PDB Short entry for 5MAS HEADER ANTIBIOTIC 04-NOV-16 5MAS TITLE PEPTAIBOL BERGOFUNGIN A COMPND MOL_ID: 1; COMPND 2 MOLECULE: BERGOFUNGIN A; COMPND 3 CHAIN: A; COMPND 4 OTHER_DETAILS: NOR00964 IN NORINE DATABASE COMPND 5 (HTTP://BIOINFO.LIFL.FR/NORINE/FORM.JSP) SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: EMERICELLOPSIS DONEZKII; SOURCE 3 ORGANISM_TAXID: 281368 KEYWDS 3(10)-HELIX, PEPTAIBOLS, ANTIBIOTIC PEPTIDES, ALPHA-HELIX, ANTIBIOTIC EXPDTA X-RAY DIFFRACTION AUTHOR R.GESSMANN,K.PETRATOS REVDAT 2 01-MAR-17 5MAS 1 JRNL REVDAT 1 22-FEB-17 5MAS 0 JRNL AUTH R.GESSMANN,D.AXFORD,H.BRUCKNER,A.BERG,K.PETRATOS JRNL TITL A NATURAL, SINGLE-RESIDUE SUBSTITUTION YIELDS A LESS ACTIVE JRNL TITL 2 PEPTAIBIOTIC: THE STRUCTURE OF BERGOFUNGIN A AT ATOMIC JRNL TITL 3 RESOLUTION. JRNL REF ACTA CRYSTALLOGR F STRUCT V. 73 95 2017 JRNL REF 2 BIOL COMMUN JRNL REFN ESSN 2053-230X JRNL PMID 28177320 JRNL DOI 10.1107/S2053230X17001236 REMARK 2 REMARK 2 RESOLUTION. 0.84 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL 2014/3 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 84.3 REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : THIN RESOLUTION SHELLS REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.104 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.103 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.131 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 660 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 12250 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.068 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.067 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.088 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 444 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 7756 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 108 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 1 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 108.50 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 120.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 985 REMARK 3 NUMBER OF RESTRAINTS : 1 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: PLATON SQUEEZE 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 5MAS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-NOV-16. REMARK 100 THE DEPOSITION ID IS D_1200002201. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUL-16 REMARK 200 TEMPERATURE (KELVIN) : 100 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 : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12250 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.840 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 84.3 REMARK 200 DATA REDUNDANCY : 1.650 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : 0.09000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 4.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.84 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 52.8 REMARK 200 DATA REDUNDANCY IN SHELL : 0.94 REMARK 200 R MERGE FOR SHELL (I) : 0.35000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.720 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING REMARK 200 SOFTWARE USED: SHELXS 2013/1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: TINY HAIR REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 19.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.53 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 24.13750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 4.46600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 24.13750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 4.46600 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 90 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 1600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 KCAL/MOL 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4G13 RELATED DB: PDB REMARK 900 RELATED ID: 4G14 RELATED DB: PDB DBREF 5MAS A 0 15 PDB 5MAS 5MAS 0 15 SEQRES 1 A 16 ACE VAL 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 *(H2 O) HELIX 1 AA1 VAL A 1 HYP A 10 1 10 HELIX 2 AA2 GLN A 11 PHL A 15 5 5 LINK C ACE A 0 N VAL A 1 1555 1555 1.34 LINK C VAL A 1 N AIB A 2 1555 1555 1.34 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 1.35 LINK C LEU A 7 N AIB A 8 1555 1555 1.36 LINK C AIB A 8 N AIB A 9 1555 1555 1.35 LINK C AIB A 9 N HYP A 10 1555 1555 1.35 LINK C HYP A 10 N GLN A 11 1555 1555 1.36 LINK C GLN A 11 N DIV A 12 1555 1555 1.33 LINK C DIV A 12 N HYP A 13 1555 1555 1.35 LINK C HYP A 13 N AIB A 14 1555 1555 1.35 LINK C AIB A 14 N PHL A 15 1555 1555 1.32 CRYST1 48.275 8.932 24.604 90.00 119.72 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 0.020715 0.000000 0.011827 0.00000 SCALE2 0.000000 0.111957 0.000000 0.00000 SCALE3 0.000000 0.000000 0.046802 0.00000 HETATM 1 C ACE A 0 -1.783 7.401 -6.696 1.00 3.41 C ANISOU 1 C ACE A 0 464 337 462 -16 -71 27 C HETATM 2 O ACE A 0 -2.203 8.287 -5.925 1.00 4.40 O ANISOU 2 O ACE A 0 830 320 479 118 51 22 O HETATM 3 CH3 ACE A 0 -1.251 7.706 -8.066 1.00 4.28 C ANISOU 3 CH3 ACE A 0 836 307 442 15 140 118 C HETATM 4 H1 ACE A 0 -0.975 6.873 -8.502 1.00 6.42 H HETATM 5 H2 ACE A 0 -1.951 8.138 -8.599 1.00 6.42 H HETATM 6 H3 ACE A 0 -0.480 8.306 -7.991 1.00 6.42 H