HEADER D-L PEPTIDE 11-SEP-03 1UNO TITLE CRYSTAL STRUCTURE OF A D,L-ALTERNATING PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: H-(L-TYR-D-TYR)4-LYS-OH; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS D-L PEPTIDE, D, L-ALTERNATING PEPTIDE, BETA-HELIX EXPDTA X-RAY DIFFRACTION AUTHOR E.ALEXOPOULOS,A.KUESEL,I.USON,U.DIEDERICHSEN,G.M.SHELDRICK REVDAT 8 23-OCT-24 1UNO 1 REMARK REVDAT 7 24-JUL-19 1UNO 1 REMARK REVDAT 6 22-MAY-19 1UNO 1 REMARK REVDAT 5 08-MAY-19 1UNO 1 REMARK LINK REVDAT 4 08-FEB-17 1UNO 1 SOURCE REMARK VERSN FORMUL REVDAT 4 2 1 SHEET REVDAT 3 24-FEB-09 1UNO 1 VERSN REVDAT 2 03-NOV-04 1UNO 1 JRNL REVDAT 1 24-SEP-04 1UNO 0 JRNL AUTH E.ALEXOPOULOS,A.KUESEL,G.M.SHELDRICK,U.DIEDERICHSEN,I.USON JRNL TITL SOLUTION AND STRUCTURE OF AN ALTERNATING D,L-PEPTIDE JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 60 1971 2004 JRNL REFN ISSN 0907-4449 JRNL PMID 15502304 JRNL DOI 10.1107/S0907444904022292 REMARK 2 REMARK 2 RESOLUTION. 1.40 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.2 REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : IN 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) : 0.222 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 406 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 8289 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)) : 0.197 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 319 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 6046 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 212 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 19 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 231.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 939 REMARK 3 NUMBER OF RESTRAINTS : 907 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 ANGLE DISTANCES (A) : 0.028 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.179 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.072 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.100 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.020 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.046 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 : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1UNO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-SEP-03. REMARK 100 THE DEPOSITION ID IS D_1290013490. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JAN-03 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.50 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X13 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8015 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8289 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.2 REMARK 200 DATA REDUNDANCY : 1.420 REMARK 200 R MERGE (I) : 0.03390 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.8200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.50 REMARK 200 R MERGE FOR SHELL (I) : 0.30830 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.420 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: SHELXD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: (NH4)2SO4,MPD,HEPES, PH 7.5,HANGING REMARK 280 DROP, PH 7.50, VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 39.46500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 13.99500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 13.99500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 59.19750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 13.99500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 13.99500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 19.73250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 13.99500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 13.99500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 59.19750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 13.99500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 13.99500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 19.73250 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 39.46500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 REMARK 400 THE H-(L-TYR-D-TYR)4-LYS-OH IS POLYPEPTIDE, A MEMBER OF ANTIBIOTIC REMARK 400 CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: H-(L-TYR-D-TYR)4-LYS-OH REMARK 400 CHAIN: A, B 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 DTY A 6 CB - CG - CD1 ANGL. DEV. = -3.7 DEGREES REMARK 500 DTY B 2 CB - CG - CD1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DTY B 4 CB - CG - CD2 ANGL. DEV. = -3.6 DEGREES REMARK 500 DTY B 4 CG - CD2 - CE2 ANGL. DEV. = -5.8 DEGREES REMARK 500 DTY B 4 CD1 - CE1 - CZ ANGL. DEV. = -6.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 DTY A 2 -84.03 151.81 REMARK 500 DTY A 6 -72.75 151.67 REMARK 500 DTY B 2 -89.73 150.68 REMARK 500 DTY B 6 -71.96 150.28 REMARK 500 REMARK 500 REMARK: NULL DBREF 1UNO A 1 9 PDB 1UNO 1UNO 1 9 DBREF 1UNO B 1 9 PDB 1UNO 1UNO 1 9 SEQRES 1 A 9 TYR DTY TYR DTY TYR DTY TYR DTY LYS SEQRES 1 B 9 TYR DTY TYR DTY TYR DTY TYR DTY LYS HET DTY A 2 12 HET DTY A 4 12 HET DTY A 6 12 HET DTY A 8 12 HET DTY B 2 12 HET DTY B 4 12 HET DTY B 6 12 HET DTY B 8 12 HETNAM DTY D-TYROSINE FORMUL 1 DTY 8(C9 H11 N O3) FORMUL 3 HOH *19(H2 O) SHEET 1 A 2 DTY A 2 LYS A 9 0 SHEET 2 A 2 DTY B 2 LYS B 9 -1 O DTY B 6 N DTY A 4 LINK C TYR A 1 N DTY A 2 1555 1555 1.33 LINK C DTY A 2 N TYR A 3 1555 1555 1.32 LINK C TYR A 3 N DTY A 4 1555 1555 1.33 LINK C DTY A 4 N TYR A 5 1555 1555 1.31 LINK C TYR A 5 N DTY A 6 1555 1555 1.32 LINK C DTY A 6 N TYR A 7 1555 1555 1.32 LINK C TYR A 7 N DTY A 8 1555 1555 1.33 LINK C DTY A 8 N LYS A 9 1555 1555 1.33 LINK C TYR B 1 N DTY B 2 1555 1555 1.33 LINK C DTY B 2 N TYR B 3 1555 1555 1.31 LINK C TYR B 3 N DTY B 4 1555 1555 1.32 LINK C DTY B 4 N TYR B 5 1555 1555 1.32 LINK C TYR B 5 N DTY B 6 1555 1555 1.33 LINK C DTY B 6 N TYR B 7 1555 1555 1.33 LINK C TYR B 7 N DTY B 8 1555 1555 1.34 LINK C DTY B 8 N LYS B 9 1555 1555 1.34 CRYST1 27.990 27.990 78.930 90.00 90.00 90.00 P 43 21 2 16 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 0.035727 0.000000 0.000000 0.00000 SCALE2 0.000000 0.035727 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012669 0.00000