HEADER ANTIBIOTIC 24-JAN-03 1OB7 TITLE CEPHAIBOL C COMPND MOL_ID: 1; COMPND 2 MOLECULE: CEPHAIBOL C; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACREMONIUM TUBAKII; SOURCE 3 ORGANISM_TAXID: 146077 KEYWDS ION CHANNEL, CEPHAIBOL, PEPTAIBOL, ANTIBACTERIAL, ANTIFUNGAL, KEYWDS 2 ANTIBIOTIC EXPDTA X-RAY DIFFRACTION AUTHOR G.BUNKOCZI,M.SCHIELL,L.VERTESY,G.M.SHELDRICK REVDAT 5 22-MAY-19 1OB7 1 REMARK HETSYN LINK REVDAT 4 30-MAY-18 1OB7 1 REMARK REVDAT 3 13-JUL-11 1OB7 1 VERSN REVDAT 2 24-FEB-09 1OB7 1 VERSN REVDAT 1 11-DEC-03 1OB7 0 JRNL AUTH G.BUNKOCZI,M.SCHIELL,L.VERTESY,G.M.SHELDRICK JRNL TITL CRYSTAL STRUCTURES OF CEPHAIBOLS JRNL REF J.PEPT.SCI. V. 9 745 2003 JRNL REFN ISSN 1075-2617 JRNL PMID 14658793 JRNL DOI 10.1002/PSC.496 REMARK 2 REMARK 2 RESOLUTION. 0.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.62 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.072 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.072 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.077 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 431 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 8776 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.071 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.071 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.076 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 424 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 8168 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 125 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 7 REMARK 3 SOLVENT ATOMS : 11 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 134.90 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 122.80 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 1 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 1294 REMARK 3 NUMBER OF RESTRAINTS : 1519 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.018 REMARK 3 ANGLE DISTANCES (A) : 0.028 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.002 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.499 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.140 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.111 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.000 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.005 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.038 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: RESTRAINTS FOR AIB, DIV, HYP AND PHL FROM REMARK 3 ANTIAMOEBIN (PDB 1JOH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1OB7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-JAN-03. REMARK 100 THE DEPOSITION ID IS D_1290012027. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-02 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 4.60 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER M06XCE REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER SMART 6000 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT REMARK 200 DATA SCALING SOFTWARE : SADABS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8776 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.890 REMARK 200 RESOLUTION RANGE LOW (A) : 28.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 8.690 REMARK 200 R MERGE (I) : 0.03060 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 50.4400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.89 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.36 REMARK 200 R MERGE FOR SHELL (I) : 0.03490 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 26.51 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: DIRECT METHODS REMARK 200 SOFTWARE USED: SHELXD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 23.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M NAAC/HAC PH=4.60, 38% ETOH, PH REMARK 280 4.60 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 4.50100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 20.55000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 14.30950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 20.55000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 4.50100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 14.30950 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 400 REMARK 400 COMPOUND REMARK 400 CEPHAIBOL C IS LINEAR PEPTIDE, A MEMBER OF THE PEPTAIBOL REMARK 400 FAMILY OF MEMBRANE CHANNEL FORMING PEPTIDES. REMARK 400 HERE, CEPHAIBOL C IS REPRESENTED BY THE SEQUENCE (SEQRES) REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: CEPHAIBOL C REMARK 400 CHAIN: A REMARK 400 COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 0 TO 16 REMARK 400 DESCRIPTION: CEPHAIBOL C IS A HEXADECAMERIC HELICAL PEPTIDE. REMARK 400 THE N-TERM IS ACETYLATED (RESIDUE 0) REMARK 400 REMARK 400 THE CEPHAIBOL C IS PEPTAIBOL, A MEMBER OF ANTIBIOTIC CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: CEPHAIBOL C REMARK 400 CHAIN: A REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: CEPHAIBOL C IS A HEXADECAMERIC HELICAL PEPTIDE. THE REMARK 400 N-TERM IS ACETYLATED (RESIDUE 0) REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 20 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HYP A 10 O REMARK 620 2 GLN A 11 OE1 88.9 REMARK 620 3 HOH A2009 O 124.4 96.2 REMARK 620 4 HOH A2008 O 125.9 94.5 2.2 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 20 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EOH A 18 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EOH A 19 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN A OF CEPHAIBOL C REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1M24 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE PEPTAIBOL TRICHOTOXIN_A50E REMARK 900 RELATED ID: 1R9U RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE PEPTAIBOL ZERVAMICIN IIB IN METHANOL REMARK 900 RELATED ID: 1DLZ RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE PEPTIABOL ZERVAMICIN IIB REMARK 900 RELATED ID: 1IH9 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE PEPTAIBOL ZERVAMICIN IIB BOUND TO DPC REMARK 900 MICELLES REMARK 900 RELATED ID: 1GQ0 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE PEPTAIBOL ANTIAMOEBIN I REMARK 900 RELATED ID: 1JOH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE PEPTAIBOL ANTIAMOEBIN I REMARK 900 RELATED ID: 1AMT RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE PEPTAIBOL ALAMETHICIN REMARK 900 RELATED ID: 1EE7 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE PEPTAIBOL CHRYSOSPERMIN C BOUND TO DPC REMARK 900 MICELLES REMARK 900 RELATED ID: 1OB6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE PEPTAIBOL CEPHAIBOL B REMARK 900 RELATED ID: 1OB4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE PEPTAIBOL CEPHAIBOL A REMARK 999 REMARK 999 SEQUENCE REMARK 999 SLIGHT CONTAMINATION CAUSED MICROHETERGENEITY AT POSITION 12 DBREF 1OB7 A 0 16 NOR NOR00972 NOR00972 0 16 SEQADV 1OB7 DIV A 12 NOR NO00972 AIB 12 MICROHETEROGENEITY SEQRES 1 A 17 ACE PHE AIB AIB AIB AIB GLY LEU DIV AIB HYP GLN DIV SEQRES 2 A 17 HYP AIB PRO PHL MODRES 1OB7 AIB A 2 ALA ALPHA-AMINOISOBUTYRIC ACID MODRES 1OB7 AIB A 3 ALA ALPHA-AMINOISOBUTYRIC ACID MODRES 1OB7 AIB A 4 ALA ALPHA-AMINOISOBUTYRIC ACID MODRES 1OB7 AIB A 5 ALA ALPHA-AMINOISOBUTYRIC ACID MODRES 1OB7 AIB A 9 ALA ALPHA-AMINOISOBUTYRIC ACID MODRES 1OB7 HYP A 10 PRO 4-HYDROXYPROLINE MODRES 1OB7 AIB A 12 ALA ALPHA-AMINOISOBUTYRIC ACID MODRES 1OB7 HYP A 13 PRO 4-HYDROXYPROLINE MODRES 1OB7 AIB A 14 ALA ALPHA-AMINOISOBUTYRIC ACID MODRES 1OB7 PHL A 16 PHE L-PHENYLALANINOL HET ACE A 0 3 HET AIB A 2 6 HET AIB A 3 6 HET AIB A 4 6 HET AIB A 5 6 HET DIV A 8 7 HET AIB A 9 6 HET HYP A 10 8 HET DIV A 12 7 HET AIB A 12 6 HET HYP A 13 8 HET AIB A 14 6 HET PHL A 16 11 HET EOH A 18 3 HET EOH A 19 6 HET NA A 20 1 HETNAM ACE ACETYL GROUP HETNAM AIB ALPHA-AMINOISOBUTYRIC ACID HETNAM DIV D-ISOVALINE HETNAM HYP 4-HYDROXYPROLINE HETNAM PHL L-PHENYLALANINOL HETNAM EOH ETHANOL HETNAM NA SODIUM ION HETSYN HYP HYDROXYPROLINE HETSYN PHL BOUND FORM OF PHENYLALANINAL FORMUL 1 ACE C2 H4 O FORMUL 1 AIB 7(C4 H9 N O2) FORMUL 1 DIV 2(C5 H11 N O2) FORMUL 1 HYP 2(C5 H9 N O3) FORMUL 1 PHL C9 H13 N O FORMUL 2 EOH 2(C2 H6 O) FORMUL 4 NA NA 1+ FORMUL 5 HOH *11(H2 O) HELIX 1 1 PHE A 1 HYP A 10 1 10 LINK C ACE A 0 N PHE A 1 1555 1555 1.33 LINK C PHE A 1 N AIB A 2 1555 1555 1.33 LINK C AIB A 2 N AIB A 3 1555 1555 1.34 LINK C AIB A 3 N AIB A 4 1555 1555 1.33 LINK C AIB A 4 N AIB A 5 1555 1555 1.34 LINK C AIB A 5 N GLY A 6 1555 1555 1.33 LINK C LEU A 7 N DIV A 8 1555 1555 1.34 LINK C DIV A 8 N AIB A 9 1555 1555 1.34 LINK C AIB A 9 N HYP A 10 1555 1555 1.34 LINK O HYP A 10 NA NA A 20 1555 1555 2.86 LINK C HYP A 10 N GLN A 11 1555 1555 1.34 LINK C GLN A 11 N BDIV A 12 1555 1555 1.34 LINK C BDIV A 12 N HYP A 13 1555 1555 1.34 LINK C HYP A 13 N AIB A 14 1555 1555 1.30 LINK C AIB A 14 N PRO A 15 1555 1555 1.31 LINK C PRO A 15 N PHL A 16 1555 1555 1.32 LINK NA NA A 20 OE1 GLN A 11 1555 1555 2.85 LINK NA NA A 20 O HOH A2009 1555 1655 2.53 LINK NA NA A 20 O HOH A2008 1555 1655 2.74 SITE 1 AC1 5 GLY A 6 HYP A 10 GLN A 11 HOH A2008 SITE 2 AC1 5 HOH A2009 SITE 1 AC2 4 AIB A 2 AIB A 3 HOH A2001 HOH A2007 SITE 1 AC3 4 ACE A 0 DIV A 12 PRO A 15 PHL A 16 SITE 1 AC4 7 EOH A 18 EOH A 19 NA A 20 HOH A2008 SITE 2 AC4 7 HOH A2009 HOH A2010 HOH A2011 CRYST1 9.002 28.619 41.100 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.111086 0.000000 0.000000 0.00000 SCALE2 0.000000 0.034942 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024331 0.00000 HETATM 1 C ACE A 0 9.727 19.397 7.312 1.00 3.62 C ANISOU 1 C ACE A 0 452 321 604 -50 19 -67 C HETATM 2 O ACE A 0 9.998 18.245 6.963 1.00 4.46 O ANISOU 2 O ACE A 0 485 403 806 -96 136 -184 O HETATM 3 CH3 ACE A 0 10.657 20.524 7.002 1.00 4.40 C ANISOU 3 CH3 ACE A 0 515 395 763 -86 30 -63 C