PDB Short entry for 4BY8 HEADER ANTIBIOTIC 18-JUL-13 4BY8 TITLE MICROHETEROGENEOUS PARACELSIN-X FROM TRICHODERMA REESEI COMPND MOL_ID: 1; COMPND 2 MOLECULE: PARACELSIN-X; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRICHODERMA REESEI; SOURCE 3 ORGANISM_TAXID: 51453; SOURCE 4 STRAIN: QM9414 KEYWDS PEPTAIBOL, PEPTAIBIOTIC, MEMBRANE ACTIVE, PEPTIDE ANTIBIOTIC, KEYWDS 2 ANTIBIOTIC EXPDTA X-RAY DIFFRACTION AUTHOR R.GESSMANN,K.PETRATOS REVDAT 4 17-APR-19 4BY8 1 REMARK HETSYN LINK REVDAT 3 02-OCT-13 4BY8 1 JRNL REVDAT 2 28-AUG-13 4BY8 1 SOURCE ATOM REVDAT 1 21-AUG-13 4BY8 0 JRNL AUTH R.GESSMANN,K.PETRATOS JRNL TITL MICROHETEROGENEOUS PARACELSIN-X FROM TRICHODERMA REESEI JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 0.94 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) : 0.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 11.31 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT 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) : 0.166 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.164 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 379 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 7699 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.158 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.156 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 285 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 5530 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 163 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 3 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 139.50 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 147.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 4 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 1305 REMARK 3 NUMBER OF RESTRAINTS : 1321 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.022 REMARK 3 ANGLE DISTANCES (A) : 0.050 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.430 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.033 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.070 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.040 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.060 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS,KRETSINGER REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4BY8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-JUL-13. REMARK 100 THE DEPOSITION ID IS D_1290057705. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAR-13 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 : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8729 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7699 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.940 REMARK 200 RESOLUTION RANGE LOW (A) : 11.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.94 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.49000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: DIRECT METHODS REMARK 200 SOFTWARE USED: SNB REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 20.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SLOW EVAPORATION AT ROOM TEMPERATURE, REMARK 280 TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 1 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -Y,-X,-Z+2/3 REMARK 290 5555 -X+Y,Y,-Z+1/3 REMARK 290 6555 X,X-Y,-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 14.05000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.10000 REMARK 290 SMTRY1 4 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 28.10000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 14.05000 REMARK 290 SMTRY1 6 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 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 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 LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ALA A 4 CA ALA A 4 CB 0.175 REMARK 500 ALA A 4 CA ALA A 4 C -0.178 REMARK 500 GLN A 19 CG GLN A 19 CD 0.148 REMARK 500 REMARK 500 REMARK: 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 ILE A 15 CB - CG1 - CD1 ANGL. DEV. = 33.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AMT RELATED DB: PDB REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1M24 RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE PEPTIDE CRYSTALLIZED IS MICROHETEROGENEIC IN 4 POSITIONS REMARK 999 IN THE SEQUENCE. ALA4 IS ALSO AIB4, AIB6 IS ALSO ALA6, VAL9 REMARK 999 IS ALSO ILE9, VAL15 IS ALSO ILE15 DBREF 4BY8 A 0 20 NOR NOR01025 NOR01025 0 20 SEQADV 4BY8 AIB A 4 PDB 4BY8 ALA 4 MICROHETEROGENEITY SEQADV 4BY8 ALA A 6 PDB 4BY8 AIB 6 MICROHETEROGENEITY SEQADV 4BY8 VAL A 9 PDB 4BY8 ILE 9 MICROHETEROGENEITY SEQADV 4BY8 VAL A 15 PDB 4BY8 ILE 15 MICROHETEROGENEITY SEQRES 1 A 21 ACE AIB ALA AIB AIB AIB ALA GLN AIB VAL AIB GLY AIB SEQRES 2 A 21 AIB PRO VAL AIB AIB GLN GLN PHL MODRES 4BY8 AIB A 1 ALA ALPHA-AMINOISOBUTYRIC ACID MODRES 4BY8 AIB A 3 ALA ALPHA-AMINOISOBUTYRIC ACID MODRES 4BY8 AIB A 4 ALA ALPHA-AMINOISOBUTYRIC ACID MODRES 4BY8 AIB A 5 ALA ALPHA-AMINOISOBUTYRIC ACID MODRES 4BY8 AIB A 6 ALA ALPHA-AMINOISOBUTYRIC ACID MODRES 4BY8 AIB A 8 ALA ALPHA-AMINOISOBUTYRIC ACID MODRES 4BY8 AIB A 10 ALA ALPHA-AMINOISOBUTYRIC ACID MODRES 4BY8 AIB A 12 ALA ALPHA-AMINOISOBUTYRIC ACID MODRES 4BY8 AIB A 13 ALA ALPHA-AMINOISOBUTYRIC ACID MODRES 4BY8 AIB A 16 ALA ALPHA-AMINOISOBUTYRIC ACID MODRES 4BY8 AIB A 17 ALA ALPHA-AMINOISOBUTYRIC ACID MODRES 4BY8 PHL A 20 PHE L-PHENYLALANINOL HET ACE A 0 6 HET AIB A 1 13 HET AIB A 3 13 HET AIB A 4 13 HET AIB A 5 13 HET AIB A 6 13 HET AIB A 8 13 HET AIB A 10 13 HET AIB A 12 13 HET AIB A 13 13 HET AIB A 16 13 HET AIB A 17 13 HET PHL A 20 27 HET MOH A 25 2 HETNAM ACE ACETYL GROUP HETNAM AIB ALPHA-AMINOISOBUTYRIC ACID HETNAM PHL L-PHENYLALANINOL HETNAM MOH METHANOL HETSYN PHL BOUND FORM OF PHENYLALANINAL FORMUL 1 ACE C2 H4 O FORMUL 1 AIB 11(C4 H9 N O2) FORMUL 1 PHL C9 H13 N O FORMUL 2 MOH C H4 O FORMUL 3 HOH *3(H2 O) HELIX 1 0 AIB A 1 GLN A 19 1 19 LINK C ACE A 0 N AIB A 1 1555 1555 1.29 LINK C AIB A 1 N ALA A 2 1555 1555 1.28 LINK C ALA A 2 N AIB A 3 1555 1555 1.32 LINK C AIB A 3 N AAIB A 4 1555 1555 1.33 LINK C AAIB A 4 N AIB A 5 1555 1555 1.32 LINK C AIB A 5 N AALA A 6 1555 1555 1.36 LINK C GLN A 7 N AIB A 8 1555 1555 1.37 LINK C AIB A 8 N AVAL A 9 1555 1555 1.33 LINK C AVAL A 9 N AIB A 10 1555 1555 1.34 LINK C AIB A 10 N GLY A 11 1555 1555 1.37 LINK C GLY A 11 N AIB A 12 1555 1555 1.25 LINK C AIB A 12 N AIB A 13 1555 1555 1.32 LINK C AIB A 13 N PRO A 14 1555 1555 1.31 LINK C AVAL A 15 N AIB A 16 1555 1555 1.34 LINK C AIB A 16 N AIB A 17 1555 1555 1.34 LINK C AIB A 17 N GLN A 18 1555 1555 1.28 LINK C GLN A 19 N PHL A 20 1555 1555 1.35 CRYST1 22.020 22.020 42.150 90.00 90.00 120.00 P 31 1 2 6 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 0.045413 0.026219 0.000000 0.00000 SCALE2 0.000000 0.052439 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023725 0.00000 HETATM 1 C ACE A 0 -5.798 20.950 47.599 1.00 16.52 C ANISOU 1 C ACE A 0 2545 2158 1574 735 -460 -685 C HETATM 2 O ACE A 0 -6.268 20.016 46.875 1.00 16.46 O ANISOU 2 O ACE A 0 2521 2112 1622 384 -368 -572 O HETATM 3 CH3 ACE A 0 -6.335 21.084 48.905 1.00 21.31 C ANISOU 3 CH3 ACE A 0 4072 3061 965 570 -608 -134 C HETATM 4 H1 ACE A 0 -6.055 20.340 49.444 1.00 31.97 H HETATM 5 H2 ACE A 0 -7.293 21.102 48.857 1.00 31.97 H HETATM 6 H3 ACE A 0 -6.019 21.901 49.299 1.00 31.97 H HETATM 7 N AIB A 1 -4.738 21.638 47.360 1.00 17.65 N ANISOU 7 N AIB A 1 2966 1910 1828 382 -860 -91 N HETATM 8 CA AIB A 1 -4.111 21.585 46.076 1.00 16.62 C ANISOU 8 CA AIB A 1 2958 1548 1809 -106 -772 -273 C HETATM 9 C AIB A 1 -3.620 20.123 45.896 1.00 15.53 C ANISOU 9 C AIB A 1 2640 1548 1714 -212 -738 -81 C HETATM 10 O AIB A 1 -3.771 19.625 44.731 1.00 13.92 O ANISOU 10 O AIB A 1 2461 1309 1516 -194 -324 113 O HETATM 11 CB1 AIB A 1 -4.861 22.160 44.909 1.00 18.16 C ANISOU 11 CB1 AIB A 1 3022 2024 1855 254 -722 -117 C HETATM 12 CB2 AIB A 1 -2.665 22.459 46.274 1.00 20.02 C ANISOU 12 CB2 AIB A 1 2969 1608 3031 -134 -876 -391 C HETATM 13 H AIB A 1 -4.404 22.134 47.977 1.00 21.17 H HETATM 14 HB11 AIB A 1 -4.457 21.861 44.091 1.00 27.24 H HETATM 15 HB12 AIB A 1 -4.830 23.118 44.949 1.00 27.24 H HETATM 16 HB13 AIB A 1 -5.775 21.867 44.940 1.00 27.24 H HETATM 17 HB21 AIB A 1 -1.920 21.905 46.030 1.00 30.03 H HETATM 18 HB22 AIB A 1 -2.577 22.728 47.191 1.00 30.03 H HETATM 19 HB23 AIB A 1 -2.683 23.237 45.712 1.00 30.03 H