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- PDB-5em0: Crystal structure of mugwort allergen Art v 4 -

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Basic information

Entry
Database: PDB / ID: 5em0
TitleCrystal structure of mugwort allergen Art v 4
ComponentsPollen allergen Art v 4.01
KeywordsALLERGEN
Function / homology
Function and homology information


oligopeptide binding / actin binding / cytoskeleton / cytoplasm
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 speciesArtemisia vulgaris (common wormwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsOffermann, L.R. / 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_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pollen allergen Art v 4.01
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6273
Polymers14,3651
Non-polymers2612
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.107, 59.180, 32.578
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-477-

HOH

21A-479-

HOH

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Components

#1: Protein Pollen allergen Art v 4.01 / Profilin-1


Mass: 14365.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Artemisia vulgaris (common wormwood) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8H2C9
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 37.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M HEPES, pH 8.5, 1.3 M Sodium Citrate / PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. all: 44768 / Num. obs: 44768 / % possible obs: 96.4 % / Redundancy: 4.3 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 36.78
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 4 % / Rmerge(I) obs: 0.724 / Mean I/σ(I) obs: 2.1 / % possible all: 90.8

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Processing

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

1cqa


Resolution: 1.1→26.38 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.251 / SU ML: 0.028 / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.034 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1902 2276 5.1 %RANDOM
Rwork0.1654 ---
obs0.1667 42383 96.21 %-
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: 54.07 Å2 / Biso mean: 17.37 Å2 / Biso min: 9.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å2-0 Å2
2---1.61 Å20 Å2
3---1.41 Å2
Refinement stepCycle: final / Resolution: 1.1→26.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 16 213 1230
Biso mean--28.41 30.46 -
Num. residues----134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191055
X-RAY DIFFRACTIONr_bond_other_d0.0010.021000
X-RAY DIFFRACTIONr_angle_refined_deg2.0641.9781428
X-RAY DIFFRACTIONr_angle_other_deg0.9043.0022316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7435139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.88425.81443
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.4815172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg40.689152
X-RAY DIFFRACTIONr_chiral_restr0.1250.2152
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021213
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02225
LS refinement shellResolution: 1.1→1.129 Å
Num. reflection% reflection
Rfree167 -
Rwork2886 -
obs-89.61 %
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)
10.4242-0.8841-0.10793.28710.45510.0645-0.0491-0.0212-0.00130.1490.04160.04310.01920.00870.00760.03660.00640.00040.04950.00180.00511.5547-6.610810.026
20.5712-0.0759-0.26342.52641.20161.7344-0.0043-0.02220.00820.11360.01340.0101-0.0039-0.0718-0.00910.02560.00850.00450.06320.0020.0012.97625.776412.8556
30.8153-0.4369-0.02670.3861-0.01150.1060.00020.0196-0.03040.00230.00220.0043-0.0066-0.0004-0.00240.0203-0.00020.00050.04690.00040.017410.933-3.27380.6333
40.20910.2170.02770.3560.27020.57650.00520.0278-0.0388-0.02070.0122-0.0515-0.00260.0214-0.01740.02970.00420.0070.0563-0.00740.014718.27411.2982-8.7437
50.5029-0.13110.19550.54460.03730.0929-0.00380.04470.0022-0.0490.0065-0.0107-0.01450.0142-0.00270.0358-0.0020.00360.04980.00490.007714.674610.1772-9.6465
61.297-0.05110.37150.41390.11760.2448-0.0063-0.0071-0.01230.02510.009-0.0245-0.0448-0.0107-0.00260.031-0.0035-0.00690.0470.00760.017216.810712.2593-0.7194
70.523-0.15120.07580.0444-0.01620.2155-0.0208-0.0150.0290.00690.01-0.0085-0.01830.01740.01080.02410.0001-0.00280.04570.00210.018114.54294.83696.0328
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 11
2X-RAY DIFFRACTION2A12 - 20
3X-RAY DIFFRACTION3A21 - 42
4X-RAY DIFFRACTION4A43 - 58
5X-RAY DIFFRACTION5A59 - 77
6X-RAY DIFFRACTION6A78 - 89
7X-RAY DIFFRACTION7A90 - 133

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