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- PDB-5ev0: Crystal structure of ragweed profilin Amb a 8 in complex with pol... -

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Basic information

Entry
Database: PDB / ID: 5ev0
TitleCrystal structure of ragweed profilin Amb a 8 in complex with poly-Pro14
Components
  • PRO-PRO-PRO-PRO-PRO-PRO-PRO-PRO-PRO
  • Profilin
KeywordsALLERGEN
Function / homology
Function and homology information


actin monomer binding / cell cortex / cytoskeleton
Similarity search - Function
Profilin conserved site / Profilin signature. / Profilin / Profilin / : / Profilin / Profilin superfamily / Dynein light chain 2a, cytoplasmic / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesAmbrosia artemisiifolia (common ragweed)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsOffermann, L.R. / He, J.Z. / Perdue, M.L. / Chruszcz, M.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural, Functional, and Immunological Characterization of Profilin Panallergens Amb a 8, Art v 4, and Bet v 2.
Authors: Offermann, L.R. / Schlachter, C.R. / Perdue, M.L. / Majorek, K.A. / He, J.Z. / Booth, W.T. / Garrett, J. / Kowal, K. / Chruszcz, M.
History
DepositionNov 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2016Group: Database references
Revision 1.2Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Oct 16, 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: Profilin
B: Profilin
C: PRO-PRO-PRO-PRO-PRO-PRO-PRO-PRO-PRO
D: PRO-PRO-PRO-PRO-PRO-PRO-PRO-PRO-PRO


Theoretical massNumber of molelcules
Total (without water)30,4774
Polymers30,4774
Non-polymers00
Water1,44180
1
A: Profilin
C: PRO-PRO-PRO-PRO-PRO-PRO-PRO-PRO-PRO


Theoretical massNumber of molelcules
Total (without water)15,2382
Polymers15,2382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-10 kcal/mol
Surface area6610 Å2
MethodPISA
2
B: Profilin
D: PRO-PRO-PRO-PRO-PRO-PRO-PRO-PRO-PRO


Theoretical massNumber of molelcules
Total (without water)15,2382
Polymers15,2382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-9 kcal/mol
Surface area6800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.132, 40.342, 60.256
Angle α, β, γ (deg.)90.000, 104.420, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 132
2010B1 - 132

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Components

#1: Protein Profilin


Mass: 14346.314 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ambrosia artemisiifolia (common ragweed)
Plasmid: pJExpress411 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2KN24
#2: Protein/peptide PRO-PRO-PRO-PRO-PRO-PRO-PRO-PRO-PRO


Mass: 892.048 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
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: 2.13 Å3/Da / Density % sol: 42.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M HEPES, pH 6.5, 1.4 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 22, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 14967 / Num. obs: 14967 / % possible obs: 98.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 22.7
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 2.7 / % possible all: 92.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMACrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5EM0

5em0


Resolution: 2.1→45.47 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.784 / SU ML: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.259 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2342 761 5 %RANDOM
Rwork0.1925 ---
obs0.1947 14328 98.93 %-
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 max: 97.94 Å2 / Biso mean: 35.564 Å2 / Biso min: 18.91 Å2
Baniso -1Baniso -2Baniso -3
1-2.64 Å20 Å2-2.96 Å2
2--1.3 Å2-0 Å2
3----2.81 Å2
Refinement stepCycle: final / Resolution: 2.1→45.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2103 0 0 80 2183
Biso mean---37.95 -
Num. residues----285
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192177
X-RAY DIFFRACTIONr_bond_other_d0.0060.022038
X-RAY DIFFRACTIONr_angle_refined_deg1.7591.9842963
X-RAY DIFFRACTIONr_angle_other_deg1.1283.0024735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2425285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.60425.580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.98515320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.722154
X-RAY DIFFRACTIONr_chiral_restr0.0920.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212483
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02441
Refine LS restraints NCS

Ens-ID: 1 / Number: 7256 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 56 -
Rwork0.286 981 -
all-1037 -
obs--93.09 %

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