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- PDB-7al0: Crystal Structure of Heymonin, a Novel Frog-derived Peptide -

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Basic information

Entry
Database: PDB / ID: 7al0
TitleCrystal Structure of Heymonin, a Novel Frog-derived Peptide
ComponentsHeymonin
KeywordsANTIMICROBIAL PROTEIN / Antimicrobial peptide / Inflammation / Microhyla heymonsivogt
Biological speciesMicrohyla heymonsi (Taiwan rice frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.2 Å
AuthorsKascakova, B. / Prudnikova, T. / Kuta Smatanova, I. / Xu, X.
CitationJournal: Elife / Year: 2021
Title: Characterization and functional analysis of cathelicidin-MH, a novel frog-derived peptide with anti-septicemic properties.
Authors: Chai, J. / Chen, X. / Ye, T. / Zeng, B. / Zeng, Q. / Wu, J. / Kascakova, B. / Martins, L.A. / Prudnikova, T. / Smatanova, I.K. / Kotsyfakis, M. / Xu, X.
History
DepositionOct 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation_author
Revision 1.2May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heymonin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,3413
Polymers4,2701
Non-polymers712
Water19811
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-12 kcal/mol
Surface area4080 Å2
Unit cell
Length a, b, c (Å)53.800, 53.800, 64.326
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-102-

CL

21A-210-

HOH

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Components

#1: Protein/peptide Heymonin


Mass: 4270.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Microhyla heymonsi (Taiwan rice frog)
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 41.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.2→37.73 Å / Num. obs: 1912 / % possible obs: 98 % / Redundancy: 6.7 % / CC1/2: 1 / Net I/σ(I): 28.83
Reflection shellResolution: 2.2→2.34 Å / Num. unique obs: 1912 / CC1/2: 0.971

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Processing

Software
NameVersionClassification
XDSdata processing
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.2→37.73 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.914 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.409 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2737 96 5 %RANDOM
Rwork0.2457 ---
obs0.2471 1816 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 152.8 Å2 / Biso mean: 57.292 Å2 / Biso min: 33.67 Å2
Baniso -1Baniso -2Baniso -3
1-2.08 Å21.04 Å20 Å2
2--2.08 Å20 Å2
3----6.76 Å2
Refinement stepCycle: final / Resolution: 2.2→37.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms297 0 2 13 312
Biso mean--75.2 64.72 -
Num. residues----39
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.013299
X-RAY DIFFRACTIONr_bond_other_d0.0320.017348
X-RAY DIFFRACTIONr_angle_refined_deg1.651.651394
X-RAY DIFFRACTIONr_angle_other_deg2.0661.617816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.523538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.085285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.3671578
X-RAY DIFFRACTIONr_chiral_restr0.1290.241
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02297
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0239
LS refinement shellResolution: 2.202→2.259 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 7 -
Rwork0.357 127 -
all-134 -
obs--97.81 %

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