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- PDB-1lxe: CRYSTAL STRUCTURE OF THE CATHELICIDIN MOTIF OF PROTEGRINS -

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Basic information

Entry
Database: PDB / ID: 1lxe
TitleCRYSTAL STRUCTURE OF THE CATHELICIDIN MOTIF OF PROTEGRINS
Componentsprotegrin-3 precursor
KeywordsANTIMICROBIAL PROTEIN / PROTEGRIN / CATHELICIDIN MOTIF / DISULFIDE / domain swapping
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 / FOURIER SYNTHESIS / Resolution: 2.5 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
DepositionJun 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: protegrin-3 precursor


Theoretical massNumber of molelcules
Total (without water)11,3231
Polymers11,3231
Non-polymers00
Water81145
1
A: protegrin-3 precursor

A: protegrin-3 precursor


Theoretical massNumber of molelcules
Total (without water)22,6452
Polymers22,6452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area4890 Å2
ΔGint-32 kcal/mol
Surface area12850 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)52.172, 52.172, 135.483
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThe second part of the biological assembly is generated by the two fold axis: Rotation : 0.5000 0.8660 0.0 0.8660 -0.5000 0.0 0.0 0.0 -1.0 Translation : -26.086 45.183 -22.580

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Components

#1: Protein protegrin-3 precursor / pg-3


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.: 45 / 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: 2.35 Å3/Da / Density % sol: 47.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: AMMONIUM SULFATE, SODIUM ACETATE, pH 3.5, 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

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 15, 2002
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→27.1 Å / Num. all: 3922 / Num. obs: 3922 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 43.8 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 18.5
Reflection shellResolution: 2.5→2.66 Å / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 4.6 / Num. unique all: 541 / Rsym value: 0.241 / % possible all: 91.3
Reflection
*PLUS
% possible obs: 93.3 % / Num. measured all: 37505
Reflection shell
*PLUS
% possible obs: 92 %

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Processing

Software
NameClassification
DENZOdata reduction
AUTOMARdata reduction
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1KWI

1kwi


Resolution: 2.5→27.1 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 1799954.7 / Data cutoff high rms absF: 1799954.7 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 386 9.8 %RANDOM
Rwork0.215 ---
all0.21501 3922 --
obs0.21501 3922 93.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 104.394 Å2 / ksol: 0.429523 e/Å3
Displacement parametersBiso mean: 33.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.32 Å27.71 Å20 Å2
2--1.32 Å20 Å2
3----2.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.5→27.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms722 0 0 45 767
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.03
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.931.5
X-RAY DIFFRACTIONc_mcangle_it8.122
X-RAY DIFFRACTIONc_scbond_it5.062
X-RAY DIFFRACTIONc_scangle_it8.052.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.268 67 11 %
Rwork0.231 541 -
obs-541 91.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Lowest resolution: 27.1 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.03

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