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- PDB-6mbx: CRYSTAL STRUCTURE OF MUSKMELON ALLERGEN CUC M 2 -

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Basic information

Entry
Database: PDB / ID: 6mbx
TitleCRYSTAL STRUCTURE OF MUSKMELON ALLERGEN CUC M 2
ComponentsProfilin
KeywordsALLERGEN / PROFILIN / FOOD ALLERGEN
Function / homology
Function and homology information


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 speciesCucumis melo (muskmelon)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKapingidza, A.B. / Hyduke, N.P. / Chruszcz, M.
CitationJournal: Mol.Immunol. / Year: 2019
Title: Comparative structural and thermal stability studies of Cuc m 2.0101, Art v 4.0101 and other allergenic profilins.
Authors: Kapingidza, A.B. / Pye, S.E. / Hyduke, N. / Dolamore, C. / Pote, S. / Schlachter, C.R. / Commins, S.P. / Kowal, K. / Chruszcz, M.
History
DepositionAug 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Profilin
B: Profilin
C: Profilin


Theoretical massNumber of molelcules
Total (without water)49,6883
Polymers49,6883
Non-polymers00
Water43224
1
A: Profilin


Theoretical massNumber of molelcules
Total (without water)16,5631
Polymers16,5631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Profilin


Theoretical massNumber of molelcules
Total (without water)16,5631
Polymers16,5631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Profilin


Theoretical massNumber of molelcules
Total (without water)16,5631
Polymers16,5631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.608, 59.237, 82.911
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 2 - 131 / Label seq-ID: 26 - 155

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Profilin / Pollen allergen Cuc m 2


Mass: 16562.635 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cucumis melo (muskmelon) / Plasmid: pJExpress411 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3)pLySs / References: UniProt: Q5FX67
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.54 Å3/Da / Density % sol: 51.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.8M sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 19535 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.026 / Rrim(I) all: 0.042 / Rsym value: 0.037 / Net I/σ(I): 31.8
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 962 / CC1/2: 0.876 / Rpim(I) all: 0.368 / Rrim(I) all: 0.607 / Rsym value: 0.309 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
SBC-Collectdata collection
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
BUCCANEERmodel building
HKL-2000data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5em0

5em0


Resolution: 2.4→32.26 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.939 / SU B: 32.381 / SU ML: 0.323 / Cross valid method: THROUGHOUT / ESU R: 0.368 / ESU R Free: 0.254 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2611 990 5.1 %RANDOM
Rwork0.23093 ---
obs0.23256 18524 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 94.246 Å2
Baniso -1Baniso -2Baniso -3
1--4.99 Å20 Å21.72 Å2
2--1.1 Å20 Å2
3---3.88 Å2
Refinement stepCycle: 1 / Resolution: 2.4→32.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2889 0 0 24 2913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0142949
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172706
X-RAY DIFFRACTIONr_angle_refined_deg1.2941.6524003
X-RAY DIFFRACTIONr_angle_other_deg0.8361.6386334
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1325387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.77525.882119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.66715477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.421154
X-RAY DIFFRACTIONr_chiral_restr0.0630.2384
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023331
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02505
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8782.1481557
X-RAY DIFFRACTIONr_mcbond_other0.8772.1471556
X-RAY DIFFRACTIONr_mcangle_it1.4933.2211941
X-RAY DIFFRACTIONr_mcangle_other1.4933.2211942
X-RAY DIFFRACTIONr_scbond_it0.8542.131392
X-RAY DIFFRACTIONr_scbond_other0.8532.131392
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3893.1782062
X-RAY DIFFRACTIONr_long_range_B_refined4.21925.1173198
X-RAY DIFFRACTIONr_long_range_B_other4.2125.0823197
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A39630.05
12B39630.05
21A39640.05
22C39640.05
31B39470.04
32C39470.04
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 76 -
Rwork0.361 1367 -
obs--99.93 %
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)
15.9658-5.7142-6.015915.87440.70359.6535-0.3579-1.02340.9886-0.4030.0012-2.4753-0.53731.74040.35671.676-0.0846-0.28110.32580.18111.354733.6124.2955.077
25.0633-2.2396-0.651416.13650.78788.81880.3580.54610.4116-3.0911-0.80561.3745-0.16450.01380.44761.83010.1893-0.31260.13440.06820.818523.0161.431-6.068
37.1104-5.7547-0.229815.4911.69118.5377-0.4463-0.6012-0.1053-1.06660.090.82670.42520.48670.35631.04470.13740.10710.10340.04740.537726.636-3.9633.054
48.6644-6.58443.204313.86543.47268.2308-0.969-0.66091.2699-0.47790.6336-1.7303-0.93921.55370.33530.65590.3474-0.20371.07510.06971.012938.62-4.78522.986
58.3262-3.5332-1.1719.03391.58339.3827-1.4391-2.2196-1.29891.4051.14270.49850.28320.21240.29640.83020.7191-0.04610.99260.29540.721230.174-11.9633.777
68.6055-5.5864-0.777213.46341.27928.0961-0.6654-1.1002-0.4843-0.13640.37940.3069-0.4866-0.1550.2860.48280.3896-0.19640.4579-0.08960.432727.941-6.00524.771
718.2892-0.69923.55052.15213.62528.12580.37630.0605-2.06570.4091-0.55490.25771.5334-0.19860.17860.76510.61050.11620.92190.03430.92934.86-3.09532.683
811.048-3.27430.07125.67090.99219.51390.99483.0660.9015-0.7851-1.4274-0.86280.02890.02250.43260.45220.55270.07191.36710.25660.8237.9247.57121.793
915.8573-0.5277-0.6115.1383-0.70267.00560.61140.55130.6691-0.1917-0.9565-0.23750.1693-0.55390.34510.31320.2803-0.10890.6056-0.17770.40171.2196.94330.365
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 30
2X-RAY DIFFRACTION2A31 - 70
3X-RAY DIFFRACTION3A71 - 131
4X-RAY DIFFRACTION4B2 - 32
5X-RAY DIFFRACTION5B33 - 69
6X-RAY DIFFRACTION6B70 - 131
7X-RAY DIFFRACTION7C2 - 30
8X-RAY DIFFRACTION8C31 - 68
9X-RAY DIFFRACTION9C69 - 131

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