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- PDB-1qnx: Ves v 5, an allergen from Vespula vulgaris venom -

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Basic information

Entry
Database: PDB / ID: 1qnx
TitleVes v 5, an allergen from Vespula vulgaris venom
ComponentsVES V 5
KeywordsALLERGEN / ANTIGEN 5 / VESPID VENOM
Function / homology
Function and homology information


extracellular space
Similarity search - Function
Venom allergen 5-like / CRISP family signature 2. / Allergen V5/Tpx-1-related, conserved site / CRISP family signature 1. / Cysteine-rich secretory protein-related / Pathogenesis-related Protein p14a / CAP / SCP / Tpx-1 / Ag5 / PR-1 / Sc7 family of extracellular domains. / CAP domain / Cysteine-rich secretory protein family ...Venom allergen 5-like / CRISP family signature 2. / Allergen V5/Tpx-1-related, conserved site / CRISP family signature 1. / Cysteine-rich secretory protein-related / Pathogenesis-related Protein p14a / CAP / SCP / Tpx-1 / Ag5 / PR-1 / Sc7 family of extracellular domains. / CAP domain / Cysteine-rich secretory protein family / CAP superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesVESPULA VULGARIS (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.9 Å
AuthorsHenriksen, A. / Gajhede, M. / Spangfort, M.D.
CitationJournal: Proteins: Struct.,Funct., Genet. / Year: 2001
Title: Major Venom Allergen of Yellow Jackets, Ves V 5: Structural Characterization of a Pathogenesis-Related Protein Superfamily.
Authors: Henriksen, A. / King, T.P. / Mirza, O. / Monsalve, R.I. / Meno, K. / Ipsen, H. / Larsen, J.N. / Gajhede, M. / Spangfort, M.D.
History
DepositionOct 25, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VES V 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8852
Polymers23,8621
Non-polymers231
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)45.359, 62.179, 82.777
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein VES V 5 / ANTIGEN 5


Mass: 23862.076 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VESPULA VULGARIS (insect) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q05110
#2: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.45 Å3/Da / Density % sol: 49.71 %
Crystal growpH: 5.6 / Details: 18% PEG6000, 0.1M CITRTE BUFFER PH 5.6
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / PH range low: 6 / PH range high: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
116-20 %(w/v)PEG60001reservoir
2100 mMcitrate1reservoir
35 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.959
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.959 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 17809 / % possible obs: 93.2 % / Redundancy: 8.1 % / Biso Wilson estimate: 8.3 Å2 / Rsym value: 0.067
Reflection shellResolution: 1.9→1.97 Å / Rsym value: 0.178 / % possible all: 98.9
Reflection
*PLUS
Rmerge(I) obs: 0.067
Reflection shell
*PLUS
% possible obs: 98.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.178 / Mean I/σ(I) obs: 6.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS0.5phasing
SHARPphasing
CNS0.5refinement
RefinementMethod to determine structure: MIRAS / Resolution: 1.9→30 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 799294.98 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.236 845 4.8 %RANDOM
Rwork0.209 ---
obs0.209 17556 92 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.9 Å2 / ksol: 0.365376 e/Å3
Displacement parametersBiso mean: 18 Å2
Baniso -1Baniso -2Baniso -3
1--4.06 Å20 Å20 Å2
2--4.19 Å20 Å2
3----0.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.03 Å
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1676 0 1 251 1928
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.491.5
X-RAY DIFFRACTIONc_mcangle_it0.852
X-RAY DIFFRACTIONc_scbond_it1.782
X-RAY DIFFRACTIONc_scangle_it2.52.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.271 136 4.5 %
Rwork0.215 2863 -
obs--96.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74

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