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- PDB-3e7u: X-ray Crystal Structure of L-Plectasin -

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Basic information

Entry
Database: PDB / ID: 3e7u
TitleX-ray Crystal Structure of L-Plectasin
ComponentsPlectasin
KeywordsANTIMICROBIAL PROTEIN / plectasin / molecular replacement / Antibiotic / Antimicrobial / Cleavage on pair of basic residues / Defensin / Pharmaceutical / Secreted
Function / homology
Function and homology information


potassium channel regulator activity / toxin activity / defense response to bacterium / host cell plasma membrane / extracellular region / membrane
Similarity search - Function
Arthropod defensin / Invertebrate defensins family profile. / Defensin, invertebrate/fungal / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Fungal defensin plectasin
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsMandal, K. / Pentelute, B.L. / Tereshko, V. / Kossiakoff, A.A. / Kent, S.B.H.
CitationJournal: Protein Sci. / Year: 2009
Title: Racemic crystallography of synthetic protein enantiomers used to determine the X-ray structure of plectasin by direct methods
Authors: Mandal, K. / Pentelute, B.L. / Tereshko, V. / Thammavongsa, V. / Schneewind, O. / Kossiakoff, A.A. / Kent, S.B.
History
DepositionAug 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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
Revision 1.3Nov 13, 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
X: Plectasin


Theoretical massNumber of molelcules
Total (without water)4,4151
Polymers4,4151
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.919, 53.919, 21.964
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein/peptide Plectasin


Mass: 4415.024 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide is naturally found in Pseudoplectania nigrella (Ebony cup).
References: UniProt: Q53I06
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.1 Å3/Da / Density % sol: 41.32 %
Crystal growTemperature: 292 K / pH: 7.5
Details: 0.1 M HEPES, 0.2 M ammonium acetate, 21% PEG 3350., pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 19, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 15193 / % possible obs: 99.1 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 23.3
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 5.2 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3E7R

3e7r


Resolution: 1.35→23.35 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.573 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.182 396 4.9 %RANDOM
Rwork0.157 ---
obs0.158 7731 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å20 Å2
2--0.08 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.35→23.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms305 0 0 48 353
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021317
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7371.914424
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.172539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.16224.66715
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.1881550
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0970.234
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02252
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.2144
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.2213
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.230
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3140.228
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1080.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8071.5197
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.842299
X-RAY DIFFRACTIONr_scbond_it9.3583143
X-RAY DIFFRACTIONr_scangle_it9.6884.5125
X-RAY DIFFRACTIONr_rigid_bond_restr10.2583340
X-RAY DIFFRACTIONr_sphericity_free9.321348
X-RAY DIFFRACTIONr_sphericity_bonded7.3573305
LS refinement shellResolution: 1.35→1.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 31 -
Rwork0.154 540 -
obs--96.13 %

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