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- PDB-1l3p: CRYSTAL STRUCTURE OF THE FUNCTIONAL DOMAIN OF THE MAJOR GRASS POL... -

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Basic information

Entry
Database: PDB / ID: 1l3p
TitleCRYSTAL STRUCTURE OF THE FUNCTIONAL DOMAIN OF THE MAJOR GRASS POLLEN ALLERGEN Phl p 5b
ComponentsPOLLEN ALLERGEN Phl p 5b
KeywordsALLERGEN / grass pollen allergen / phl p 5b / allergy
Function / homology
Function and homology information


RNA nuclease activity
Similarity search - Function
Group V grass pollen allergen / Pollen allergen Poa p IX/Phl p VI / Pollen allergen/Uncharacterized protein Os / Ribonuclease (pollen allergen) / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Pollen allergen Phl p 5b
Similarity search - Component
Biological speciesPhleum pratense (timothy grass)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.98 Å
AuthorsRajashankar, K.R. / Bufe, A. / Weber, W. / Eschenburg, S. / Lindner, B. / Betzel, C.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Structure of the functional domain of the major grass-pollen allergen Phlp 5b.
Authors: Rajashankar, K. / Bufe, A. / Weber, W. / Eschenburg, S. / Lindner, B. / Betzel, C.
#1: Journal: J.Biol.Chem. / Year: 1996
Title: Crystallization and preliminary diffraction data of a major pollen allergen. Crystal growth separates a low molecular weight form with elevated biological activity
Authors: Bufe, A. / Betzel, C. / Schramm, G. / Petersen, A. / Becker, W.M. / Schlaak, M. / Perbandt, M. / Dauter, Z. / Weber, W.
History
DepositionFeb 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Feb 8, 2017Group: Database references
Revision 1.5Oct 11, 2017Group: Refinement description / Category: software
Revision 1.6Apr 3, 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 / 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.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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE Author states that residue 195 is serine, but both serine and threonine are in dual conformation.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POLLEN ALLERGEN Phl p 5b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7313
Polymers10,6121
Non-polymers1192
Water1,74797
1
A: POLLEN ALLERGEN Phl p 5b
hetero molecules

A: POLLEN ALLERGEN Phl p 5b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4636
Polymers21,2242
Non-polymers2394
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area1990 Å2
ΔGint-44 kcal/mol
Surface area9780 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)38.975, 50.355, 107.804
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-255-

HOH

21A-302-

HOH

31A-303-

HOH

DetailsThe second part of the dimer is generated by the symmetry operation x,-y,-z

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Components

#1: Protein POLLEN ALLERGEN Phl p 5b / Phl p VB


Mass: 10612.089 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phleum pratense (timothy grass) / Plasmid: pMalc / Production host: Escherichia coli (E. coli) / References: UniProt: Q40963
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.52 Å3/Da / Density % sol: 51.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 1.6M phosphate, 0.5mM MgCl2, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K
Crystal grow
*PLUS
Temperature: 295 K / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16 mg/mlprotein1drop
21.6 Mphosphate1reservoirpH4.0
30.5 mM1reservoirMgCl2
40.1 mMATP1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.2 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 2, 1997
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 1.98→27 Å / Num. all: 7641 / Num. obs: 7037 / % possible obs: 96.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.38 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 31.21
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 7 % / Rmerge(I) obs: 0.117 / Mean I/σ(I) obs: 12.23 / Num. unique all: 374 / % possible all: 98.7
Reflection
*PLUS
Num. obs: 7641 / Num. measured all: 56414
Reflection shell
*PLUS
% possible obs: 92.1 %

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
CCP4model building
CNSrefinement
CCP4phasing
RefinementMethod to determine structure: SIRAS
Starting model: HG DERIVATIVE

Resolution: 1.98→27 Å / Data cutoff high absF: 10000 / Data cutoff high rms absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 350 -RANDOM
Rwork0.193 ---
all0.209 7641 --
obs0.197 7037 92 %-
Refinement stepCycle: LAST / Resolution: 1.98→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms738 0 6 97 841
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
Refinement
*PLUS
Lowest resolution: 27 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.3

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