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- PDB-1k9u: Crystal Structure of the Calcium-Binding Pollen Allergen Phl p 7 ... -

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Basic information

Entry
Database: PDB / ID: 1k9u
TitleCrystal Structure of the Calcium-Binding Pollen Allergen Phl p 7 (Polcalcin) at 1.75 Angstroem
ComponentsPolcalcin Phl p 7
KeywordsALLERGEN / pollen allergen / calcium-binding / EF-hand / cross-reactivity
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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesPhleum pratense (timothy grass)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsVerdino, P. / Westritschnig, K. / Valenta, R. / Keller, W.
CitationJournal: EMBO J. / Year: 2002
Title: The cross-reactive calcium-binding pollen allergen, Phl p 7, reveals a novel dimer assembly
Authors: Verdino, P. / Westritschnig, K. / Valenta, R. / Keller, W.
History
DepositionOct 30, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: 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 / diffrn_source / pdbx_struct_conn_angle / software / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX determination method: author determined

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polcalcin Phl p 7
B: Polcalcin Phl p 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8189
Polymers17,3692
Non-polymers4497
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-130 kcal/mol
Surface area7970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.084, 56.205, 37.238
Angle α, β, γ (deg.)90.00, 90.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Polcalcin Phl p 7 / Timothy Grass Pollen Allergen Phl p 7 / P7


Mass: 8684.694 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phleum pratense (timothy grass) / Gene: Phlpr / Plasmid: pET 17b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL 21 (DE 3) / References: UniProt: O82040
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 1.87 Å3/Da / Density % sol: 34.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.3
Details: ammonium sulfate, PEG 4000, alanine/HCl, pH 3.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / PH range low: 3.4 / PH range high: 3.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15.0 mg/mlprotein1drop
20.2 Mammonium sulfate1reservoir
324-28 %PEG40001reservoir
40.1 Malanine/HCl1reservoirpH3.2-3.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8482 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 8, 2001
RadiationMonochromator: triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8482 Å / Relative weight: 1
ReflectionResolution: 1.75→14 Å / Num. all: 13072 / Num. obs: 13072 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 26.5 Å2 / Rsym value: 0.047 / Net I/σ(I): 35.3
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 7.9 / Num. unique all: 638 / Rsym value: 0.185 / % possible all: 99.8
Reflection
*PLUS
Lowest resolution: 14 Å / % possible obs: 100 % / Num. measured all: 122317 / Rmerge(I) obs: 0.047
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 7.3

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: SAD / Resolution: 1.75→13.92 Å / Isotropic thermal model: isotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.223 664 5.1 %RANDOM
Rwork0.192 ---
all-12982 --
obs-12982 99.6 %-
Displacement parametersBiso mean: 22.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→13.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1282 0 19 157 1458
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg0.97
X-RAY DIFFRACTIONc_bond_d0.0046
X-RAY DIFFRACTIONc_dihedral_angle_d18.76
X-RAY DIFFRACTIONc_improper_angle_d0.66
LS refinement shellResolution: 1.75→1.81 Å
RfactorNum. reflection% reflection
Rfree0.313 73 -
Rwork0.233 --
obs-1294 100 %
Refinement
*PLUS
Lowest resolution: 14 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.2252 / Rfactor Rwork: 0.1984
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.76
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.66

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