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- PDB-2ygu: Crystal structure of fire ant venom allergen, Sol I 2 -

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Basic information

Entry
Database: PDB / ID: 2ygu
TitleCrystal structure of fire ant venom allergen, Sol I 2
ComponentsVENOM ALLERGEN 2
KeywordsALLERGEN / HYDROPHOBIC CAVITY / INSECT ODORANT BINDING PROTEIN
Function / homologyRecoverin; domain 1 - #190 / Ant venom allergen, Sol i 2 / Ant venom allergen, Sol i 2/4 superfamily / Recoverin; domain 1 / extracellular region / Orthogonal Bundle / Mainly Alpha / HEPTANE / Venom allergen 2
Function and homology information
Biological speciesSOLENOPSIS INVICTA (red fire ant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsBorer, A.S. / Wassmann, P. / Schirmer, T. / Markovic-Housley, Z.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Crystal Structure of Sol I 2, a Major Allergen from Fire Ant Venom
Authors: Borer, A.S. / Wassmann, P. / Schmidt, M. / Hoffman, D.R. / Zhou, J.J. / Wright, C. / Schirmer, T. / Markovic-Housley, Z.
History
DepositionApr 20, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2011Group: Other
Revision 1.2Feb 1, 2012Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VENOM ALLERGEN 2
B: VENOM ALLERGEN 2
C: VENOM ALLERGEN 2
D: VENOM ALLERGEN 2
E: VENOM ALLERGEN 2
F: VENOM ALLERGEN 2
G: VENOM ALLERGEN 2
H: VENOM ALLERGEN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,37316
Polymers112,5718
Non-polymers8028
Water1,42379
1
A: VENOM ALLERGEN 2
B: VENOM ALLERGEN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3434
Polymers28,1432
Non-polymers2002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-11.1 kcal/mol
Surface area10820 Å2
MethodPISA
2
C: VENOM ALLERGEN 2
D: VENOM ALLERGEN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3434
Polymers28,1432
Non-polymers2002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-9.5 kcal/mol
Surface area10850 Å2
MethodPISA
3
E: VENOM ALLERGEN 2
F: VENOM ALLERGEN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3434
Polymers28,1432
Non-polymers2002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-10.4 kcal/mol
Surface area11020 Å2
MethodPISA
4
G: VENOM ALLERGEN 2
H: VENOM ALLERGEN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3434
Polymers28,1432
Non-polymers2002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-11.8 kcal/mol
Surface area11050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.211, 139.160, 62.093
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS oper:
IDCodeMatrixVector
1given(-0.820122, -0.279169, -0.499463), (-0.27394, -0.574791, 0.771085), (-0.502351, 0.769207, 0.394924)130.39331, 157.1152, -40.00195
2given(0.986226, 0.014641, 0.164754), (0.004721, 0.993177, -0.116521), (-0.165336, 0.115694, 0.979428)51.95231, -34.32674, -41.15942
3given(-0.747003, -0.32934, -0.577513), (-0.380576, -0.500426, 0.777648), (-0.545113, 0.800693, 0.248481)116.22147, 132.14749, -108.78986
4given(0.998654, -0.014597, 0.049761), (0.018685, 0.996399, -0.082699), (-0.048374, 0.083518, 0.995331)3.49769, -73.6613, -6.83435
5given(-0.809925, -0.299829, -0.504107), (-0.301247, -0.524802, 0.796137), (-0.503261, 0.796672, 0.334728)151.44754, 194.50041, -98.96213
6given(0.991853, -0.010667, 0.126938), (0.007081, 0.999564, 0.028668), (-0.127189, -0.027535, 0.991496)54.87603, -104.25691, -25.56086
7given(-0.750545, -0.264782, -0.605453), (-0.364229, -0.598722, 0.713351), (-0.55138, 0.755925, 0.352926)128.75276, 183.22346, -156.42894

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Components

#1: Protein
VENOM ALLERGEN 2 / ALLERGEN SOL I II / VENOM ALLERGEN II / ALLERGEN=SOL I 2 / SOL I 2


Mass: 14071.392 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: CYS 22 DISULFIDE INTERCHAIN LINKS FOR CHAINS A WITH B, C WITH D, E WITH F, AND G WITH H.
Source: (gene. exp.) SOLENOPSIS INVICTA (red fire ant) / Organ: VENOM GLAND / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P35775
#2: Chemical
ChemComp-HP6 / HEPTANE / Heptane


Mass: 100.202 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C7H16
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 1-19 NOT EXPRESSED (SIGNAL SEQUENCE).

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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: 2.1 Å3/Da / Density % sol: 41.4 % / Description: NONE
Crystal growpH: 9.2
Details: PROTEIN WAS CRYSTALLIZED FROM 35% PEG 8000, 0.1M NAACETATE, PH 9.2 .

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 9, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.58→69.66 Å / Num. obs: 28662 / % possible obs: 95 % / Observed criterion σ(I): 1.9 / Redundancy: 3.2 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.3
Reflection shellResolution: 2.58→2.72 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.8 / % possible all: 86.3

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
SHARPphasing
DMphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.6→15 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.902 / SU B: 30.851 / SU ML: 0.29 / Cross valid method: THROUGHOUT / ESU R: 0 / ESU R Free: 0.372 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE TRANSFORMATIONS PRESENTED IN MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN .THIS ENTRY. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE TRANSFORMATIONS PRESENTED IN MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN .THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE ORIGINAL RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE TRANSFORMED RESIDUES LISTED SECOND AND GIVE THE FOLLOWING RMSD VALUES ON CA: ORIGINAL TRANSFORMED RMSD (ANGSTROM UNITS) RESIDUES RESIDUES FOR CA ATOMS A1-117 B1-117 0.13 A1-117 C1-117 0.09 A1-117 D1-117 0.08 A1-117 E1-117 0.11 A1-117 F1-117 0.11 A1-117 G1-117 0.13 A3-117 H3-117 0.11
RfactorNum. reflection% reflectionSelection details
Rfree0.27046 1434 5.1 %RANDOM
Rwork0.23714 ---
obs0.23887 26886 94.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.676 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20 Å2
2---1.01 Å20 Å2
3---1.34 Å2
Refinement stepCycle: LAST / Resolution: 2.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6872 0 56 79 7007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227031
X-RAY DIFFRACTIONr_bond_other_d0.0020.024948
X-RAY DIFFRACTIONr_angle_refined_deg1.0051.9739541
X-RAY DIFFRACTIONr_angle_other_deg0.9123.00211857
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2365935
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.36324.504262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.595151183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.981560
X-RAY DIFFRACTIONr_chiral_restr0.0510.21131
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217813
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021207
X-RAY DIFFRACTIONr_nbd_refined0.2170.21767
X-RAY DIFFRACTIONr_nbd_other0.1690.24441
X-RAY DIFFRACTIONr_nbtor_refined0.1710.23572
X-RAY DIFFRACTIONr_nbtor_other0.0830.23645
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2118
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2070.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.121.54711
X-RAY DIFFRACTIONr_mcbond_other0.6821.51864
X-RAY DIFFRACTIONr_mcangle_it3.25827586
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.37932320
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.6344.51955
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: 1252 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.010.02
2Btight positional0.010.02
3Ctight positional0.010.02
4Dtight positional0.010.02
5Etight positional0.010.02
6Ftight positional0.010.02
7Gtight positional0.010.02
8Htight positional0.010.02
1Atight thermal2.5610
2Btight thermal2.4410
3Ctight thermal2.7810
4Dtight thermal2.3810
5Etight thermal2.4710
6Ftight thermal2.710
7Gtight thermal2.510
8Htight thermal2.9210
LS refinement shellResolution: 2.6→2.665 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 96 -
Rwork0.376 1615 -
obs--81.36 %
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)
13.60151.4472-1.72865.4534-2.36132.76850.1009-0.07160.4202-0.3292-0.12450.2274-0.0085-0.04030.02360.06350.01860.00950.0997-0.03810.184760.02766.652-27.635
23.59970.5326-0.62626.3452-0.42524.8730.0147-0.3337-0.0967-0.2003-0.1692-0.73520.0310.47020.15450.07140.00910.07220.18490.02660.342776.50481.029-29.799
34.36610.4085-2.81356.3099-1.72892.28050.1670.10650.4516-0.6501-0.0554-0.4028-0.1078-0.1388-0.11160.32770.0420.00970.1832-0.02180.24286.042101.8972.77
45.7475-0.3312-1.00074.98020.30295.5496-0.0645-0.28730.4995-0.3592-0.0442-0.9304-0.22960.54310.10860.2484-0.07730.24840.1548-0.03620.692522.752116.2031.612
52.3402-0.1171-1.92754.9993-1.34844.0021-0.0516-0.00560.2232-0.41160.04220.2177-0.1569-0.2080.00930.0932-0.0027-0.04770.1917-0.04420.200160.023137.196-29.679
64.366-0.223-1.35975.790.66844.4925-0.02-0.54650.3502-0.32680.044-0.3331-0.21490.5129-0.0240.1109-0.0880.03480.2433-0.06550.242676.874151.093-31.949
74.81342.3365-1.84018.8056-2.66072.9147-0.03070.10370.3331-0.5574-0.05990.45240.0566-0.14760.09060.04720.0276-0.05040.1261-0.05380.13246.581170.8683.242
83.52020.41080.07657.035-0.24913.20260.0151-0.4158-0.0006-0.0892-0.1114-0.6374-0.020.37810.09630.04540.02280.02050.2147-0.03440.216723.302185.0823.623
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 400
2X-RAY DIFFRACTION2B1 - 400
3X-RAY DIFFRACTION3C1 - 400
4X-RAY DIFFRACTION4D1 - 400
5X-RAY DIFFRACTION5E1 - 400
6X-RAY DIFFRACTION6F1 - 400
7X-RAY DIFFRACTION7G1 - 400
8X-RAY DIFFRACTION8H1 - 400

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