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- PDB-4n42: Crystal structure of allergen protein scam1 from Scadoxus multiflorus -

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Basic information

Entry
Database: PDB / ID: 4n42
TitleCrystal structure of allergen protein scam1 from Scadoxus multiflorus
ComponentsXylanase and alpha-amylase inhibitor protein isoform III
KeywordsHYDROLASE INHIBITOR / Tim Barrel
Function / homology
Function and homology information


alpha-amylase inhibitor activity / chitinase activity / chitinase / xylan catabolic process / extracellular region
Similarity search - Function
Chitinase Cts1-like / : / Glycosyl hydrolases family 18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / chitinase
Similarity search - Component
Biological speciesScadoxus multiflorus (plant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSingh, A. / Kumar, S. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To be published
Title: Crystal structure of allergen protein scam1 from Scadoxus multiflorus
Authors: Singh, A. / Kumar, S. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionOct 8, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Experimental preparation
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Xylanase and alpha-amylase inhibitor protein isoform III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7242
Polymers29,6291
Non-polymers951
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.736, 65.265, 49.320
Angle α, β, γ (deg.)90.00, 102.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Xylanase and alpha-amylase inhibitor protein isoform III


Mass: 29629.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Scadoxus multiflorus (plant) / References: UniProt: E3VTL0
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.1M sodium acetate, 20% PEG 6000, VAPOR DIFFUSION, HANGING DROP, pH 7.2, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.514 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 5, 2013 / Details: Mirror
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.514 Å / Relative weight: 1
ReflectionResolution: 2.2→65.26 Å / Num. obs: 15078 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.064 / Net I/σ(I): 7.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O9N

3o9n


Resolution: 2.2→65.2 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.264 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19618 667 4.9 %RANDOM
Rwork0.15334 ---
obs0.15545 12838 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.726 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20.16 Å2
2--0.17 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.2→65.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2094 0 5 154 2253
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.016
X-RAY DIFFRACTIONr_angle_refined_deg1.724
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.507
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.141
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.47
X-RAY DIFFRACTIONr_chiral_restr0.114
X-RAY DIFFRACTIONr_gen_planes_refined0.01
X-RAY DIFFRACTIONr_mcbond_it
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 44 -
Rwork0.184 979 -
obs--100 %

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