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- PDB-1ob6: Cephaibol B -

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Basic information

Entry
Database: PDB / ID: 1ob6
TitleCephaibol B
ComponentsCEPHAIBOL B
KeywordsANTIBIOTIC / CEPHAIBOL / PEPTAIBOL / ANTIBACTERIAL / ANTIFUNGAL / ION CHANNEL
Function / homologyCephaibol B / ACETATE ION / ETHANOL / :
Function and homology information
Biological speciesACREMONIUM TUBAKII (fungus)
MethodX-RAY DIFFRACTION / DIRECT METHODS / Resolution: 0.89 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
Revision 1.5Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _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

Downloads & links

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Assembly

Deposited unit
A: CEPHAIBOL B
B: CEPHAIBOL B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,4895
Polymers3,3382
Non-polymers1513
Water46826
1
A: CEPHAIBOL B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,7152
Polymers1,6691
Non-polymers461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CEPHAIBOL B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,7743
Polymers1,6691
Non-polymers1052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)32.146, 9.126, 37.982
Angle α, β, γ (deg.)90.00, 111.36, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99446, 0.01694, 0.10371), (-0.01634, 0.99984, -0.00666), (-0.10381, 0.00493, 0.99458)
Vector: 19.39953, 5.28985, -19.99939)

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Components

#1: Protein/peptide CEPHAIBOL B


Type: Peptaibol / Class: Antibiotic / Mass: 1669.017 Da / Num. of mol.: 2 / 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: NOR00971, Cephaibol B
#2: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCEPHAIBOL B IS LINEAR PEPTIDE, A MEMBER OF THE PEPTAIBOL FAMILY OF MEMBRANE CHANNEL FORMING ...CEPHAIBOL B IS LINEAR PEPTIDE, A MEMBER OF THE PEPTAIBOL FAMILY OF MEMBRANE CHANNEL FORMING PEPTIDES. HERE, CEPHAIBOL B IS REPRESENTED BY THE SEQUENCE (SEQRES) GROUP: 1 NAME: CEPHAIBOL B CHAIN: A, B COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 0 TO 16 DESCRIPTION: CEPHAIBOL A IS A HEXADECAMERIC HELICAL PEPTIDE. THE N-TERM IS ACETYLATED (RESIDUE 0)
Has protein modificationY

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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: 1.54 Å3/Da / Density % sol: 20 %
Crystal growpH: 4.6 / Details: 0.1 M NAAC/HAC PH=4.6, 32% 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: May 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: 0.89→35.4 Å / Num. obs: 16045 / % possible obs: 97 % / Redundancy: 4.44 % / Rmerge(I) obs: 0.0437 / Net I/σ(I): 23.29
Reflection shellResolution: 0.89→1 Å / Redundancy: 2.16 % / Rmerge(I) obs: 0.0786 / Mean I/σ(I) obs: 10.37 / % possible all: 90
Reflection
*PLUS
Highest resolution: 0.89 Å / Redundancy: 4.44 % / Num. measured all: 73436 / Rmerge(I) obs: 0.0437
Reflection shell
*PLUS
% possible obs: 90 % / Rmerge(I) obs: 0.0786 / Mean I/σ(I) obs: 10.37

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Processing

Software
NameClassification
SHELXL-97refinement
SAINTdata reduction
SADABSdata scaling
SHELXDphasing
RefinementMethod to determine structure: DIRECT METHODS / Resolution: 0.89→35.4 Å / Num. parameters: 3121 / Num. restraintsaints: 4640 / 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
Rfree0.0793 778 5 %THIN SHELLS
all0.0746 16045 --
obs0.0744 -97 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 10 / Occupancy sum hydrogen: 252 / Occupancy sum non hydrogen: 267.5
Refinement stepCycle: LAST / Resolution: 0.89→35.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms240 0 10 26 276
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.021
X-RAY DIFFRACTIONs_angle_d0.04
X-RAY DIFFRACTIONs_similar_dist0.012
X-RAY DIFFRACTIONs_from_restr_planes0.505
X-RAY DIFFRACTIONs_zero_chiral_vol0.131
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.093
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.05
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.04
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 35.37 Å / Rfactor Rwork: 0.0746
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.505
X-RAY DIFFRACTIONs_chiral_restr0.131

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