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- PDB-2opo: Crystal structure of the calcium-binding pollen allergen Che a 3 -

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Basic information

Entry
Database: PDB / ID: 2opo
TitleCrystal structure of the calcium-binding pollen allergen Che a 3
ComponentsPolcalcin Che a 3
KeywordsALLERGEN / calcium-binding protein / dimer / domain-swapping / EF-hand
Function / homology
Function and homology information


calcium ion binding
Similarity search - Function
: / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair ...: / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesChenopodium album (lamb's-quarters)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsVerdino, P. / Keller, W.
Citation
Journal: J.Immunol. / Year: 2008
Title: Three-dimensional structure of the cross-reactive pollen allergen Che a 3: visualizing cross-reactivity on the molecular surfaces of weed, grass, and tree pollen allergens.
Authors: Verdino, P. / Barderas, R. / Villalba, M. / Westritschnig, K. / Valenta, R. / Rodriguez, R. / Keller, W.
#1: Journal: J.Allergy Clin.Immunol. / Year: 2004
Title: Profilin (Che a 2) and polcalcin (Che a 3) are relevant allergens of Chenopodium album pollen: isolation, amino acid sequences, and immunologic properties
Authors: Barderas, R. / Villalba, M. / Pascual, C.Y. / Batanero, E. / Rodriguez, R.
History
DepositionJan 29, 2007Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 6, 2007ID: 1PMZ
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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

Downloads & links

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Assembly

Deposited unit
A: Polcalcin Che a 3
B: Polcalcin Che a 3
C: Polcalcin Che a 3
D: Polcalcin Che a 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,95916
Polymers38,2544
Non-polymers70512
Water4,900272
1
A: Polcalcin Che a 3
B: Polcalcin Che a 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4808
Polymers19,1272
Non-polymers3526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-116 kcal/mol
Surface area8950 Å2
MethodPISA, PQS
2
C: Polcalcin Che a 3
D: Polcalcin Che a 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4808
Polymers19,1272
Non-polymers3526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-101 kcal/mol
Surface area9340 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)72.240, 73.874, 68.939
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Polcalcin Che a 3 / Calcium-binding pollen allergen Che a 3


Mass: 9563.561 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chenopodium album (lamb's-quarters) / Plasmid: pET-11b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q84V36
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.4
Details: 0.2 M ammonium sulfate, 22% PEG 4000, 0.1 M alanine/HCl, pH 3.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 6, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. all: 37929 / Num. obs: 37132 / % possible obs: 97.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.8 % / Biso Wilson estimate: 24.7 Å2 / Rsym value: 0.057 / Net I/σ(I): 18.1
Reflection shellResolution: 1.75→1.81 Å / Mean I/σ(I) obs: 3.2 / Num. unique all: 3151 / Rsym value: 0.283 / % possible all: 84.5

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Processing

Software
NameVersionClassification
REFMAC5.3.0017refinement
HKL-2000data reduction
HKL-2000data scaling
BEASTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1K9U

1k9u


Resolution: 1.75→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.618 / SU ML: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.137 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24713 2815 7.8 %RANDOM
Rwork0.19802 ---
all0.20172 37132 --
obs0.20172 33503 95.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.066 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20 Å2
2---1.47 Å20 Å2
3---1.8 Å2
Refinement stepCycle: LAST / Resolution: 1.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2575 0 28 272 2875
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222822
X-RAY DIFFRACTIONr_bond_other_d0.0020.022057
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.9743817
X-RAY DIFFRACTIONr_angle_other_deg0.95634959
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9255373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.42322.857154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.65415534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6761541
X-RAY DIFFRACTIONr_chiral_restr0.1010.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023240
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02649
X-RAY DIFFRACTIONr_nbd_refined0.2440.2863
X-RAY DIFFRACTIONr_nbd_other0.20.22259
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21462
X-RAY DIFFRACTIONr_nbtor_other0.0850.21566
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2225
X-RAY DIFFRACTIONr_metal_ion_refined0.1170.240
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.230.275
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1020.232
X-RAY DIFFRACTIONr_mcbond_it1.1621.51784
X-RAY DIFFRACTIONr_mcbond_other0.3271.5703
X-RAY DIFFRACTIONr_mcangle_it1.75822783
X-RAY DIFFRACTIONr_scbond_it2.6331155
X-RAY DIFFRACTIONr_scangle_it3.9124.51011
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 116 -
Rwork0.267 1343 -
obs-1343 53.38 %
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)
14.68525.2724-1.74865.9332-1.96770.6526-0.29580.33930.076-0.4370.33580.07930.0875-0.0913-0.040.0495-0.01940.01150.00950.0373-0.008514.829816.715230.888
22.57512.0834-2.1981.9615-1.52852.2909-0.18850.2241-0.2124-0.34870.0879-0.20330.0483-0.04080.10070.0059-0.0140.0279-0.0352-0.0263-0.077319.960512.623233.3173
31.5116-1.97810.95752.697-1.12810.75-0.0775-0.11590.12530.13430.0647-0.1616-0.09970.03910.0128-0.0871-0.00990.0213-0.03050.011-0.072620.249815.680464.4486
41.0309-1.56141.28012.4017-1.86481.7387-0.1071-0.0210.16160.03210.0359-0.3279-0.07670.02420.0712-0.0682-0.00460.0074-0.02320.002-0.039124.375720.318667.9675
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 866 - 86
2X-RAY DIFFRACTION2BB6 - 866 - 86
3X-RAY DIFFRACTION3CC2 - 862 - 86
4X-RAY DIFFRACTION4DD5 - 865 - 86

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