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- PDB-3e7r: X-ray Crystal Structure of Racemic Plectasin -

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Basic information

Entry
Database: PDB / ID: 3e7r
TitleX-ray Crystal Structure of Racemic Plectasin
ComponentsPlectasin
KeywordsANTIMICROBIAL PROTEIN / plectasin / racemic protein crystallography / Antibiotic / Antimicrobial / Cleavage on pair of basic residues / Defensin / 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 / AB INITIO PHASING / Resolution: 1 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 1.2Mar 28, 2012Group: Other
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
L: Plectasin


Theoretical massNumber of molelcules
Total (without water)4,4151
Polymers4,4151
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)23.581, 23.812, 24.492
Angle α, β, γ (deg.)109.65, 94.95, 97.69
Int Tables number2
Space group name H-MP-1

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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.: 24 / 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: 1.41 Å3/Da / Density % sol: 14.53 %
Crystal growTemperature: 292 K / pH: 7
Details: 0.1 M HEPES, 22.5% (w/v) Jeffamine ED-2001, pH 7, 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: Oct 24, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1→50 Å / Num. obs: 22253 / % possible obs: 83.2 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 12
Reflection shellResolution: 1→1.04 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 4.8 / % possible all: 32

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1→22.84 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.955 / SU B: 0.522 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1100 5 %RANDOM
Rwork0.202 ---
obs0.203 21051 83.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.08 Å20.03 Å2
2---0.03 Å2-0.05 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1→22.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms302 0 0 24 326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021322
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7491.91432
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.453539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.39124.37516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.5441548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.090.234
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02260
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1920.2135
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3230.2220
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0690.210
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.241
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9271.5196
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.8252299
X-RAY DIFFRACTIONr_scbond_it4.2463151
X-RAY DIFFRACTIONr_scangle_it5.8734.5133
X-RAY DIFFRACTIONr_rigid_bond_restr2.233347
X-RAY DIFFRACTIONr_sphericity_free12.1324
X-RAY DIFFRACTIONr_sphericity_bonded7.0423309
LS refinement shellResolution: 1→1.03 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 30 -
Rwork0.323 574 -
obs--30.41 %

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