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- PDB-3mq1: Crystal Structure of Dust Mite Allergen Der p 5 -

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Basic information

Entry
Database: PDB / ID: 3mq1
TitleCrystal Structure of Dust Mite Allergen Der p 5
ComponentsMite allergen Der p 5
KeywordsALLERGEN / DUST MITE
Function / homologyMethane Monooxygenase Hydroxylase; Chain G, domain 1 - #970 / Mite allergen, group 5/21 / Mite allergen, group 5/21 superfamily / Mite allergen Blo t 5 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha / PHOSPHATE ION / Mite allergen Der p 5
Function and homology information
Biological speciesDermatophagoides pteronyssinus (European house dust mite)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsMueller, G.A. / Gosavi, R.A. / Krahn, J.M. / Edwards, L.L. / Cuneo, M.J. / Glesner, J. / Pomes, A. / Chapman, M.D. / London, R.E. / Pedersen, L.C.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Der p 5 crystal structure provides insight into the group 5 dust mite allergens.
Authors: Mueller, G.A. / Gosavi, R.A. / Krahn, J.M. / Edwards, L.L. / Cuneo, M.J. / Glesner, J. / Pomes, A. / Chapman, M.D. / London, R.E. / Pedersen, L.C.
History
DepositionApr 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mite allergen Der p 5
B: Mite allergen Der p 5
C: Mite allergen Der p 5
D: Mite allergen Der p 5
E: Mite allergen Der p 5
F: Mite allergen Der p 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,97241
Polymers72,8596
Non-polymers4,11335
Water81145
1
E: Mite allergen Der p 5
F: Mite allergen Der p 5
hetero molecules

A: Mite allergen Der p 5
B: Mite allergen Der p 5
C: Mite allergen Der p 5
D: Mite allergen Der p 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,97241
Polymers72,8596
Non-polymers4,11335
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation2_665-x+3/2,-y+1,z+1/21
identity operation1_555x,y,z1
Buried area23650 Å2
ΔGint-266 kcal/mol
Surface area29890 Å2
MethodPISA
2
A: Mite allergen Der p 5
B: Mite allergen Der p 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,50821
Polymers24,2862
Non-polymers2,22219
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9280 Å2
ΔGint-122 kcal/mol
Surface area11080 Å2
MethodPISA
3
C: Mite allergen Der p 5
D: Mite allergen Der p 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,46812
Polymers24,2862
Non-polymers1,18210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-92 kcal/mol
Surface area10850 Å2
MethodPISA
4
E: Mite allergen Der p 5
F: Mite allergen Der p 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9958
Polymers24,2862
Non-polymers7096
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-13 kcal/mol
Surface area10880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.780, 96.570, 167.890
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
Mite allergen Der p 5 / Allergen Der P V / IgE-binding allergen


Mass: 12143.111 Da / Num. of mol.: 6 / Fragment: UNP residues 34-132
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dermatophagoides pteronyssinus (European house dust mite)
Gene: DERP5 / Plasmid: PGEX4T3(tev) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P14004
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.6 Å3/Da / Density % sol: 52.74 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 31.5% MPD, 90 mM Na/K phosphate, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: May 8, 2009 / Details: VariMax HF
RadiationMonochromator: VariMaxHF mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 19292 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Rsym value: 0.069 / Net I/σ(I): 15.7
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 1883 / Rsym value: 0.518 / % possible all: 98.5

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.8→33.598 Å / SU ML: 0.38 / σ(F): 0.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2789 822 4.84 %Random
Rwork0.2259 ---
obs0.2287 16987 87.22 %-
all-19292 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.539 Å2 / ksol: 0.287 e/Å3
Refinement stepCycle: LAST / Resolution: 2.8→33.598 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4624 0 250 45 4919
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0014942
X-RAY DIFFRACTIONf_angle_d0.3076661
X-RAY DIFFRACTIONf_dihedral_angle_d8.7841836
X-RAY DIFFRACTIONf_chiral_restr0.022790
X-RAY DIFFRACTIONf_plane_restr0.001834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.97560.31061110.25892198X-RAY DIFFRACTION73
2.9756-3.20510.3241310.25662380X-RAY DIFFRACTION79
3.2051-3.52740.32531320.22352719X-RAY DIFFRACTION89
3.5274-4.03710.26051240.20892921X-RAY DIFFRACTION94
4.0371-5.08340.23661580.18632922X-RAY DIFFRACTION94
5.0834-33.60030.27551660.243025X-RAY DIFFRACTION93
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined4.2871-0.42630.10733.5666-0.13232.3081-0.099-0.00030.6388-0.26410.0947-0.0854-0.24980.0565-0.0174-0.084-0.00260.06620.0458-0.06050.094843.221156.238255.6252
23.426-0.45930.12543.3812-1.71683.26070.0292-0.42951.04830.7659-0.06260.1789-0.6572-0.0374-0.0216-0.0020.0670.06820.0268-0.21150.5021
31.9801-0.5347-1.0923.14270.54942.48450.3436-0.65340.6169-0.23590.2768-0.0668-0.90330.7180.00340.4151-0.35210.19440.5036-0.36330.2919
43.0705-0.7673-1.43252.12171.76293.76090.0597-0.84690.42130.5710.31250.16360.20860.2652-0.00050.3694-0.09230.09450.5319-0.1660.1317
52.8838-0.0025-0.70871.2466-0.6822.90180.36590.49220.5130.08530.1773-0.3410.89760.86580.00220.58750.2199-0.09670.5197-0.01410.3638
61.5375-0.09851.74940.63530.20452.49020.05770.30380.6817-0.11370.18840.0371-0.64560.8039-00.6191-0.1687-0.01740.45240.10710.8005
Refinement TLS groupSelection details: chain F

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