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- PDB-1pfp: CATHELIN-LIKE MOTIF OF PROTEGRIN-3 -

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Basic information

Entry
Database: PDB / ID: 1pfp
TitleCATHELIN-LIKE MOTIF OF PROTEGRIN-3
ComponentsProtegrin 3
KeywordsANTIMICROBIAL PROTEIN / PG-3 / SeMet / SeCys / diselenide
Function / homology
Function and homology information


lipopolysaccharide binding / antimicrobial humoral immune response mediated by antimicrobial peptide / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / innate immune response / extracellular space
Similarity search - Function
Cathelicidins signature 1. / Cathelicidin, conserved site / Cathelicidins signature 2. / Cathelicidin-like / Cathelicidin / Nuclear Transport Factor 2; Chain: A, - #10 / Cystatin superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsStrub, M.-P. / Hoh, F. / Sanchez, J.-F. / Strub, J.M. / Bock, A. / Aumelas, A. / Dumas, C.
Citation
Journal: Structure / Year: 2003
Title: Selenomethionine and Selenocysteine Double Labeling Strategy for Crystallographic Phasing
Authors: Strub, M.-P. / Hoh, F. / Sanchez, J.-F. / Strub, J.M. / Bock, A. / Aumelas, A. / Dumas, C.
#1: Journal: Structure / Year: 2002
Title: Structure of the cathelicidin motif of protegrin-3 precursor: structural insights into the activation mechanism of an antimicrobial protein.
Authors: Sanchez, J.-F. / Hoh, F. / Strub, M.-P. / Aumelas, A. / Dumas, C.
History
DepositionMay 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 19, 2014Group: Atomic model / Structure summary
Revision 1.4Aug 6, 2014Group: Derived calculations / Structure summary
Revision 1.5Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protegrin 3


Theoretical massNumber of molelcules
Total (without water)11,9711
Polymers11,9711
Non-polymers00
Water63135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.541, 51.541, 134.512
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Protegrin 3 / PG-3


Mass: 11970.686 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: NPG3 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)selB::kan cys51E / References: UniProt: P32196
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.15 Å3/Da / Density % sol: 42.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 3.8
Details: ammonium sulfate, sodium acetate, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110-15 mg/mlprotein1drop
22.1 Mammonium sulfate1reservoir
3sodium acetate1reservoirpH3.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97992 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 1, 2002 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97992 Å / Relative weight: 1
ReflectionResolution: 2.3→23.5 Å / Num. all: 5162 / Num. obs: 5162 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Biso Wilson estimate: 30.7 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 13.1
Reflection shellResolution: 2.3→2.36 Å / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.295 / % possible all: 98.1
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 23 Å / Num. measured all: 48282
Reflection shell
*PLUS
% possible obs: 98.6 %

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→23.5 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.905 / SU B: 9.501 / SU ML: 0.218 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.353 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: restrained and TLS refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.28357 659 12.8 %RANDOM
Rwork0.21932 ---
all0.22713 5162 --
obs0.22713 4503 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.847 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å2-0.23 Å20 Å2
2---0.46 Å20 Å2
3---0.7 Å2
Refinement stepCycle: LAST / Resolution: 2.3→23.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms685 0 0 35 720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021694
X-RAY DIFFRACTIONr_bond_other_d0.0020.02638
X-RAY DIFFRACTIONr_angle_refined_deg1.562.013940
X-RAY DIFFRACTIONr_angle_other_deg0.85931489
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.19584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0820.2111
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02752
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02127
X-RAY DIFFRACTIONr_nbd_refined0.2540.2147
X-RAY DIFFRACTIONr_nbd_other0.2360.2750
X-RAY DIFFRACTIONr_nbtor_other0.1010.2438
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.225
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1360.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2560.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.7651.5437
X-RAY DIFFRACTIONr_mcangle_it1.482713
X-RAY DIFFRACTIONr_scbond_it1.9783257
X-RAY DIFFRACTIONr_scangle_it3.1914.5227
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.323 43
Rwork0.279 333
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 23 Å / Rfactor Rfree: 0.283 / Rfactor Rwork: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.016
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.56

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