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- PDB-6shk: High resolution structure of the antimicrobial peptide Dermcidin ... -

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Basic information

Entry
Database: PDB / ID: 6shk
TitleHigh resolution structure of the antimicrobial peptide Dermcidin from human
ComponentsDermcidin
KeywordsANTIMICROBIAL PROTEIN / AMP / antimicrobial peptides / channel / barrel stave model
Function / homology
Function and homology information


killing by host of symbiont cells / Hydrolases; Acting on peptide bonds (peptidases) / Antimicrobial peptides / monoatomic ion channel activity / defense response to fungus / peptidase activity / defense response to bacterium / lipid binding / proteolysis / RNA binding ...killing by host of symbiont cells / Hydrolases; Acting on peptide bonds (peptidases) / Antimicrobial peptides / monoatomic ion channel activity / defense response to fungus / peptidase activity / defense response to bacterium / lipid binding / proteolysis / RNA binding / extracellular exosome / extracellular region / membrane / metal ion binding
Similarity search - Function
Dermcidin / Dermcidin/Lacritin / Dermcidin, antibiotic peptide
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.992 Å
AuthorsZeth, K.
Citation
Journal: To be published
Title: Crystal Structure and Functional Mechanism of a Human Antimicrobial Membrane Channel
Authors: Zeth, K.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Crystal structure and functional mechanism of a human antimicrobial membrane channel.
Authors: Song, C. / Weichbrodt, C. / Salnikov, E.S. / Dynowski, M. / Forsberg, B.O. / Bechinger, B. / Steinem, C. / de Groot, B.L. / Zachariae, U. / Zeth, K.
History
DepositionAug 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dermcidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,9573
Polymers4,8271
Non-polymers1312
Water00
1
A: Dermcidin
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)29,74418
Polymers28,9596
Non-polymers78512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area10600 Å2
ΔGint-429 kcal/mol
Surface area17620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.758, 50.758, 105.880
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein/peptide Dermcidin / Preproteolysin


Mass: 4826.503 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCD, AIDD, DSEP / Production host: Escherichia coli (E. coli)
References: UniProt: P81605, Hydrolases; Acting on peptide bonds (peptidases)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.72 Å3/Da / Density % sol: 54.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 4000, Ph 7, 200 mM Zinc

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 6939 / % possible obs: 99.4 % / Redundancy: 9.34 % / CC1/2: 0.99 / Rmerge(I) obs: 0.092 / Rrim(I) all: 0.098 / Net I/σ(I): 11.32
Reflection shellResolution: 1.99→2.11 Å / Rmerge(I) obs: 3.5 / Mean I/σ(I) obs: 0.48 / Num. unique obs: 1072 / CC1/2: 0.54 / Rrim(I) all: 3.8

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YMK

2ymk


Resolution: 1.992→35.293 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 43.89
RfactorNum. reflection% reflection
Rfree0.2737 341 4.96 %
Rwork0.281 --
obs0.2806 6870 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 157.98 Å2 / Biso mean: 79.3895 Å2 / Biso min: 39.72 Å2
Refinement stepCycle: final / Resolution: 1.992→35.293 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms337 0 2 0 339
Biso mean--103.97 --
Num. residues----48
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.992-2.50910.41461700.3625323798
2.5091-35.290.25511710.2679329299
Refinement TLS params.Method: refined / Origin x: 0.3332 Å / Origin y: 10.2572 Å / Origin z: 50.5063 Å
111213212223313233
T0.5015 Å2-0.1075 Å2-0.0244 Å2-0.6228 Å20.0234 Å2--0.5298 Å2
L1.3203 °2-0.7765 °2-1.2003 °2-1.6843 °20.9691 °2--2.2863 °2
S-0.1149 Å °0.1617 Å °-0.012 Å °0.0442 Å °0.0399 Å °0.1186 Å °1.2991 Å °-1.3064 Å °0.0277 Å °
Refinement TLS groupSelection details: chain 'A' and (resid 1 through 48 )

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