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- PDB-1o84: Crystal Structure of Bacteriocin AS-48. N-decyl-beta-D-maltoside ... -

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Basic information

Entry
Database: PDB / ID: 1o84
TitleCrystal Structure of Bacteriocin AS-48. N-decyl-beta-D-maltoside Bound.
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
alpha-maltose / DECANE / AS-48 protein
Similarity search - Component
Biological speciesENTEROCOCCUS FAECALIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 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 1.3May 30, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.4Oct 16, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,41210
Polymers14,3552
Non-polymers1,0578
Water45025
1
A: PEPTIDE ANTIBIOTIC AS-48
B: PEPTIDE ANTIBIOTIC AS-48
hetero molecules

A: PEPTIDE ANTIBIOTIC AS-48
B: PEPTIDE ANTIBIOTIC AS-48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,82420
Polymers28,7104
Non-polymers2,11416
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
MethodPQS
Unit cell
Length a, b, c (Å)76.488, 76.488, 51.517
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-1072-

SO4

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.6455, 0.1237, 0.7537), (0.0138, -0.9847, 0.1735), (0.7637, 0.1224, 0.6339)
Vector: 26.4733, 42.3851, -17.938)

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Components

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Protein / Sugars , 2 types, 3 molecules AB

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


Mass: 7177.538 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: CYCLIC PROTEIN, LINK BETWEEN M1 AND W70 / Source: (natural) ENTEROCOCCUS FAECALIS (bacteria) / References: UniProt: Q47765
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 32 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.69 Å3/Da / Density % sol: 54 %
Crystal growMethod: vapor diffusion / pH: 7.5
Details: CRYSTALS WERE GROWN USING VAPOUR DIFFUSION TECHNIQUES FROM DROPS CONTAINING AS48 (20 MG/ML), 18 MM N-DECYL-BETA-D-MALTOSIDE AND RESERVOIR SOLUTION (0.2 M AMMONIUM SULPHATE,25 % W/V ...Details: CRYSTALS WERE GROWN USING VAPOUR DIFFUSION TECHNIQUES FROM DROPS CONTAINING AS48 (20 MG/ML), 18 MM N-DECYL-BETA-D-MALTOSIDE AND RESERVOIR SOLUTION (0.2 M AMMONIUM SULPHATE,25 % W/V POLYETHYLENE GLYCOL 4000) IN A RATIO 4:1:5, pH 7.50
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
210 mMTris-HCl1droppH7.5
30.2 Mammonium sulfate1reservoir
425 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF NONIUS / 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: 2.7→34.3 Å / Num. obs: 4544 / % possible obs: 100 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.138 / Net I/σ(I): 5.1
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 9 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.3 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 34.3 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.138
Reflection shell
*PLUS
% possible obs: 100 % / Redundancy: 9 % / Rmerge(I) obs: 0.591 / Mean I/σ(I) obs: 1.3

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→10 Å / SU B: 15.606 / SU ML: 0.313 / Cross valid method: THROUGHOUT / ESU R Free: 0.393 / Details: NCS RESTRAINTS USED
RfactorNum. reflection% reflectionSelection details
Rfree0.25607 185 4.7 %RANDOM
Rwork0.23576 ---
obs0.23669 3777 100 %-
Displacement parametersBiso mean: 44.965 Å2
Baniso -1Baniso -2Baniso -3
1--3.56 Å20 Å20 Å2
2---3.56 Å20 Å2
3---7.12 Å2
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1008 0 64 25 1097
Refinement
*PLUS
Highest resolution: 2.8 Å / Rfactor Rfree: 0.256 / Rfactor Rwork: 0.236
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.022
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg2.141
X-RAY DIFFRACTIONplanar_d0.006
LS refinement shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.85 Å / Rfactor Rfree: 0.309 / Rfactor Rwork: 0.286

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