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- PDB-2vzn: Crystal structure of the major allergen from fire ant venom, Sol i 3 -

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Basic information

Entry
Database: PDB / ID: 2vzn
TitleCrystal structure of the major allergen from fire ant venom, Sol i 3
ComponentsVENOM ALLERGEN 3
KeywordsALLERGEN / MAJOR FIRE ANT ALLERGEN / SOL I 3 / SECRETED / CROSS-REACTIVITY
Function / homology
Function and homology information


extracellular region
Similarity search - Function
Venom allergen 3, insect / 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 ...Venom allergen 3, insect / 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 speciesSOLENOPSIS INVICTA (red fire ant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsPadavattan, S. / Markovic-Housley, Z.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal Structure of the Major Allergen from Fire Ant Venom, Sol I 3
Authors: Padavattan, S. / Schmidt, M. / Hoffman, D.R. / Markovic-Housley, Z.
History
DepositionAug 5, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 15, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VENOM ALLERGEN 3
B: VENOM ALLERGEN 3


Theoretical massNumber of molelcules
Total (without water)49,6542
Polymers49,6542
Non-polymers00
Water00
1
A: VENOM ALLERGEN 3


Theoretical massNumber of molelcules
Total (without water)24,8271
Polymers24,8271
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: VENOM ALLERGEN 3


Theoretical massNumber of molelcules
Total (without water)24,8271
Polymers24,8271
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)93.355, 93.355, 144.051
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A3 - 6
2111B3 - 6
1211A15 - 28
2211B15 - 28
1311A33 - 62
2311B33 - 62
1411A63 - 70
2411B63 - 70
1511A71 - 73
2511B71 - 73
1611A76 - 99
2611B76 - 99
1711A101 - 119
2711B101 - 119
1811A126 - 143
2811B126 - 143
1911A144 - 156
2911B144 - 156
11011A158 - 160
21011B158 - 160
11111A161 - 181
21111B161 - 181
11211A188 - 192
21211B188 - 192
11311A194 - 210
21311B194 - 210

NCS oper: (Code: given
Matrix: (0.8875, -0.4511, -0.09406), (-0.4532, -0.8914, -0.001191), (-0.08331, 0.04368, -0.9956)
Vector: 2.931, 4.283, 43.13)

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Components

#1: Protein VENOM ALLERGEN 3 / VENOM ALLERGEN III / ALLERGEN SOL I III / VENOM ALLERGEN SOLI 3


Mass: 24827.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SOLENOPSIS INVICTA (red fire ant) / Tissue: VENOM GLAND / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P35778

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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: 3.77 Å3/Da / Density % sol: 67 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: THE HANGING-DROP VAPOR WATER (9.9 MG/ML) WAS MIXED WITH RESERVOIR SOLUTION (19% (W/V) POLYETHYLENE GLYCOL (PEG) 1000, 100 MM TRIS-HCL, PH 8.5) AT A RATIO OF 1:1.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.978
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 2, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.04→80.85 Å / Num. obs: 13121 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 2.68 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.07
Reflection shellResolution: 3.04→3.07 Å / Redundancy: 2.52 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 1.37 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALATRUNCATEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QNX

1qnx


Resolution: 3.05→30 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.905 / SU B: 35.351 / SU ML: 0.31 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0 / ESU R Free: 0.383 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY AND HAVE OCCUPANCY OF ZERO
RfactorNum. reflection% reflectionSelection details
Rfree0.239 652 5.02 %RANDOM
Rwork0.201 ---
obs0.203 13061 96.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 47.89 Å2
Baniso -1Baniso -2Baniso -3
1-0.163 Å20.082 Å2-0 Å2
2--0.163 Å20 Å2
3----0.245 Å2
Refinement stepCycle: LAST / Resolution: 3.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3219 0 0 0 3219
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0213314
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0161.9064528
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1965412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.23424.167156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.36515470
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2791516
X-RAY DIFFRACTIONr_chiral_restr0.0620.2485
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023762
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.2769
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21669
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.288
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.222
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6921.52128
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.02923348
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.55931371
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3114.51180
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2233 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.040.05
2Btight thermal0.090.5
LS refinement shellResolution: 3.05→3.13 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.278 47
Rwork0.332 893
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)
13.31541.3440.72696.883-2.42076.9935-0.14620.00230.2648-0.6970.2201-0.20570.54420.0252-0.0739-0.1405-0.01250.0792-0.311-0.0088-0.051139.2662.4548.222
24.145-3.0863-1.28179.32430.65792.90850.1743-0.3182-0.51420.3472-0.1550.4036-0.0798-0.0496-0.0194-0.09560.0567-0.1074-0.09630.0822-0.032836.163-15.67331.258
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 204
2X-RAY DIFFRACTION2B2 - 204

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