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- PDB-2wql: CRYSTAL STRUCTURE OF THE MAJOR CARROT ALLERGEN DAU C 1 -

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Basic information

Entry
Database: PDB / ID: 2wql
TitleCRYSTAL STRUCTURE OF THE MAJOR CARROT ALLERGEN DAU C 1
ComponentsMAJOR ALLERGEN DAU C 1
KeywordsALLERGEN / PATHOGENESIS-RELATED PROTEIN / PLANT DEFENSE
Function / homology
Function and homology information


response to biotic stimulus / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / defense response / signaling receptor activity
Similarity search - Function
Pathogenesis-related protein Bet v I family / Pathogenesis-related proteins Bet v I family signature. / Bet v I type allergen / Bet v I/Major latex protein / Pathogenesis-related protein Bet v 1 family / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL / DI(HYDROXYETHYL)ETHER / Major allergen Dau c 1
Similarity search - Component
Biological speciesDAUCUS CAROTA (carrot)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMarkovic-Housley, Z. / Basle, A. / Padavattan, S. / Hoffmann-Sommergruber, K. / Schirmer, T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structure of the Major Carrot Allergen Dau C 1.
Authors: Markovic-Housley, Z. / Basle, A. / Padavattan, S. / Maderegger, B. / Schirmer, T. / Hoffmann-Sommergruber, K.
History
DepositionAug 24, 2009Deposition site: PDBE / Processing site: PDBE
SupersessionSep 1, 2009ID: 2VJG
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 / _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: MAJOR ALLERGEN DAU C 1
B: MAJOR ALLERGEN DAU C 1
C: MAJOR ALLERGEN DAU C 1
D: MAJOR ALLERGEN DAU C 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,84230
Polymers64,3414
Non-polymers2,50126
Water28816
1
A: MAJOR ALLERGEN DAU C 1
B: MAJOR ALLERGEN DAU C 1
hetero molecules

A: MAJOR ALLERGEN DAU C 1
B: MAJOR ALLERGEN DAU C 1
hetero molecules

A: MAJOR ALLERGEN DAU C 1
B: MAJOR ALLERGEN DAU C 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,58148
Polymers96,5116
Non-polymers4,07142
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_545-y,z-1/2,-x+1/21
crystal symmetry operation7_555-z+1/2,-x,y+1/21
Buried area18270 Å2
ΔGint-208.52 kcal/mol
Surface area40910 Å2
MethodPISA
2
C: MAJOR ALLERGEN DAU C 1
D: MAJOR ALLERGEN DAU C 1
hetero molecules

C: MAJOR ALLERGEN DAU C 1
D: MAJOR ALLERGEN DAU C 1
hetero molecules

C: MAJOR ALLERGEN DAU C 1
D: MAJOR ALLERGEN DAU C 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,94542
Polymers96,5116
Non-polymers3,43436
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_545-y,z-1/2,-x+1/21
crystal symmetry operation7_555-z+1/2,-x,y+1/21
Buried area18060 Å2
ΔGint-206.46 kcal/mol
Surface area39560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.948, 189.948, 189.948
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALALEULEUAA3 - 83 - 8
21ALAALALEULEUBB3 - 83 - 8
31ALAALALEULEUCC3 - 83 - 8
41ALAALALEULEUDD3 - 83 - 8
12ILEILELYSLYSAA10 - 7610 - 76
22ILEILELYSLYSBB10 - 7610 - 76
32ILEILELYSLYSCC10 - 7610 - 76
42ILEILELYSLYSDD10 - 7610 - 76
13ALAALATHRTHRAA78 - 11478 - 114
23ALAALATHRTHRBB78 - 11478 - 114
33ALAALATHRTHRCC78 - 11478 - 114
43ALAALATHRTHRDD78 - 11478 - 114
14THRTHRASNASNAA116 - 154116 - 154
24THRTHRASNASNBB116 - 154116 - 154
34THRTHRASNASNCC116 - 154116 - 154
44THRTHRASNASNDD116 - 154116 - 154
15P4CP4CPEGPEGAE - F200 - 201
25P4CP4CPEGPEGBK - L200 - 201
35P4CP4CPEGPEGCS - T200 - 201
45P4CP4CPEGPEGDY - Z200 - 201
16CLCLCLCLAG - H300 - 301
26CLCLCLCLBO - P300 - 301
36CLCLCLCLCU - V300 - 301
46CLCLCLCLDAA - BA300 - 301

NCS oper:
IDCodeMatrixVector
1given(-0.416841, 0.852809, -0.314579), (0.851775, 0.245638, -0.462754), (-0.317368, -0.460846, -0.828793)101.96425, -35.89702, 91.29668
2given(-0.416841, 0.852809, -0.314579), (0.851775, 0.245638, -0.462754), (-0.317368, -0.460846, -0.828793)101.96425, -35.89702, 91.29668
3given(0.109675, 0.993967, -0.000922), (0.993725, -0.109628, 0.022204), (0.021969, -0.003352, -0.999753)42.13312, -47.90314, 136.95863
4given(0.796621, 0.322027, -0.51156), (-0.51674, 0.801902, -0.29989), (0.313648, 0.503242, 0.805216)18.2924, 60.24236, 48.93366

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Components

#1: Protein
MAJOR ALLERGEN DAU C 1 / CR16 / PATHOGENESIS-RELATED PROTEIN GEA20


Mass: 16085.151 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DAUCUS CAROTA (carrot) / Plasmid: PDS 56 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 / References: UniProt: O04298
#2: Chemical
ChemComp-P4C / O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL / POLYETHYLENE 400


Mass: 324.367 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H28O8
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, PRO 36 TO THR ENGINEERED RESIDUE IN CHAIN A, SER 66 TO THR ...ENGINEERED RESIDUE IN CHAIN A, PRO 36 TO THR ENGINEERED RESIDUE IN CHAIN A, SER 66 TO THR ENGINEERED RESIDUE IN CHAIN A, THR 80 TO SER ENGINEERED RESIDUE IN CHAIN A, LEU 102 TO MET ENGINEERED RESIDUE IN CHAIN B, PRO 36 TO THR ENGINEERED RESIDUE IN CHAIN B, SER 66 TO THR ENGINEERED RESIDUE IN CHAIN B, THR 80 TO SER ENGINEERED RESIDUE IN CHAIN B, LEU 102 TO MET ENGINEERED RESIDUE IN CHAIN C, PRO 36 TO THR ENGINEERED RESIDUE IN CHAIN C, SER 66 TO THR ENGINEERED RESIDUE IN CHAIN C, THR 80 TO SER ENGINEERED RESIDUE IN CHAIN C, LEU 102 TO MET ENGINEERED RESIDUE IN CHAIN D, PRO 36 TO THR ENGINEERED RESIDUE IN CHAIN D, SER 66 TO THR ENGINEERED RESIDUE IN CHAIN D, THR 80 TO SER ENGINEERED RESIDUE IN CHAIN D, LEU 102 TO MET
Sequence detailsDAU C 1 VARIANT WITH THE FOLLOWING MUTATIONS P36T S66T T80S L102M

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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: 4.1 Å3/Da / Density % sol: 70 % / Description: NONE
Crystal growpH: 5.4
Details: 2% PEG 400, 100MM NA CITRATE PH 5.4, 2M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.978
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 27, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.7→77.6 Å / Num. obs: 31520 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.1 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BK0

2bk0


Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.915 / SU B: 18.814 / SU ML: 0.174 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.386 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23734 1596 5.1 %RANDOM
Rwork0.22149 ---
obs0.22228 29881 96.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.404 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4464 0 146 16 4626
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224578
X-RAY DIFFRACTIONr_bond_other_d0.0020.022950
X-RAY DIFFRACTIONr_angle_refined_deg1.2171.9786195
X-RAY DIFFRACTIONr_angle_other_deg0.86937297
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5045604
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.91625.946148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.14715707
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.581158
X-RAY DIFFRACTIONr_chiral_restr0.0650.2783
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024992
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02792
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_it0.3271.53007
X-RAY DIFFRACTIONr_mcbond_other0.0691.51240
X-RAY DIFFRACTIONr_mcangle_it0.7124881
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.47831571
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.644.51314
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1810 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.030.05
2Btight positional0.030.05
3Ctight positional0.030.05
4Dtight positional0.030.05
1Atight thermal0.060.5
2Btight thermal0.050.5
3Ctight thermal0.050.5
4Dtight thermal0.050.5
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 102 -
Rwork0.373 2154 -
obs--94.75 %
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)
11.7675-0.50290.23711.57640.73553.3501-0.0250.22790.1571-0.12960.006-0.18-0.30210.21710.0190.1113-0.018-0.02360.13560.04880.060754.264-19.29958.245
21.86940.10990.70992.17950.0413.8688-0.04970.15880.0343-0.17890.0502-0.1928-0.05790.5302-0.00050.1197-0.0375-0.00010.150.05960.070344.338-21.16434.738
32.4715-0.3269-1.39892.03740.16023.560.0287-0.18330.18860.2093-0.0095-0.2021-0.16260.4128-0.01930.1603-0.0405-0.05260.10030.05040.086128.7219.60279.908
42.10420.3549-0.53232.3809-1.3754.75440.0421-0.21490.26540.1829-0.0802-0.0206-0.50660.19830.03810.1398-0.0278-0.05990.12370.01580.082225.691-0.954103.205
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 154
2X-RAY DIFFRACTION2B3 - 154
3X-RAY DIFFRACTION3C3 - 154
4X-RAY DIFFRACTION4D3 - 154

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