HEADER ANTIBIOTIC 10-JUL-12 4G14 TITLE CRYSTAL STRUCTURE OF SAMAROSPORIN I AT 293K 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 6 06-DEC-23 4G14 1 REMARK REVDAT 5 13-SEP-23 4G14 1 HETSYN LINK REVDAT 4 18-JUL-18 4G14 1 REMARK REVDAT 3 26-DEC-12 4G14 1 COMPND DBREF REVDAT 2 31-OCT-12 4G14 1 JRNL REVDAT 1 03-OCT-12 4G14 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. 1.09 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) : 1.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.59 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 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) : 0.123 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.120 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.171 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 206 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 4194 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.112 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.157 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 166 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 3432 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 : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 1022 REMARK 3 NUMBER OF RESTRAINTS : 1001 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 4G14 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JUL-12. REMARK 100 THE DEPOSITION ID IS D_1000073605. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAR-12 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 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 : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4194 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.090 REMARK 200 RESOLUTION RANGE LOW (A) : 22.590 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.09 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 4G13 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 18.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.52 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 23.14000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 4.58500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 23.14000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 4.58500 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: AS PER AUTHORS THE BIOLOGICAL ASSEMBLY IS MULTIMERIC OF REMARK 300 UNKNOWN STOICHIOMETRY 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 PEPT 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PHE A 1 CB - CG - CD2 ANGL. DEV. = -4.8 DEGREES REMARK 500 REMARK 500 REMARK: 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: 4G13 RELATED DB: PDB REMARK 900 SAMAROSPORIN I DBREF 4G14 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 HETSYN PHL BOUND FORM OF PHENYLALANINAL 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 1.40 LINK C PHE A 1 N AIB A 2 1555 1555 1.27 LINK C AIB A 2 N AIB A 3 1555 1555 1.33 LINK C AIB A 3 N AIB A 4 1555 1555 1.34 LINK C AIB A 4 N VAL A 5 1555 1555 1.33 LINK C LEU A 7 N AIB A 8 1555 1555 1.34 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 1.35 LINK C GLN A 11 N DIV A 12 1555 1555 1.36 LINK C DIV A 12 N HYP A 13 1555 1555 1.35 LINK C HYP A 13 N AIB A 14 1555 1555 1.32 LINK C AIB A 14 N PHL A 15 1555 1555 1.34 CRYST1 46.280 9.170 25.250 90.00 116.59 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 0.021608 0.000000 0.010816 0.00000 SCALE2 0.000000 0.109051 0.000000 0.00000 SCALE3 0.000000 0.000000 0.044288 0.00000 HETATM 1 C ACE A 0 15.060 3.440 30.292 1.00 9.95 C ANISOU 1 C ACE A 0 1120 1145 1515 -314 -77 119 C HETATM 2 O ACE A 0 15.252 4.498 29.750 1.00 13.00 O ANISOU 2 O ACE A 0 2084 1093 1764 -278 182 100 O HETATM 3 CH3 ACE A 0 15.505 2.971 31.620 1.00 11.17 C ANISOU 3 CH3 ACE A 0 1347 1505 1391 -189 -228 -106 C HETATM 4 H1 ACE A 0 15.164 2.088 31.778 1.00 16.75 H HETATM 5 H2 ACE A 0 15.175 3.567 32.297 1.00 16.75 H HETATM 6 H3 ACE A 0 16.464 2.954 31.648 1.00 16.75 H