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- PDB-1joh: THE STRUCTURE OF ANTIAMOEBIN I, A MEMBRANE-ACTIVE PEPTIDE -

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Entry
Database: PDB / ID: 1joh
TitleTHE STRUCTURE OF ANTIAMOEBIN I, A MEMBRANE-ACTIVE PEPTIDE
ComponentsANTIAMOEBIN I
KeywordsANTIBIOTIC / ANTIAMOEBIN I / PEPTAIBOL / ANTIBACTERIAL / ANTIFUNGAL
Function / homologyAntiamoebin 1 / METHANOL / :
Function and homology information
Biological speciesEMERICELLOPSIS (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSnook, C.F. / Wallace, B.A.
Citation
Journal: Structure / Year: 1998
Title: The Structure and Function of Antiamoebin I, a Proline-Rich Membrane-Active Polypeptide.
Authors: Snook, C.F. / Woolley, G.A. / Oliva, G. / Pattabhi, V. / Wood, S.F. / Blundell, T.L. / Wallace, B.A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: The Molecular-Replacement Solution of an Intermediate-Sized Helical Polypeptide, Antiamoebin I.
Authors: Snook, C.F. / Wallace, B.A.
#2: Journal: Thesis, University of London / Year: 1997
Title: The Structure and Function of Antiamoebin I, a Membrane-Active Peptide
Authors: Snook, C.F.
#3: Journal: Thesis, University of London / Year: 1988
Title: Molecular Redundancy and Protein Crystallography : X-Ray Structure Analysis of Antiamoebin I, Bovine Pancreatic Polypeptide and Human Serum Amyloid P Component
Authors: Oliva, G.
History
DepositionOct 11, 1997Processing site: BNL
Revision 1.0Jan 20, 1999Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Dec 12, 2012Group: Other
Revision 1.5Mar 4, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / pdbx_database_status ...chem_comp / pdbx_database_status / refine / reflns / struct_conn
Item: _chem_comp.pdbx_synonyms / _pdbx_database_status.process_site ..._chem_comp.pdbx_synonyms / _pdbx_database_status.process_site / _refine.ls_R_factor_obs / _refine.ls_number_reflns_obs / _reflns.pdbx_Rmerge_I_obs / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6Apr 3, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.7Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ANTIAMOEBIN I
B: ANTIAMOEBIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,04725
Polymers3,3102
Non-polymers73723
Water00
1
A: ANTIAMOEBIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,00712
Polymers1,6551
Non-polymers35211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ANTIAMOEBIN I
hetero molecules


  • defined by author
  • 2.04 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)2,03913
Polymers1,6551
Non-polymers38512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.530, 28.820, 9.060
Angle α, β, γ (deg.)88.90, 96.64, 123.85
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (1), (1), (-1) / Vector: 115.46)

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Components

#1: Protein/peptide ANTIAMOEBIN I


Type: Peptaibol / Class: Antibiotic / Mass: 1654.991 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: ANTIAMOEBIN I IS A HEXADECAMERIC HELICAL PEPTIDE. THE N-TERM IS ACETYLATED (RESIDUE 0)
Source: (natural) EMERICELLOPSIS (fungus) / References: NOR: NOR00945, Antiamoebin 1
#2: Chemical...
ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: CH4O
Compound detailsANTIAMOEBIN I IS LINEAR PEPTIDE, A MEMBER OF THE PEPTAIBOL FAMILY OF MEMBRANE CHANNEL FORMING ...ANTIAMOEBIN I IS LINEAR PEPTIDE, A MEMBER OF THE PEPTAIBOL FAMILY OF MEMBRANE CHANNEL FORMING PEPTIDES. HERE, ANTIAMOEBIN I IS REPRESENTED BY THE SEQUENCE (SEQRES)
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: 1.71 Å3/Da / Density % sol: 28 % / Description: USED NORMALISED STRUCTURE FACTORS
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
Conc.: 170 mg/ml / Common name: peptide

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SEALED TUBE / Wavelength: 1.5418
DetectorType: HILGER-WATTS / Detector: DIFFRACTOMETER / Date: 1986
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.2→25 Å / Num. obs: 6715 / % possible obs: 93.7 % / Observed criterion σ(I): 0 / Redundancy: 1 % / Rmerge(I) obs: 0.012 / Net I/σ(I): 10.5

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Processing

Software
NameClassification
SHELXL-93model building
SHELXL-93refinement
SHELXL-93phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RESIDUES 6 - 16 OF LEU1-ZERVAMICIN WITH ALL NON -EQUIVALENT SIDE-CHAINS TRIMMED TO ALA.

Resolution: 1.4→25 Å / Num. parameters: 1074 / Num. restraintsaints: 982 / σ(F): 0 / StereochEM target val spec case: HETATM DATA FROM CCSD / Stereochemistry target values: ENGH AND HUBER
Details: REFINEMENT STARTED USING 10.0 TO 2.5A AND DATA CUT-OFF AT 2 SIGMA IN X-PLOR. HIGH RESOLUTION LIMIT INCREASED TO 2.0A, LOW RESOLUTION DECREASED TO 25.0A AND DATA CUT-OFF DECREASED TO 0.0 ...Details: REFINEMENT STARTED USING 10.0 TO 2.5A AND DATA CUT-OFF AT 2 SIGMA IN X-PLOR. HIGH RESOLUTION LIMIT INCREASED TO 2.0A, LOW RESOLUTION DECREASED TO 25.0A AND DATA CUT-OFF DECREASED TO 0.0 SIGMA AT 2.0A RESOLUTION. RESOLUTION INCREASED FROM 2.0A TO 1.4A WITH ALL DATA USING SHELXL-93. REFINEMENT CEASED AFTER RESIDUES 1 TO 5 IN B-CHAIN IDENTIFIED AS DISORDERED IN DENSITY.
RfactorNum. reflection% reflection
all0.156 4359 -
obs0.156 4359 95.4 %
Refine analyzeOccupancy sum non hydrogen: 268
Refinement stepCycle: LAST / Resolution: 1.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms238 0 30 0 268
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.036
X-RAY DIFFRACTIONs_angle_d3.152
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.016
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.022
X-RAY DIFFRACTIONs_approx_iso_adps0.065
Refinement
*PLUS
Rfactor all: 0.156
Solvent computation
*PLUS
Displacement parameters
*PLUS

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