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- PDB-4g14: Crystal structure of samarosporin I at 293K -

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Basic information

Entry
Database: PDB / ID: 4g14
TitleCrystal structure of samarosporin I at 293K
ComponentsSAMAROSPORIN I
KeywordsANTIBIOTIC / peptaibol / 3(10)-alpha Helix / antibiotic peptide / membrane / extracellular
Function / homologySAMAROSPORIN I / :
Function and homology information
Biological speciessamarospora rostrup (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å
AuthorsGessmann, R. / Axford, D. / Petratos, K.
CitationJournal: J.Pept.Sci. / Year: 2012
Title: The crystal structure of samarosporin I at atomic resolution.
Authors: Gessmann, R. / Axford, D. / Evans, G. / Bruckner, H. / Petratos, K.
History
DepositionJul 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Dec 26, 2012Group: Database references / Structure summary
Revision 1.3Jul 18, 2018Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SAMAROSPORIN I


Theoretical massNumber of molelcules
Total (without water)1,5581
Polymers1,5581
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.280, 9.170, 25.250
Angle α, β, γ (deg.)90.00, 116.59, 90.00
Int Tables number5
Space group name H-MC121
DetailsAS PER AUTHORS THE BIOLOGICAL ASSEMBLY IS MULTIMERIC OF UNKNOWN STOICHIOMETRY

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Components

#1: Protein/peptide SAMAROSPORIN I / EMERIMICIN IV / STILBELLIN I


Type: Peptaibol / Class: Antibiotic / Mass: 1557.876 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) samarospora rostrup (unknown) / Strain: F-7762 / References: NOR: NOR00986, SAMAROSPORIN I
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Compound detailsSAMAROSPORIN I/EMERIMICIN IV IS LINEAR PEPTIDE, A MEMBER OF THE PEPT FAMILY OF MEMBRANE CHANNEL ...SAMAROSPORIN I/EMERIMICIN IV IS LINEAR PEPTIDE, A MEMBER OF THE PEPT FAMILY OF MEMBRANE CHANNEL FORMING PEPTIDES. HERE, SAMAROSPORIN I/EMERIMICIN IV IS REPRESENTED BY THE SEQUENCE (SEQRES) THE N-TERM IS ACETYLATED (RESIDUE 0)

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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: 1.52 Å3/Da / Density % sol: 18.4 %
Crystal growTemperature: 293 K / Method: evaporation / Details: methanol/water, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.7293 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 3, 2012
RadiationMonochromator: ACCEL FIXED EXIT DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7293 Å / Relative weight: 1
ReflectionResolution: 1.09→22.59 Å / Num. all: 4194 / Num. obs: 4194 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Net I/σ(I): 4.2
Reflection shellResolution: 1.09→1.12 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.6 / % possible all: 99.2

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Processing

Software
NameClassification
SHELXL-97refinement
xia2data reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4G13

4g13


Resolution: 1.09→22.59 Å / Num. parameters: 1022 / Num. restraintsaints: 1001 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.171 206 5 %random
Rwork0.12 ---
obs0.123 4194 99.2 %-
all-4194 --
Solvent computationSolvent model: BABINET
Refine analyzeOccupancy sum hydrogen: 112 / Occupancy sum non hydrogen: 114
Refinement stepCycle: LAST / Resolution: 1.09→22.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms112 0 0 2 114

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