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- PDB-5em1: Crystal structure of ragweed allergen Amb a 8 -

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Basic information

Entry
Database: PDB / ID: 5em1
TitleCrystal structure of ragweed allergen Amb a 8
ComponentsProfilin
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
BENZOIC ACID / Profilin
Similarity search - Component
Biological speciesAmbrosia artemisiifolia (common ragweed)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 5, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7503
Polymers14,5931
Non-polymers1582
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.228, 58.466, 60.596
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Profilin /


Mass: 14592.689 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ambrosia artemisiifolia (common ragweed)
Plasmid: pJ411 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2KN24
#2: Chemical ChemComp-BEZ / BENZOIC ACID / Benzoic acid


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 1.96 Å3/Da / Density % sol: 37.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M HEPES, pH 6.5, 1.3 M sodium citrate / PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. all: 20925 / Num. obs: 20925 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 32.2
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.5 / % possible all: 98.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CQA

1cqa


Resolution: 1.45→30.32 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.991 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.165 1067 5.1 %RANDOM
Rwork0.1419 ---
obs0.1431 19808 99.83 %-
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: 51.32 Å2 / Biso mean: 17.471 Å2 / Biso min: 8.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20 Å2
2---0.56 Å2-0 Å2
3---0.91 Å2
Refinement stepCycle: final / Resolution: 1.45→30.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1017 0 10 201 1228
Biso mean--15.01 29.49 -
Num. residues----135
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191118
X-RAY DIFFRACTIONr_bond_other_d0.0010.021062
X-RAY DIFFRACTIONr_angle_refined_deg2.3132.021522
X-RAY DIFFRACTIONr_angle_other_deg0.92332458
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1785151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24425.34943
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.41915150
X-RAY DIFFRACTIONr_dihedral_angle_4_deg31.443153
X-RAY DIFFRACTIONr_chiral_restr0.1170.2164
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211292
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02243
LS refinement shellResolution: 1.451→1.489 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.205 61 -
Rwork0.199 1402 -
all-1463 -
obs--97.73 %
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)
10.2755-0.11140.02170.18290.05220.02890.00210.03-0.05050.0130.00220.0240.00510.0069-0.00430.0390.0022-0.0010.04240.00780.0187-10.1587-17.43339.8169
24.6941-3.54772.63175.454-4.8454.41760.20290.2720.32780.1545-0.01680.1141-0.2014-0.0361-0.1860.0640.02990.04270.05410.04330.0757-12.3131-3.62672.1122
30.38410.05650.2470.1958-0.00190.1714-0.00390.026-0.019-0.00630.0153-0.02990.01090.0131-0.01140.0420.0016-0.00210.0344-0.0030.01553.5945-15.561410.7299
40.47560.23340.05930.4704-0.18460.3087-0.0107-0.0462-0.01370.03430.0045-0.07440.01210.01270.00620.04830.0123-0.01320.0354-0.00870.01959.2203-6.035819.2474
51.2065-0.1377-1.33360.7772-0.09371.5563-0.00270.00550.01930.07390.0069-0.0399-0.0115-0.0021-0.00430.04350.00090.0020.0314-0.00190.01695.6571.136714.7357
60.33050.18640.15580.8682-0.17250.16450.00120.01290.0081-0.00340.00730.03750.00540.0141-0.00850.0538-0.00480.00340.036-0.00470.0025-0.2965-6.14415.7534
76.9445-0.82084.01180.0985-0.364810.22470.16570.06670.2688-0.0243-0.0043-0.0363-0.32090.0895-0.16150.0858-0.01610.00580.00890.00780.0304-3.2711-0.18042.8926
80.64110.2812-0.26441.8457-1.10680.6965-0.02790.00280.02080.04190.05910.0213-0.0388-0.0595-0.03110.05420.01660.01340.04070.01580.0145-10.1923-8.316.1055
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 13
2X-RAY DIFFRACTION2A14 - 21
3X-RAY DIFFRACTION3A22 - 49
4X-RAY DIFFRACTION4A50 - 71
5X-RAY DIFFRACTION5A72 - 80
6X-RAY DIFFRACTION6A81 - 107
7X-RAY DIFFRACTION7A108 - 112
8X-RAY DIFFRACTION8A113 - 133

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