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- PDB-3uv1: Crystal structure a major allergen from dust mite -

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Basic information

Entry
Database: PDB / ID: 3uv1
TitleCrystal structure a major allergen from dust mite
ComponentsDer f 7 allergen
KeywordsALLERGEN / Super-roll
Function / homology
Function and homology information


extracellular region
Similarity search - Function
Bactericidal permeability-increasing protein; domain 1 - #50 / Mite allergen, group-7 / Mite allergen, group-7 superfamily / Group 7 allergen / Bactericidal permeability-increasing protein; domain 1 / Super Roll / Alpha Beta
Similarity search - Domain/homology
Der f 7 allergen / Mite allergen Der f 7
Similarity search - Component
Biological speciesDermatophagoides farinae (American house dust mite)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2 Å
AuthorsTan, K.W. / Kumar, T. / Chew, F.T. / Mok, Y.K.
CitationJournal: Plos One / Year: 2012
Title: Crystal Structure of Der f 7, a Dust Mite Allergen from Dermatophagoides farinae.
Authors: Tan, K.W. / Jobichen, C. / Ong, T.C. / Gao, Y.F. / Tiong, Y.S. / Wong, K.N. / Chew, F.T. / Sivaraman, J. / Mok, Y.K.
History
DepositionNov 29, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Der f 7 allergen
B: Der f 7 allergen


Theoretical massNumber of molelcules
Total (without water)44,3952
Polymers44,3952
Non-polymers00
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-8 kcal/mol
Surface area17090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.092, 58.234, 128.978
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 6:48 OR RESSEQ 50:130 OR RESSEQ 132:196 )
211CHAIN B AND (RESSEQ 6:48 OR RESSEQ 50:130 OR RESSEQ 132:196 )

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Components

#1: Protein Der f 7 allergen


Mass: 22197.369 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 18-213
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dermatophagoides farinae (American house dust mite)
Production host: Escherichia coli (E. coli) / References: UniProt: A1KXH4, UniProt: Q26456*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.06 Å3/Da / Density % sol: 40.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1 M Bis-Tris pH 7.4 and 28% PEG MME 2000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5417 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jan 5, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 30870 / % possible obs: 97.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3 % / Rsym value: 0.031
Reflection shellResolution: 2→2.03 Å

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2→19.903 Å / SU ML: 0.51 / σ(F): 1.33 / Phase error: 27.26 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflectionSelection details
Rfree0.2801 3227 6.52 %random
Rwork0.2241 ---
obs0.2276 30870 98.68 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.854 Å2 / ksol: 0.316 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.1707 Å2-0 Å2-0 Å2
2--6.0432 Å20 Å2
3----4.8726 Å2
Refinement stepCycle: LAST / Resolution: 2→19.903 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2867 0 0 281 3148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092909
X-RAY DIFFRACTIONf_angle_d1.1883938
X-RAY DIFFRACTIONf_dihedral_angle_d16.0311060
X-RAY DIFFRACTIONf_chiral_restr0.084470
X-RAY DIFFRACTIONf_plane_restr0.004513
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0001-2.02990.33691350.2664193594
2.0299-2.06160.29651360.2573190594
2.0616-2.09530.29031340.2429198197
2.0953-2.13140.25221410.2408202798
2.1314-2.17010.28171370.2561197499
2.1701-2.21180.44531490.3495208299
2.2118-2.25690.43561380.37951976100
2.2569-2.30590.37431450.3064202699
2.3059-2.35950.29591380.2625203599
2.3595-2.41840.37161390.2275204099
2.4184-2.48370.27541370.2318199798
2.4837-2.55660.2861450.2267201198
2.5566-2.63890.36511330.2474198198
2.6389-2.7330.31511420.2379201599
2.733-2.84220.31521470.24372047100
2.8422-2.97110.26291450.22532031100
2.9711-3.12720.28411350.22742033100
3.1272-3.32230.23721410.21182038100
3.3223-3.57740.23121420.2138203099
3.5774-3.93490.25841440.20322068100
3.9349-4.49860.24861390.1724199599
4.4986-5.64620.24031420.17132047100
5.6462-19.9040.24661430.20932027100

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