HEADER ANTIBIOTIC 10-JUL-12 4G13 TITLE CRYSTAL STRUCTURE OF SAMAROSPORIN I AT 100K COMPND MOL_ID: 1; COMPND 2 MOLECULE: SAMAROSPORIN I; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: EMERIMICIN IV, STILBELLIN I SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SAMAROSPORA ROSTRUP; SOURCE 3 STRAIN: F-7762 KEYWDS PEPTAIBOL, 3(10)-ALPHA HELIX, ANTIBIOTIC PEPTIDE, MEMBRANE, KEYWDS 2 EXTRACELLULAR, ANTIBIOTIC EXPDTA X-RAY DIFFRACTION AUTHOR R.GESSMANN,D.AXFORD,K.PETRATOS REVDAT 4 18-JUL-18 4G13 1 REMARK REVDAT 3 26-DEC-12 4G13 1 COMPND DBREF REVDAT 2 31-OCT-12 4G13 1 JRNL REVDAT 1 03-OCT-12 4G13 0 JRNL AUTH R.GESSMANN,D.AXFORD,G.EVANS,H.BRUCKNER,K.PETRATOS JRNL TITL THE CRYSTAL STRUCTURE OF SAMAROSPORIN I AT ATOMIC JRNL TITL 2 RESOLUTION. JRNL REF J.PEPT.SCI. V. 18 678 2012 JRNL REFN ISSN 1075-2617 JRNL PMID 23019149 JRNL DOI 10.1002/PSC.2454 REMARK 2 REMARK 2 RESOLUTION. 0.80 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) : 0.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.61 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.8 REMARK 3 CROSS-VALIDATION METHOD : NULL 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) : 0.078 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.078 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.081 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 466 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 9272 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.067 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.067 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.071 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 389 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 7856 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 112 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 2 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 114.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 112.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 1 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 1061 REMARK 3 NUMBER OF RESTRAINTS : 99 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 ANGLE DISTANCES (A) : NULL REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: BABINET REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4G13 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JUL-12. REMARK 100 THE DEPOSITION ID IS D_1000073604. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-FEB-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.7293 REMARK 200 MONOCHROMATOR : ACCEL FIXED EXIT DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9272 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.800 REMARK 200 RESOLUTION RANGE LOW (A) : 22.610 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.8 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 50.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING REMARK 200 SOFTWARE USED: ACORN REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 15.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: METHANOL/WATER, EVAPORATION, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 22.55450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 4.53750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 22.55450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 4.53750 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 300 REMARK: AUTHORS STATE THAT THE BIOLOGICALLY SIGNIFICANT REMARK 300 OLIGOMERIZATION STATE IN THE MEMBRANE IS UNKNOWN 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 SAMAROSPORIN I/EMERIMICIN IV IS LINEAR PEPTIDE, A MEMBER OF THE REMARK 400 PEPTAIBOL FAMILY OF MEMBRANE CHANNEL FORMING PEPTIDES. HERE, REMARK 400 SAMAROSPORIN I/EMERIMICIN IV IS REPRESENTED BY THE SEQUENCE (SEQRES) REMARK 400 THE N-TERM IS ACETYLATED (RESIDUE 0) REMARK 400 REMARK 400 THE SAMAROSPORIN I IS PEPTAIBOL, A MEMBER OF ANTIBIOTIC CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: SAMAROSPORIN I REMARK 400 CHAIN: A REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JOH RELATED DB: PDB REMARK 900 ANTIAMOEBIN IN METHANOL/WATER REMARK 900 RELATED ID: 1OB4 RELATED DB: PDB REMARK 900 CEPHAIBOL A REMARK 900 RELATED ID: 1OB6 RELATED DB: PDB REMARK 900 CEPHAIBOL B REMARK 900 RELATED ID: 1OB7 RELATED DB: PDB REMARK 900 CEPHAIBOL C REMARK 900 RELATED ID: 4G14 RELATED DB: PDB REMARK 900 SAMAROSPORIN I DBREF 4G13 A 0 15 NOR NOR00986 NOR00986 0 15 SEQRES 1 A 16 ACE PHE AIB AIB AIB VAL GLY LEU AIB AIB HYP GLN DIV SEQRES 2 A 16 HYP AIB PHL HET ACE A 0 6 HET AIB A 2 13 HET AIB A 3 13 HET AIB A 4 13 HET AIB A 8 13 HET AIB A 9 13 HET HYP A 10 15 HET DIV A 12 16 HET HYP A 13 15 HET AIB A 14 13 HET PHL A 15 23 HETNAM ACE ACETYL GROUP HETNAM AIB ALPHA-AMINOISOBUTYRIC ACID HETNAM HYP 4-HYDROXYPROLINE HETNAM DIV D-ISOVALINE HETNAM PHL L-PHENYLALANINOL HETSYN HYP HYDROXYPROLINE FORMUL 1 ACE C2 H4 O FORMUL 1 AIB 6(C4 H9 N O2) FORMUL 1 HYP 2(C5 H9 N O3) FORMUL 1 DIV C5 H11 N O2 FORMUL 1 PHL C9 H13 N O FORMUL 2 HOH *2(H2 O) HELIX 1 1 PHE A 1 HYP A 10 1 10 HELIX 2 2 GLN A 11 PHL A 15 5 5 LINK C ACE A 0 N PHE A 1 1555 1555 1.35 LINK C PHE A 1 N AIB A 2 1555 1555 1.34 LINK C AIB A 2 N AIB A 3 1555 1555 1.35 LINK C AIB A 3 N AIB A 4 1555 1555 1.33 LINK C AIB A 4 N VAL A 5 1555 1555 1.35 LINK C LEU A 7 N AIB A 8 1555 1555 1.33 LINK C AIB A 8 N AIB A 9 1555 1555 1.34 LINK C AIB A 9 N HYP A 10 1555 1555 1.35 LINK C HYP A 10 N GLN A 11 1555 1555 1.34 LINK C GLN A 11 N DIV A 12 1555 1555 1.33 LINK C DIV A 12 N HYP A 13 1555 1555 1.34 LINK C HYP A 13 N AIB A 14 1555 1555 1.35 LINK C AIB A 14 N PHL A 15 1555 1555 1.35 CRYST1 45.109 9.075 25.067 90.00 115.60 90.00 C 1 2 1 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 0.022169 0.000000 0.010621 0.00000 SCALE2 0.000000 0.110193 0.000000 0.00000 SCALE3 0.000000 0.000000 0.044236 0.00000