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- PDB-3ehk: Crystal structure of Pru du amandin, an allergenic protein from p... -

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Basic information

Entry
Database: PDB / ID: 3ehk
TitleCrystal structure of Pru du amandin, an allergenic protein from prunus dulcis
ComponentsPrunin
KeywordsPLANT PROTEIN / Globulin / 11S seed storage protein
Function / homology
Function and homology information


cotyledon development / extraorganismal space / seed development / nutrient reservoir activity / protein hexamerization / metal ion binding
Similarity search - Function
11-S seed storage protein, conserved site / 11-S plant seed storage proteins signature. / 11-S seed storage protein, plant / Cupin / Cupin 1 / Cupin / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls ...11-S seed storage protein, conserved site / 11-S plant seed storage proteins signature. / 11-S seed storage protein, plant / Cupin / Cupin 1 / Cupin / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesPrunus dulcis (almond)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsGaur, V. / Salunke, D.M.
CitationJournal: To be published
Title: Crystal structure of Pru du amandin, an allergenic protein from prunus dulcis
Authors: Gaur, V. / Salunke, D.M.
History
DepositionSep 13, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prunin
B: Prunin
C: Prunin
D: Prunin
E: Prunin
F: Prunin


Theoretical massNumber of molelcules
Total (without water)365,6296
Polymers365,6296
Non-polymers00
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area48510 Å2
ΔGint-132.2 kcal/mol
Surface area66050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.099, 151.099, 164.628
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
Prunin


Mass: 60938.148 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Prunus dulcis (almond) / References: UniProt: Q43607
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.57 Å3/Da / Density % sol: 52.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl (pH8.5), 2.0M Ammonium Sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 7, 2006 / Details: Osmic Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 59067 / Num. obs: 59067 / % possible obs: 96.6 % / Redundancy: 2.56 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 4.1
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 2.43 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 1.7 / % possible all: 98.4

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.2.0019refinement
AUTOMARdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UD1

1ud1


Resolution: 3.2→33.31 Å / Cor.coef. Fo:Fc: 0.86 / Cor.coef. Fo:Fc free: 0.813 / SU B: 56.962 / SU ML: 0.428 / Cross valid method: THROUGHOUT / ESU R Free: 0.654 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27899 4859 10.1 %RANDOM
Rwork0.2543 ---
obs0.25679 43052 78.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.023 Å2
Baniso -1Baniso -2Baniso -3
1-2.88 Å20 Å20 Å2
2--2.88 Å20 Å2
3----5.76 Å2
Refinement stepCycle: LAST / Resolution: 3.2→33.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18252 0 0 107 18359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02118612
X-RAY DIFFRACTIONr_angle_refined_deg1.8911.91125236
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.94952280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.76924.6491110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.706152940
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6715168
X-RAY DIFFRACTIONr_chiral_restr0.1280.22682
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214958
X-RAY DIFFRACTIONr_nbd_refined0.3130.210112
X-RAY DIFFRACTIONr_nbtor_refined0.3430.212371
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2734
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3580.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.27
X-RAY DIFFRACTIONr_mcbond_it7.9711.511424
X-RAY DIFFRACTIONr_mcangle_it11.989218276
X-RAY DIFFRACTIONr_scbond_it4.95437188
X-RAY DIFFRACTIONr_scangle_it5.8094.56960
LS refinement shellResolution: 3.199→3.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 363 -
Rwork0.346 3163 -
obs--78.6 %
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)
10.0933-0.01170.07330.1386-0.1340.83180.0197-0.02280.02-0.0292-0.04630.0425-0.111-0.19370.0265-0.10450.0460.03210.0199-0.051-0.0044110.483487.58011.5233
20.5369-0.14230.21760.1355-0.1220.69270.06180.05890.1637-0.0207-0.0915-0.0235-0.35850.23260.0297-0.0149-0.09320.009-0.00870.015-0.0453142.8064100.9674-13.7254
31.09290.2425-0.21880.1975-0.13530.90950.0042-0.08780.02920.0299-0.04710.01480.01810.14180.0428-0.1548-0.0234-0.00930.03560.0041-0.0709143.93275.851715.0335
40.1878-0.0746-0.02270.4193-0.2871.04140.01780.106-0.06380.0582-0.02530.06020.1614-0.16270.0074-0.1524-0.035-0.03470.0288-0.06880.0035110.496463.4546-21.5551
50.45230.0867-0.20210.2224-0.12230.61610.0306-0.0857-0.15380.0114-0.0815-0.03840.40670.2460.0510.00230.079-0.001-0.01240.0193-0.0368142.814650.1439-6.333
60.5909-0.04120.2750.113-0.07590.75190.0208-0.03930.0009-0.0696-0.02060.01820.0410.1494-0.0003-0.13240.01440.01210.05720.0012-0.0614143.971775.2018-35.0603
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 523
3X-RAY DIFFRACTION2B10 - 523
5X-RAY DIFFRACTION3C10 - 523
7X-RAY DIFFRACTION4D10 - 523
9X-RAY DIFFRACTION5E10 - 523
11X-RAY DIFFRACTION6F10 - 523

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