PDB Short entry for 4G13 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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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 HETATM 1 C ACE A 0 14.843 3.351 30.322 1.00 4.37 C ANISOU 1 C ACE A 0 759 385 515 47 62 -28 C HETATM 2 O ACE A 0 14.883 4.472 29.898 1.00 6.36 O ANISOU 2 O ACE A 0 1350 379 686 16 -95 -49 O HETATM 3 CH3 ACE A 0 15.285 2.976 31.733 1.00 5.33 C ANISOU 3 CH3 ACE A 0 887 581 556 -164 -44 -42 C HETATM 4 H1 ACE A 0 15.164 2.033 31.866 1.00 7.99 H HETATM 5 H2 ACE A 0 14.757 3.460 32.373 1.00 7.99 H HETATM 6 H3 ACE A 0 16.211 3.200 31.849 1.00 7.99 H