Dermatophagoides farinae (American house dust mite)
References: UniProt: I2CMD3, UniProt: P16311*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: 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 / N-Acetylglucosamine


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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.14 Å3/Da / Density % sol: 42.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 10.5
Details: PROTEIN SOLUTION: 0.5M L-ARGININE, 0.12M LI SULFATE, 0.004M EDTA, 0.1M CAPS, PH 10.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, PH 10.50
PH range: 10.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 24, 2008
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.597
11-H, K, -L20.403
ReflectionResolution: 2→50 Å / Num. obs: 40623 / % possible obs: 94.1 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 34.2
Reflection shellResolution: 2→2.03 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.591 / Mean I/σ(I) obs: 4.2 / CC1/2: 0.86 / Rsym value: 0.591 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
MOLREPphasing
PHASERphasing
REFMAC5.8.0158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AS8

2as8


Resolution: 2→36.1 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.949 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.036 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21008 1958 4.9 %RANDOM
Rwork0.17954 ---
obs0.18099 37834 92.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.655 Å2
Baniso -1Baniso -2Baniso -3
1--15.61 Å2-0 Å2-0 Å2
2---15.61 Å2-0 Å2
3---31.22 Å2
Refinement stepCycle: LAST / Resolution: 2→36.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5238 0 58 289 5585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195463
X-RAY DIFFRACTIONr_bond_other_d00.024629
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.9317463
X-RAY DIFFRACTIONr_angle_other_deg3.872310730
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3495672
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.79123.869274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.29715807
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7061537
X-RAY DIFFRACTIONr_chiral_restr0.0860.2799
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026227
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021160
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.91.642687
X-RAY DIFFRACTIONr_mcbond_other0.91.642687
X-RAY DIFFRACTIONr_mcangle_it1.4422.4533359
X-RAY DIFFRACTIONr_mcangle_other1.4422.4533360
X-RAY DIFFRACTIONr_scbond_it1.1891.8462776
X-RAY DIFFRACTIONr_scbond_other1.1141.8112761
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8032.6714081
X-RAY DIFFRACTIONr_long_range_B_refined5.5919.8776168
X-RAY DIFFRACTIONr_long_range_B_other5.5919.8816169
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A145380.09
12B145380.09
21A140560.08
22C140560.08
31B139780.09
32C139780.09
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 167 -
Rwork0.206 2978 -
obs--100 %
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)
11.2877-0.29040.27032.15570.02221.349-0.0055-0.0658-0.0668-0.07750.07840.0991-0.12840.0052-0.0730.25610.03250.0410.19780.02670.0171-23.1971.3866.819
23.0374-0.02040.15041.35610.00491.22410.0149-0.4093-0.1658-0.01560.04540.0579-0.0190.0127-0.06020.20290.0206-0.01250.32080.00470.0154-44.26322.44-6.532
33.67671.1214-1.39342.0239-2.01883.643-0.08610.67410.3328-0.08130.38390.2235-0.0513-0.4039-0.29770.260.0068-0.02090.44990.10010.0444-61.794-14.8450.047
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 223
2X-RAY DIFFRACTION2B1 - 223
3X-RAY DIFFRACTION3C1 - 223

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