HEADER ANTIBIOTIC 01-NOV-17 6EVH TITLE LIPOAMINOPEPTIDE HELIOFERIN A AND B FROM MYCOGONE ROSEA COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIPOAMINOPEPTIDE HELIOFERIN A AND B; COMPND 3 CHAIN: A; COMPND 4 OTHER_DETAILS: MOO IS 2-METHYL-N-1-OXOOCTANOIC ACID,AMO IS AHMOD IS COMPND 5 (2S, 4S, 6S)-2-AMINO-6-HYDROXY-4-METHYL-8-OXODECANOYL,AIB IS ALPHA- COMPND 6 AMINOISOBUTYRIC ACID,C9K IS APAE IS CONFORMATION A 2-(2-AMINOPROPYL) COMPND 7 AMINOETHANOL AND C9N, CONFORMATION B AMAE IS 2-[(2-AMINOPROPYL)- COMPND 8 METHYLAMINO]-ETHANOL SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOGONE ROSEA; SOURCE 3 ORGANISM_TAXID: 129585 KEYWDS LIPOAMINOPEPTIDE, PROTONOPHORIC, PEPTAIBOL, PEPTAIBIOTIC, ANTIBIOTIC EXPDTA X-RAY DIFFRACTION AUTHOR R.GESSMANN,K.PETRATOS REVDAT 3 15-NOV-23 6EVH 1 LINK ATOM REVDAT 2 29-MAY-19 6EVH 1 KEYWDS REVDAT 1 18-JUL-18 6EVH 0 JRNL AUTH R.GESSMANN,K.PETRATOS JRNL TITL AMINOLIPOPEPTIDE HELIOFERIN A AND B JRNL REF ACTA CRYST. D V. 74 2018 JRNL REFN ISSN 2058-7983 JRNL PMID 29652258 JRNL DOI 10.1107/S2059798318001857 REMARK 2 REMARK 2 RESOLUTION. 0.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : THIN SHELLS REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL 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)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 88 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL 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: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE LAST AMINO ALCOHOL RESIDUE IS APAE IN HELIOFERIN A AND AMAE IN REMARK 3 HELIOFERIN B. REMARK 3 THE DEPOSITED STRUCTURE IS NEUTRAL REMARK 3 THE PRESENCE OF A PROTON AT N2 OF THE LAST RESIDUE APAE/AMAE IS REMARK 3 IMPLICATED. REMARK 4 REMARK 4 6EVH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1200007280. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUN-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER IMUS MICROFOCUS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CMOS REMARK 200 DETECTOR MANUFACTURER : RDI CMOS_8M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PROTEUM PLUS REMARK 200 DATA SCALING SOFTWARE : SAINT REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11314 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.820 REMARK 200 RESOLUTION RANGE LOW (A) : 17.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 200 DATA REDUNDANCY : 9.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.00 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING REMARK 200 SOFTWARE USED: SHELXS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: PLATE, 0.5 MM X 0.2 MM X 0.03 REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SLOW EVAPORATION IN A CLOSED VIAL, REMARK 280 TEMPERATURE 297K 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 17.35550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 5.44300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 17.35550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 5.44300 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: 110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 1390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 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 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 ILE A 6 CG1 - CB - CG2 ANGL. DEV. = -19.7 DEGREES REMARK 500 ILE A 6 CA - CB - CG1 ANGL. DEV. = -17.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue F A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues AIB A 7 and AIB A 8 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues AIB A 8 and C9N A 9 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues AIB A 8 and C9K A 9 DBREF 6EVH A 0 9 PDB 6EVH 6EVH 0 9 SEQRES 1 A 10 C9T PRO BZK ALA AIB ILE ILE AIB AIB C9K HET C9T A 0 33 HET BZK A 2 34 HET AIB A 4 13 HET AIB A 7 21 HET AIB A 8 13 HET C9K A 9 20 HET C9N A 9 22 HET CL A 101 1 HET F A 102 1 HETNAM C9T (2~{R})-2-METHYLOCTANOIC ACID HETNAM BZK (2S, 4S, 6S)-2-AMINO-6-HYDROXY-4-METHYL-8-OXODECANOIC HETNAM 2 BZK ACID HETNAM AIB ALPHA-AMINOISOBUTYRIC ACID HETNAM C9K 2-[[(2~{S})-2-AZANYLPROPYL]AMINO]ETHANOL HETNAM C9N 2-[[(2~{S})-2-AZANYLPROPYL]-METHYL-AMINO]ETHANOL HETNAM CL CHLORIDE ION HETNAM F FLUORIDE ION FORMUL 1 C9T C9 H18 O2 FORMUL 1 BZK C11 H21 N O4 FORMUL 1 AIB 3(C4 H9 N O2) FORMUL 1 C9K C5 H14 N2 O FORMUL 1 C9N C6 H16 N2 O FORMUL 2 CL CL 1- FORMUL 3 F F 1- HELIX 1 AA1 PRO A 1 AIB A 8 1 8 LINK C C9T A 0 N PRO A 1 1555 1555 1.33 LINK C PRO A 1 N BZK A 2 1555 1555 1.34 LINK C BZK A 2 N ALA A 3 1555 1555 1.33 LINK C ALA A 3 N AIB A 4 1555 1555 1.33 LINK C AIB A 4 N ILE A 5 1555 1555 1.31 LINK C ILE A 6 N AIB A 7 1555 1555 1.35 LINK C AIB A 7 N AIB A 8 1555 1555 1.33 LINK C AIB A 8 N AC9K A 9 1555 1555 1.32 LINK C AIB A 8 N BC9N A 9 1555 1555 1.32 SITE 1 AC1 6 C9T A 0 PRO A 1 BZK A 2 ALA A 3 SITE 2 AC1 6 C9N A 9 C9K A 9 SITE 1 AC2 5 C9T A 0 PRO A 1 BZK A 2 C9N A 9 SITE 2 AC2 5 C9K A 9 SITE 1 AC3 8 PRO A 1 BZK A 2 ALA A 3 AIB A 4 SITE 2 AC3 8 ILE A 5 ILE A 6 C9N A 9 C9K A 9 SITE 1 AC4 9 PRO A 1 BZK A 2 ALA A 3 AIB A 4 SITE 2 AC4 9 ILE A 5 ILE A 6 AIB A 7 CL A 101 SITE 3 AC4 9 F A 102 SITE 1 AC5 9 PRO A 1 BZK A 2 ALA A 3 AIB A 4 SITE 2 AC5 9 ILE A 5 ILE A 6 AIB A 7 CL A 101 SITE 3 AC5 9 F A 102 CRYST1 34.711 10.886 17.150 90.00 93.05 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 0.028809 0.000000 0.001536 0.00000 SCALE2 0.000000 0.091860 0.000000 0.00000 SCALE3 0.000000 0.000000 0.058391 0.00000 HETATM 1 C1 AC9T A 0 12.906 1.446 8.581 0.67 6.89 C ANISOU 1 C1 AC9T A 0 1617 553 385 293 -193 -79 C HETATM 2 C2 AC9T A 0 14.081 1.967 7.972 0.67 5.71 C ANISOU 2 C2 AC9T A 0 1011 346 757 -139 -306 -91 C HETATM 3 C3 AC9T A 0 14.981 2.605 9.093 0.67 5.32 C ANISOU 3 C3 AC9T A 0 590 588 795 17 -35 -45 C HETATM 4 C3 BC9T A 0 13.569 2.859 9.635 0.33 5.98 C ANISOU 4 C3 BC9T A 0 854 606 755 -178 -99 -219 C HETATM 5 C4 AC9T A 0 14.394 3.866 9.704 0.67 4.30 C ANISOU 5 C4 AC9T A 0 675 192 728 -30 -202 -154 C HETATM 6 C4 BC9T A 0 14.817 3.325 9.556 0.33 11.47 C ANISOU 6 C4 BC9T A 0 1240 403 2610 19 597 -943 C HETATM 7 C5 C9T A 0 15.190 4.311 10.897 1.00 6.07 C ANISOU 7 C5 C9T A 0 608 846 794 -142 -94 -208 C HETATM 8 C6 C9T A 0 16.650 4.636 10.705 1.00 5.54 C ANISOU 8 C6 C9T A 0 548 775 729 -106 -40 -287 C HETATM 9 C7 C9T A 0 17.297 5.303 11.924 1.00 4.66 C ANISOU 9 C7 C9T A 0 413 756 558 -85 -69 -107 C HETATM 10 C7B C9T A 0 17.516 4.354 13.077 1.00 6.62 C ANISOU 10 C7B C9T A 0 526 934 994 -221 -102 126 C HETATM 11 C C9T A 0 18.609 5.943 11.459 1.00 4.15 C ANISOU 11 C C9T A 0 359 681 498 -45 -55 -182 C HETATM 12 O C9T A 0 19.703 5.350 11.642 1.00 5.25 O ANISOU 12 O C9T A 0 375 669 901 -6 -98 -49 O HETATM 13 H11AC9T A 0 12.333 1.044 7.895 0.67 10.34 H HETATM 14 H13AC9T A 0 12.421 2.171 9.028 0.67 10.34 H HETATM 15 H12AC9T A 0 13.154 0.764 9.240 0.67 10.34 H HETATM 16 H21AC9T A 0 13.839 2.653 7.301 0.67 8.56 H HETATM 17 H22AC9T A 0 14.575 1.242 7.513 0.67 8.56 H HETATM 18 H32AC9T A 0 15.867 2.820 8.707 0.67 7.99 H HETATM 19 H32BC9T A 0 13.470 2.327 10.452 0.33 8.97 H HETATM 20 H31AC9T A 0 15.120 1.937 9.810 0.67 7.99 H HETATM 21 H31BC9T A 0 13.380 2.297 8.854 0.33 8.97 H HETATM 22 H41AC9T A 0 14.386 4.587 9.026 0.67 6.46 H HETATM 23 H41BC9T A 0 14.920 3.851 8.723 0.33 17.21 H HETATM 24 H42AC9T A 0 13.458 3.693 9.978 0.67 6.46 H HETATM 25 H42BC9T A 0 15.450 2.566 9.519 0.33 17.21 H HETATM 26 H52AC9T A 0 14.750 5.115 11.271 1.00 9.10 H HETATM 27 H51AC9T A 0 15.128 3.599 11.583 1.00 9.10 H HETATM 28 H61 C9T A 0 16.744 5.237 9.924 1.00 8.31 H HETATM 29 H62 C9T A 0 17.140 3.799 10.501 1.00 8.31 H HETATM 30 H7 C9T A 0 16.689 6.034 12.235 1.00 6.99 H HETATM 31 HB2 C9T A 0 18.127 3.639 12.800 1.00 9.93 H HETATM 32 HB1 C9T A 0 16.659 3.964 13.348 1.00 9.93 H HETATM 33 HB3 C9T A 0 17.906 4.842 13.833 1.00 9.93 H