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- PDB-1o83: Crystal Structure of Bacteriocin AS-48 at pH 7.5, phosphate bound... -

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Basic information

Entry
Database: PDB / ID: 1o83
TitleCrystal Structure of Bacteriocin AS-48 at pH 7.5, phosphate bound. Crystal form I
ComponentsPEPTIDE ANTIBIOTIC AS-48
KeywordsPEPTIDE ANTIBIOTIC / BACTERIOCIN / ANTIBACTERIAL PEPTIDE / MEMBRANE PERMEABILIZATION / PROTEIN CRYSTALLOGRAPHY / CYCLIC POLYPEPTIDE / PROTEIN MEMBRANE INTERACTION
Function / homology
Function and homology information


killing of cells of another organism / defense response to bacterium / extracellular region / membrane
Similarity search - Function
Bacteriocin AS-48 / Bacteriocin AS-48 / Circular bacteriocin / Bacteriocin class IId cyclical uberolysin-like / Bacteriocin As-48; Chain A / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / AS-48 protein
Similarity search - Component
Biological speciesENTEROCOCCUS FAECALIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.64 Å
AuthorsSanchez-Barrena, M.J. / Martinez-Ripoll, M. / Galvez, A. / Valdivia, E. / Maqueda, M. / Cruz, V. / Albert, A.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Structure of Bacteriocin as-48: From Soluble State to Membrane Bound State
Authors: Sanchez-Barrena, M.J. / Martinez-Ripoll, M. / Galvez, A. / Valdivia, E. / Maqueda, M. / Cruz, V. / Albert, A.
History
DepositionNov 25, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2019Group: Data collection / Experimental preparation / Other
Category: diffrn_source / exptl_crystal_grow / pdbx_database_status
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site ..._diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.source / _diffrn_source.type / _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PEPTIDE ANTIBIOTIC AS-48
B: PEPTIDE ANTIBIOTIC AS-48
C: PEPTIDE ANTIBIOTIC AS-48
D: PEPTIDE ANTIBIOTIC AS-48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9927
Polymers28,7104
Non-polymers2823
Water6,900383
1
A: PEPTIDE ANTIBIOTIC AS-48


Theoretical massNumber of molelcules
Total (without water)7,1781
Polymers7,1781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PEPTIDE ANTIBIOTIC AS-48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3653
Polymers7,1781
Non-polymers1872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: PEPTIDE ANTIBIOTIC AS-48


Theoretical massNumber of molelcules
Total (without water)7,1781
Polymers7,1781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: PEPTIDE ANTIBIOTIC AS-48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2732
Polymers7,1781
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)79.670, 83.880, 99.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2026-

HOH

21A-2056-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.6347, -0.4502, -0.6281), (-0.6012, -0.2229, 0.7674), (-0.4854, 0.8647, -0.1292)67.2556, 22.6595, 15.5881
2given(0.0364, 0.9985, -0.0411), (0.9991, -0.0355, 0.0226), (0.0211, -0.0419, -0.9989)-3.9841, 0.927, 0.5753
3given(-0.5225, -0.2441, 0.817), (0.5656, 0.6177, 0.5463), (-0.638, 0.7475, -0.1847)25.7128, 18.6244, 28.8505

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Components

#1: Protein
PEPTIDE ANTIBIOTIC AS-48 / BACTERIOCIN AS-48


Mass: 7177.538 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: PEPTIDE LINK BETWEEN RESIDUES 1 AND 70 / Source: (natural) ENTEROCOCCUS FAECALIS (bacteria) / References: UniProt: Q47765
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55 %
Crystal growMethod: vapor diffusion / pH: 7.5
Details: CRYSTAL WAS GROWN USING VAPOUR DIFFUSION TECHNIQUES FROM DROPS CONTAINING AS-48 (20 MG/ML) AND RESERVOIR SOLUTION (0.1 M HEPES-NA PH 7.5, 0.8 M MONO-SODIUM DIHYDROGEN PHOSPHATE) IN A 1:1 RATIO
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
210 mMTris-HCl1droppH7.5
30.2 Mammonium sulfate1reservoir
40.1 Msodium acetate trihydrate1reservoirpH4.5
515 %(w/v)PEG40001reservoir
60.1 Msodium-Hepes1reservoirpH7.5
70.8 Mmono-sodium dihydrogen phosphate1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.64→19.43 Å / Num. obs: 37078 / % possible obs: 90 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 19.43
Reflection shellResolution: 1.64→1.73 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 1.4 / % possible all: 90
Reflection
*PLUS
Highest resolution: 1.64 Å / Lowest resolution: 19.43 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.085
Reflection shell
*PLUS
% possible obs: 90 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 1.4

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.64→15 Å / SU B: 1.95 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.098
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1806 4.9 %RANDOM
Rwork0.193 ---
obs0.195 35069 89.51 %-
Displacement parametersBiso mean: 19.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2--0.12 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.64→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2016 0 16 383 2415
Refinement
*PLUS
Lowest resolution: 15 Å / Rfactor Rfree: 0.2148 / Rfactor Rwork: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.01
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.314
X-RAY DIFFRACTIONplanar_d0.005
LS refinement shell
*PLUS
Highest resolution: 1.64 Å / Lowest resolution: 1.73 Å / Rfactor Rfree: 0.4 / Rfactor Rwork: 0.38

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