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- PDB-5eve: Crystal structure of Amb a 8 in complex with poly-Pro10 -

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Basic information

Entry
Database: PDB / ID: 5eve
TitleCrystal structure of Amb a 8 in complex with poly-Pro10
Components
  • Poly-Proline peptide
  • Profilin
KeywordsALLERGEN
Function / homology
Function and homology information


sequestering of actin monomers / 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: 2.55 Å
AuthorsOffermann, L.R. / Schlachter, C.R. / Garrett, J. / 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 10, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Profilin
B: Poly-Proline peptide


Theoretical massNumber of molelcules
Total (without water)15,1152
Polymers15,1152
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-8 kcal/mol
Surface area6920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.473, 40.424, 42.004
Angle α, β, γ (deg.)90.000, 91.880, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Profilin


Mass: 14126.067 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ambrosia artemisiifolia (common ragweed)
Plasmid: pJExpress411 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2KN24
#2: Protein/peptide Poly-Proline peptide


Mass: 989.163 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 1.99 Å3/Da / Density % sol: 38.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1 M Sodium Citrate, pH 6.5, 100 mM sodium cacodylate
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 24, 2015
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 3959 / Num. obs: 3959 / % possible obs: 97.1 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.051 / Rrim(I) all: 0.096 / Χ2: 1.875 / Net I/av σ(I): 23.333 / Net I/σ(I): 11 / Num. measured all: 13348
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.55-2.592.80.4522.461790.7970.3010.5451.06491.3
2.59-2.6430.4111770.7790.2640.4910.995.2
2.64-2.693.10.3952170.8560.2570.4731.1895.2
2.69-2.753.20.3731930.9070.2360.4430.98397.5
2.75-2.813.40.321890.8940.1960.3761.26296.9
2.81-2.873.40.2861930.9030.1780.3381.16997.5
2.87-2.943.50.2312070.9610.1390.271.42399
2.94-3.023.50.1982070.9720.1210.2321.38398.6
3.02-3.113.70.1831830.9770.110.2151.40698.4
3.11-3.213.60.1731960.9670.1060.2041.51199.5
3.21-3.333.50.1272030.9890.0780.151.61198.5
3.33-3.463.60.12000.9890.0610.1171.97399
3.46-3.623.40.0982100.990.060.1152.54198.1
3.62-3.813.50.0931970.9890.0590.112.58298.5
3.81-4.053.50.0652000.9960.040.0772.31998.5
4.05-4.363.30.0581960.9950.0360.0682.7197.5
4.36-4.83.40.0512040.9970.0320.0612.68596.7
4.8-5.493.50.0522010.9960.0330.0622.91797.6
5.49-6.923.40.0462080.9960.0290.0542.1598.6
6.92-503.10.0481990.9940.0330.0593.2289.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
REFMAC5.8.0131refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EM0

5em0


Resolution: 2.55→41.98 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.2128 / WRfactor Rwork: 0.1878 / FOM work R set: 0.7858 / SU B: 30.298 / SU ML: 0.27 / SU R Cruickshank DPI: 0.2849 / SU Rfree: 0.3283 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2334 199 5.2 %RANDOM
Rwork0.2005 ---
obs0.2023 3663 97.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 129.37 Å2 / Biso mean: 59.397 Å2 / Biso min: 35.98 Å2
Baniso -1Baniso -2Baniso -3
1-4.36 Å20 Å24.22 Å2
2---4.17 Å2-0 Å2
3----0.47 Å2
Refinement stepCycle: final / Resolution: 2.55→41.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1047 0 0 8 1055
Biso mean---43.82 -
Num. residues----142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191079
X-RAY DIFFRACTIONr_bond_other_d0.0020.021011
X-RAY DIFFRACTIONr_angle_refined_deg1.1821.9781469
X-RAY DIFFRACTIONr_angle_other_deg0.87832350
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.325140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44725.38539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.60515159
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.096152
X-RAY DIFFRACTIONr_chiral_restr0.0620.2155
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211224
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02218
X-RAY DIFFRACTIONr_mcbond_it0.5333.924566
X-RAY DIFFRACTIONr_mcbond_other0.5333.917565
X-RAY DIFFRACTIONr_mcangle_it0.9915.874704
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 10 -
Rwork0.357 246 -
all-256 -
obs--91.76 %
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)
13.62120.1534-0.03096.7865-1.97725.080.1037-0.04360.0853-0.0386-0.2127-0.42110.13970.29430.1090.07570.0196-0.01940.09620.0050.03728.12880.67979.0273
26.16017.4985-1.38379.1362-1.46246.37340.4475-0.4714-0.41060.5608-0.5804-0.49740.10160.04570.13290.1756-0.0926-0.01120.05990.02380.02993.7228-8.607223.2888
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 133
2X-RAY DIFFRACTION2B1 - 10

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