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- PDB-5zjl: Crystal Structure of the dust mite allergen Der f 23 from Dermato... -

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Basic information

Entry
Database: PDB / ID: 5zjl
TitleCrystal Structure of the dust mite allergen Der f 23 from Dermatophagoides farinae
ComponentsDer f 23 allergen
KeywordsALLERGEN
Function / homologyChitin binding domain / Chitin binding Peritrophin-A domain / Chitin-binding type-2 domain profile. / Chitin binding domain superfamily / chitin binding / extracellular region / Der f 23 allergen
Function and homology information
Biological speciesDermatophagoides farinae (American house dust mite)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsJi, K. / Chen, J. / Sun, J.L. / Hu, J. / Cai, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation (China)81571570 China
National Science Foundation (China)30671943 China
CitationJournal: To Be Published
Title: Crystal Structure of the dust mite allergen Der f 23 from Dermatophagoides farinae
Authors: Ji, K. / Chen, J. / Sun, J.L. / Hu, J. / Cai, Z.
History
DepositionMar 20, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Der f 23 allergen
B: Der f 23 allergen


Theoretical massNumber of molelcules
Total (without water)7,3302
Polymers7,3302
Non-polymers00
Water00
1
A: Der f 23 allergen


Theoretical massNumber of molelcules
Total (without water)3,6651
Polymers3,6651
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Der f 23 allergen


Theoretical massNumber of molelcules
Total (without water)3,6651
Polymers3,6651
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.049, 39.048, 109.970
Angle α, β, γ (deg.)90.00, 89.99, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: THR / End label comp-ID: THR / Refine code: _ / Auth seq-ID: 9 - 39 / Label seq-ID: 1 - 31

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein/peptide Der f 23 allergen


Mass: 3665.183 Da / Num. of mol.: 2 / Fragment: UNP residues 144-174
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dermatophagoides farinae (American house dust mite)
Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A0U3JM87
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: 5.72 Å3/Da / Density % sol: 78.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M MgCl2, 0.1 Sodium Citrate (pH 5.0), 2% PEG2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.25
11-K, -H, -L20.248
11K, H, -L30.234
11-h,-k,l40.268
ReflectionResolution: 1.7→25 Å / Num. obs: 15991 / % possible obs: 87 % / Redundancy: 5.8 % / Net I/σ(I): 10
Reflection shellResolution: 1.7→1.73 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZCE

4zce


Resolution: 1.7→21.99 Å / Cor.coef. Fo:Fc: 0.783 / Cor.coef. Fo:Fc free: 0.779 / SU B: 5.321 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.024 / ESU R Free: 0.021 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30091 818 5.2 %RANDOM
Rwork0.2863 ---
obs0.28712 15058 86.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.562 Å2
Baniso -1Baniso -2Baniso -3
1--7.81 Å20 Å2-1.25 Å2
2---7.41 Å20 Å2
3---15.22 Å2
Refinement stepCycle: 1 / Resolution: 1.7→21.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms508 0 0 0 508
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0420.02525
X-RAY DIFFRACTIONr_bond_other_d0.0070.02448
X-RAY DIFFRACTIONr_angle_refined_deg2.981.89710
X-RAY DIFFRACTIONr_angle_other_deg1.9431052
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.465560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62224.16724
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.3241588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.389152
X-RAY DIFFRACTIONr_chiral_restr0.2040.272
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.02562
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02112
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_it2.1951.183246
X-RAY DIFFRACTIONr_mcbond_other2.19352.029245
X-RAY DIFFRACTIONr_mcangle_it2.2831.787304
X-RAY DIFFRACTIONr_mcangle_other2.281305
X-RAY DIFFRACTIONr_scbond_it2.4281.189276
X-RAY DIFFRACTIONr_scbond_other2.424277
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1781.783405
X-RAY DIFFRACTIONr_long_range_B_refined2.25513.47624
X-RAY DIFFRACTIONr_long_range_B_other2.25313.65625
X-RAY DIFFRACTIONr_rigid_bond_restr15.483522
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded4.9815508
Refine LS restraints NCS

Ens-ID: 1 / Number: 1690 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.22 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.701→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.589 60 -
Rwork0.34 1217 -
obs--95.66 %
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)
10.3799-0.2454-0.06240.17680.00270.3603-0.0043-0.01150.0027-0.0073-0.0133-0.0110.05030.00220.01760.055-0.00170.00060.09190.00410.006113.1016.800211.6117
20.0004-0.00090.00030.6824-0.25370.0943-0.0064-0.000700.01780.0048-0.0077-0.0055-0.00360.00160.0654-0.00020.00160.1075-0.0010.000816.0565-9.710815.9782
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 39
2X-RAY DIFFRACTION2B9 - 39

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