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- PDB-1ob4: Cephaibol A -

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Basic information

Entry
Database: PDB / ID: 1ob4
TitleCephaibol A
ComponentsCEPHAIBOL A
KeywordsANTIBIOTIC / ION CHANNEL / CEPHAIBOL / PEPTAIBOL / ANTIBACTERIAL / ANTIFUNGAL
Function / homologyCephaibol A / ETHANOL / :
Function and homology information
Biological speciesACREMONIUM TUBAKII (fungus)
MethodX-RAY DIFFRACTION / DIRECT METHODS / Resolution: 0.95 Å
AuthorsBunkoczi, G. / Schiell, M. / Vertesy, L. / Sheldrick, G.M.
CitationJournal: J.Pept.Sci. / Year: 2003
Title: Crystal Structures of Cephaibols
Authors: Bunkoczi, G. / Schiell, M. / Vertesy, L. / Sheldrick, G.M.
History
DepositionJan 24, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Structure summary / Version format compliance
Revision 1.2Nov 30, 2012Group: Other
Revision 1.3May 30, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.4May 22, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp / refine / struct_conn
Item: _chem_comp.pdbx_synonyms / _refine.pdbx_ls_cross_valid_method / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CEPHAIBOL A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,7012
Polymers1,6551
Non-polymers461
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)30.534, 37.787, 9.115
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein/peptide CEPHAIBOL A


Type: Peptaibol / Class: Antibiotic / Mass: 1654.991 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: CEPHAIBOL A IS A HEXADECAMERIC HELICAL PEPTIDE. THE N-TERM IS ACETYLATED (RESIDUE 0)
Source: (natural) ACREMONIUM TUBAKII (fungus) / References: NOR: NOR00969, Cephaibol A
#2: Chemical ChemComp-EOH / ETHANOL / Ethanol


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCEPHAIBOL A IS LINEAR PEPTIDE, A MEMBER OF THE PEPTAIBOL FAMILY OF MEMBRANE CHANNEL FORMING ...CEPHAIBOL A IS LINEAR PEPTIDE, A MEMBER OF THE PEPTAIBOL FAMILY OF MEMBRANE CHANNEL FORMING PEPTIDES. HERE, CEPHAIBOL A IS REPRESENTED BY THE SEQUENCE (SEQRES) GROUP: 1 NAME: CEPHAIBOL A CHAIN: A COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 0 TO 16 DESCRIPTION: CEPHAIBOL A IS A HEXADECAMERIC HELICAL PEPTIDE. 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: 1.57 Å3/Da / Density % sol: 22 %
Crystal growpH: 4.6 / Details: 0.1 M NAAC/HAC PH=4.6, 34% ETOH, pH 4.60
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 4.8 / PH range high: 4.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlcephaibol1drop
20.1 MNaAc/HAc1reservoirpH4.2-4.8
330-38 %ethanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER M06XCE / Wavelength: 1.5418
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Feb 15, 2002 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 0.95→37.8 Å / Num. obs: 7025 / % possible obs: 98.6 % / Redundancy: 9.45 % / Rmerge(I) obs: 0.0431 / Net I/σ(I): 29.21
Reflection shellResolution: 0.95→1.05 Å / Redundancy: 4.66 % / Rmerge(I) obs: 0.1156 / Mean I/σ(I) obs: 10.67 / % possible all: 96.6
Reflection
*PLUS
Highest resolution: 0.95 Å / Redundancy: 9.45 % / Num. measured all: 67303 / Rmerge(I) obs: 0.0431
Reflection shell
*PLUS
% possible obs: 96.6 % / Rmerge(I) obs: 0.1156 / Mean I/σ(I) obs: 10.67

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Processing

Software
NameClassification
SHELXL-97refinement
SAINTdata reduction
SADABSdata scaling
SHELXDphasing
RefinementMethod to determine structure: DIRECT METHODS / Resolution: 0.95→37.8 Å / Num. parameters: 1429 / Num. restraintsaints: 2016 / Cross valid method: FREE R-VALUE / σ(F): 0
StereochEM target val spec case: RESTRAINTS FOR AIB, DIV, HYP AND PHL FROM ANTIAMOEBIN (PDB 1JOH)
Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.112 353 5 %RANDOM
all0.0872 7025 --
obs0.0858 -98.6 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 2 / Occupancy sum hydrogen: 124 / Occupancy sum non hydrogen: 133.28
Refinement stepCycle: LAST / Resolution: 0.95→37.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms119 0 3 15 137
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d0.035
X-RAY DIFFRACTIONs_similar_dist0.015
X-RAY DIFFRACTIONs_from_restr_planes0.416
X-RAY DIFFRACTIONs_zero_chiral_vol0.149
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.112
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.035
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.046
X-RAY DIFFRACTIONs_approx_iso_adps0.082
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 37.79 Å / Rfactor Rwork: 0.0872
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.416
X-RAY DIFFRACTIONs_chiral_restr0.149

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