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- PDB-5yny: Structure of house dust mite allergen Der F 21 in PEG2KMME -

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Basic information

Entry
Database: PDB / ID: 5yny
TitleStructure of house dust mite allergen Der F 21 in PEG2KMME
ComponentsAllergen Der f 21
KeywordsALLERGEN / House dust mite (HDM)
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 / protein homodimerization activity / Mainly Alpha / Mite allergen Der f 21.0101
Function and homology information
Biological speciesDermatophagoides farinae (American house dust mite)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNg, C.L. / Chew, F.T. / Pang, S.L. / Ho, K.L. / Teh, A.H. / Waterman, J. / Rambo, R. / Mathavan, I.
Funding support Malaysia, 1items
OrganizationGrant numberCountry
Other governmentGUP-2014- 010 Malaysia
Citation
Journal: Sci Rep / Year: 2019
Title: Crystal structure and epitope analysis of house dust mite allergen Der f 21.
Authors: Pang, S.L. / Ho, K.L. / Waterman, J. / Rambo, R.P. / Teh, A.H. / Mathavan, I. / Harris, G. / Beis, K. / Say, Y.H. / Anusha, M.S. / Sio, Y.Y. / Chew, F.T. / Ng, C.L.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Cloning, expression, purification, characterization, crystallization and X-ray crystallographic analysis of recombinant Der f 21 (rDer f 21) from Dermatophagoides farinae.
Authors: Ng, C.L. / Chew, F.T. / Pang, S.L. / Ho, K.L. / Teh, A.H. / Waterman, J.
History
DepositionOct 25, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Allergen Der f 21
B: Allergen Der f 21
C: Allergen Der f 21
D: Allergen Der f 21


Theoretical massNumber of molelcules
Total (without water)60,7984
Polymers60,7984
Non-polymers00
Water1,04558
1
A: Allergen Der f 21
B: Allergen Der f 21


Theoretical massNumber of molelcules
Total (without water)30,3992
Polymers30,3992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-16 kcal/mol
Surface area12650 Å2
MethodPISA
2
C: Allergen Der f 21
D: Allergen Der f 21


Theoretical massNumber of molelcules
Total (without water)30,3992
Polymers30,3992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-14 kcal/mol
Surface area11690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.237, 50.934, 69.642
Angle α, β, γ (deg.)90.000, 97.330, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALVALVALAA3 - 11512 - 124
21VALVALVALVALBB3 - 11512 - 124
12ARGARGVALVALAA5 - 11514 - 124
22ARGARGVALVALCC5 - 11514 - 124
13ARGARGALAALAAA5 - 11414 - 123
23ARGARGALAALADD5 - 11414 - 123
14ARGARGVALVALBB5 - 11514 - 124
24ARGARGVALVALCC5 - 11514 - 124
15ARGARGALAALABB5 - 11414 - 123
25ARGARGALAALADD5 - 11414 - 123
16ARGARGALAALACC5 - 11414 - 123
26ARGARGALAALADD5 - 11414 - 123

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Allergen Der f 21 / Der f 5.02 allergen


Mass: 15199.378 Da / Num. of mol.: 4 / Fragment: UNP residues 25-136
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: B2GM84
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.01 Å3/Da / Density % sol: 32.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M Tris (pH 8.0) and 30% PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→28.74 Å / Num. obs: 19287 / % possible obs: 97.8 % / Redundancy: 3.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.023 / Rsym value: 0.046 / Net I/σ(I): 16.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 6969 / CC1/2: 0.903 / Rpim(I) all: 0.244 / Rsym value: 0.476 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→28.74 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.919 / SU B: 18.93 / SU ML: 0.218 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.511 / ESU R Free: 0.287
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2726 973 5 %RANDOM
Rwork0.2207 ---
obs0.2232 18302 97.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 139.05 Å2 / Biso mean: 68.436 Å2 / Biso min: 38.24 Å2
Baniso -1Baniso -2Baniso -3
1--5.9 Å20 Å2-0.07 Å2
2--4.01 Å20 Å2
3---1.85 Å2
Refinement stepCycle: final / Resolution: 2.3→28.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3544 0 0 58 3602
Biso mean---69.45 -
Num. residues----451
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193621
X-RAY DIFFRACTIONr_bond_other_d0.0080.023512
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.9744867
X-RAY DIFFRACTIONr_angle_other_deg1.48538043
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6355462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.82725.031163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.98515708
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1441521
X-RAY DIFFRACTIONr_chiral_restr0.0870.2559
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024071
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02790
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A58530.19
12B58530.19
21A58190.18
22C58190.18
31A47180.2
32D47180.2
41B57310.17
42C57310.17
51B47380.19
52D47380.19
61C46920.18
62D46920.18
LS refinement shellResolution: 2.3→2.359 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 76 -
Rwork0.271 1333 -
all-1409 -
obs--97.58 %
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)
15.43950.07580.33010.0588-0.12110.43930.18030.01530.04840.0123-0.08060.0277-0.0740.0604-0.09970.2002-0.0251-0.00870.19040.00560.0464-10.826811.158419.8909
24.8077-0.0811-0.02040.1373-0.14010.15950.121-0.0807-0.1428-0.0042-0.0810.0201-0.00790.0374-0.040.14350.00370.01130.21580.04680.0679-1.94610.222333.5364
37.36790.16530.63510.0154-0.00640.69450.07340.08640.19660.018-0.0321-0.0045-0.026-0.017-0.04130.20960.00050.01180.09410.02790.1018-30.9437-10.4555-0.0539
46.81480.3464-0.04850.2923-0.41130.64460.1557-0.418-0.37770.0772-0.1257-0.0002-0.16280.0924-0.030.2072-0.00960.00020.24370.02080.0224-21.037-16.54316.227
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 117
2X-RAY DIFFRACTION2B1 - 116
3X-RAY DIFFRACTION3C5 - 116
4X-RAY DIFFRACTION4D5 - 115

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