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- PDB-4rgd: The structure a AS-48 G13K/L40K mutant -

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Basic information

Entry
Database: PDB / ID: 4rgd
TitleThe structure a AS-48 G13K/L40K mutant
ComponentsBacteriocin AS-48
KeywordsANTIBIOTIC / Circular Bacteriocin / membrane interaction / plasma membrane
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
CITRIC ACID / AS-48 protein
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsSanchez-Barrena, M.J.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: The bacteriocin AS-48 requires dimer dissociation followed by hydrophobic interactions with the membrane for antibacterial activity.
Authors: Cebrian, R. / Martinez-Bueno, M. / Valdivia, E. / Albert, A. / Maqueda, M. / Sanchez-Barrena, M.J.
History
DepositionSep 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacteriocin AS-48
B: Bacteriocin AS-48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7243
Polymers14,5312
Non-polymers1921
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-9 kcal/mol
Surface area7440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.820, 49.910, 41.720
Angle α, β, γ (deg.)90.00, 98.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Bacteriocin AS-48 / AS-48A / Enterocin proprotein / Peptide antibiotic AS-48


Mass: 7265.688 Da / Num. of mol.: 2 / Fragment: UNP residues 36-105 / Mutation: G13K, L40K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: as-48, as48A / Production host: Enterococcus faecalis (bacteria) / References: UniProt: Q47765
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.33 Å3/Da / Density % sol: 47.16 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M ammonium acetate, 30% PEG4K, 0.1M sodium citrate tribasic dihydrate plus ANAPOE-58, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.2→24.9 Å / Num. all: 41746 / Num. obs: 41746 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2
Reflection shellResolution: 1.2→1.22 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.8.0049refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O82

1o82


Resolution: 1.2→24.1 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.974 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.033 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14704 2103 5 %RANDOM
Rwork0.11819 ---
obs0.11969 39619 99.96 %-
all-39619 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.541 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å2-0.34 Å2
2---0.16 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.2→24.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1020 0 13 305 1338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.021104
X-RAY DIFFRACTIONr_bond_other_d00.021208
X-RAY DIFFRACTIONr_angle_refined_deg2.0391.9911493
X-RAY DIFFRACTIONr_angle_other_deg3.46632795
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2795155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.66522.524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.07415227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.613155
X-RAY DIFFRACTIONr_chiral_restr0.1320.2181
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021186
X-RAY DIFFRACTIONr_gen_planes_other0.0220.02211
X-RAY DIFFRACTIONr_mcbond_it0.9930.677576
X-RAY DIFFRACTIONr_mcbond_other0.9980.677575
X-RAY DIFFRACTIONr_mcangle_it1.2011.028721
X-RAY DIFFRACTIONr_mcangle_other1.2021.028722
X-RAY DIFFRACTIONr_scbond_it4.6491.257528
X-RAY DIFFRACTIONr_scbond_other4.6451.258529
X-RAY DIFFRACTIONr_scangle_other5.161.639764
X-RAY DIFFRACTIONr_long_range_B_refined6.0049.8471711
X-RAY DIFFRACTIONr_long_range_B_other5.1347.6721477
X-RAY DIFFRACTIONr_rigid_bond_restr13.95532312
X-RAY DIFFRACTIONr_sphericity_free51.32527
X-RAY DIFFRACTIONr_sphericity_bonded11.40152570
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 135 -
Rwork0.212 2938 -
obs--99.93 %

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