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- PDB-1kwi: Crystal Structure Analysis of the Cathelicidin Motif of Protegrins -

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Basic information

Entry
Database: PDB / ID: 1kwi
TitleCrystal Structure Analysis of the Cathelicidin Motif of Protegrins
ComponentsProtegrin-3 Precursor
KeywordsANTIMICROBIAL PROTEIN / protegrin / cathelicidin motif / disulfide / MAD / selenocystine
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
Cathelicidin / Cathelicidins signature 1. / Cathelicidin, conserved site / Cathelicidins signature 2. / Cathelicidin-like / 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 / MAD / Resolution: 2.19 Å
AuthorsSanchez, J.F. / Hoh, F. / Strub, M.P. / Aumelas, A. / Dumas, C.
CitationJournal: 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
DepositionJan 29, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protegrin-3 Precursor


Theoretical massNumber of molelcules
Total (without water)11,3231
Polymers11,3231
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.360, 51.360, 133.677
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 Precursor


Mass: 11322.741 Da / Num. of mol.: 1 / Fragment: RESIDUES 30-130
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: pg3 / Plasmid: pET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P32196
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O

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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: 2.25 Å3/Da / Density % sol: 40 %
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
Temperature: 18 ℃ / PH range low: 3.7 / PH range high: 3.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
20.1 Msodium citrate1reservoirpH3.5-3.7
31.5 Mammonium sulfate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF BM1410.9791, 0.9793, 0.9717
SYNCHROTRONESRF BM30A20.9881
Detector
TypeIDDetectorDateDetails
MARRESEARCH1CCDSep 16, 2001mirrors
MARRESEARCH2CCDMar 29, 2001mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1mirrorsMADMx-ray1
2mirrorsSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97931
30.97171
40.98811
ReflectionResolution: 2.19→24 Å / Num. all: 5386 / Num. obs: 5360 / % possible obs: 91.1 % / Observed criterion σ(F): 1 / Redundancy: 7.6 % / Biso Wilson estimate: 31.9 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 12.2
Reflection shellResolution: 2.19→2.29 Å / % possible all: 94.3
Reflection
*PLUS
Highest resolution: 2.19 Å / Num. obs: 9865 / % possible obs: 93.1 % / Num. measured all: 99989 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 90 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEmodel building
CNS1refinement
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.19→23.97 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 1501596 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.291 568 10.6 %RANDOM
Rwork0.229 ---
all0.248 5360 --
obs0.229 5360 91.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 85.8159 Å2 / ksol: 0.415484 e/Å3
Displacement parametersBiso mean: 37.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.09 Å22.65 Å20 Å2
2--2.09 Å20 Å2
3----4.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.19→23.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms668 0 0 73 741
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.19→2.33 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.313 99 11.1 %
Rwork0.231 790 -
obs--93.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Lowest resolution: 23.97 Å / % reflection Rfree: 10.5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.64
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.04

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