HEADER HYDROLASE INHIBITOR 22-JUN-14 4TTK TITLE RACEMIC STRUCTURE OF SUNFLOWER TRYPSIN INHIBITOR-1 (SFTI-1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUNFLOWER TRYPSIN INHIBITOR-1 (SFTI-1) (D-FORM); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HELIANTHUS ANNUUS; SOURCE 4 ORGANISM_COMMON: 3; SOURCE 5 ORGANISM_TAXID: 4232; SOURCE 6 OTHER_DETAILS: CHEMICAL SYNTHESIS KEYWDS CYCLIC PEPTIDE, DISULFIDE BOND, HYDROLASE INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR C.K.WANG,G.J.KING,D.J.CRAIK REVDAT 5 27-DEC-23 4TTK 1 REMARK LINK REVDAT 4 01-JAN-20 4TTK 1 REMARK REVDAT 3 06-SEP-17 4TTK 1 SOURCE JRNL REMARK REVDAT 2 22-OCT-14 4TTK 1 JRNL REVDAT 1 10-SEP-14 4TTK 0 JRNL AUTH C.K.WANG,G.J.KING,S.E.NORTHFIELD,P.G.OJEDA,D.J.CRAIK JRNL TITL RACEMIC AND QUASI-RACEMIC X-RAY STRUCTURES OF CYCLIC JRNL TITL 2 DISULFIDE-RICH PEPTIDE DRUG SCAFFOLDS. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 53 11236 2014 JRNL REFN ESSN 1521-3773 JRNL PMID 25168664 JRNL DOI 10.1002/ANIE.201406563 REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 13.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 7286 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.264 REMARK 3 R VALUE (WORKING SET) : 0.262 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.350 REMARK 3 FREE R VALUE TEST SET COUNT : 754 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 13.9581 - 2.1357 0.99 1293 141 0.2793 0.2796 REMARK 3 2 2.1357 - 1.6961 1.00 1335 151 0.2408 0.2636 REMARK 3 3 1.6961 - 1.4820 1.00 1289 157 0.2569 0.2711 REMARK 3 4 1.4820 - 1.3466 1.00 1307 150 0.2504 0.3075 REMARK 3 5 1.3466 - 1.2502 1.00 1308 155 0.2634 0.2673 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.780 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 46.92 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 110 REMARK 3 ANGLE : 1.253 146 REMARK 3 CHIRALITY : 0.053 16 REMARK 3 PLANARITY : 0.011 19 REMARK 3 DIHEDRAL : 7.834 43 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4TTK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JUN-14. REMARK 100 THE DEPOSITION ID IS D_1000202131. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-NOV-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7289 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 21.460 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 11.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 45.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.22100 REMARK 200 R SYM FOR SHELL (I) : 0.22100 REMARK 200 FOR SHELL : 7.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.5, 1.0 M AMMONIUM REMARK 280 SULFATE, 3% W/V POLYETHYLENE GLYCOL 8,000, 0.14 M SODIUM REMARK 280 THIOCYANATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P -3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,-Z REMARK 290 5555 Y,-X+Y,-Z REMARK 290 6555 X-Y,X,-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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 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 300 REMARK: CRYSTAL OBTAINED FROM RACEMIC MIXTURE OF D- AND L- REMARK 300 ENANTIOMERS OF SFTI-1. THE D-FORM IS REPRESENTED IN THE ASYMMETRIC REMARK 300 UNIT. 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: 140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 1480 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: 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 DLY A 5 -50.28 90.59 REMARK 500 REMARK 500 REMARK: NULL DBREF 4TTK A 1 14 PDB 4TTK 4TTK 1 14 SEQRES 1 A 14 GLY DAR DCY DTH DLY DSN DIL DPR DPR DIL DCY DPN DPR SEQRES 2 A 14 DAS HET DAR A 2 11 HET DCY A 3 6 HET DTH A 4 7 HET DLY A 5 9 HET DSN A 6 6 HET DIL A 7 8 HET DPR A 8 7 HET DPR A 9 7 HET DIL A 10 8 HET DCY A 11 6 HET DPN A 12 11 HET DPR A 13 7 HET DAS A 14 8 HETNAM DAR D-ARGININE HETNAM DCY D-CYSTEINE HETNAM DTH D-THREONINE HETNAM DLY D-LYSINE HETNAM DSN D-SERINE HETNAM DIL D-ISOLEUCINE HETNAM DPR D-PROLINE HETNAM DPN D-PHENYLALANINE HETNAM DAS D-ASPARTIC ACID FORMUL 1 DAR C6 H15 N4 O2 1+ FORMUL 1 DCY 2(C3 H7 N O2 S) FORMUL 1 DTH C4 H9 N O3 FORMUL 1 DLY C6 H14 N2 O2 FORMUL 1 DSN C3 H7 N O3 FORMUL 1 DIL 2(C6 H13 N O2) FORMUL 1 DPR 3(C5 H9 N O2) FORMUL 1 DPN C9 H11 N O2 FORMUL 1 DAS C4 H7 N O4 FORMUL 2 HOH *7(H2 O) SSBOND 1 DCY A 3 DCY A 11 1555 1555 2.05 LINK C GLY A 1 N DAR A 2 1555 1555 1.33 LINK N GLY A 1 C DAS A 14 1555 1555 1.33 LINK C DAR A 2 N DCY A 3 1555 1555 1.33 LINK C DCY A 3 N DTH A 4 1555 1555 1.33 LINK C DTH A 4 N DLY A 5 1555 1555 1.33 LINK C DLY A 5 N DSN A 6 1555 1555 1.32 LINK C DSN A 6 N DIL A 7 1555 1555 1.33 LINK C DIL A 7 N DPR A 8 1555 1555 1.35 LINK C DPR A 8 N DPR A 9 1555 1555 1.34 LINK C DPR A 9 N DIL A 10 1555 1555 1.33 LINK C DIL A 10 N DCY A 11 1555 1555 1.33 LINK C DCY A 11 N DPN A 12 1555 1555 1.33 LINK C DPN A 12 N DPR A 13 1555 1555 1.35 LINK C DPR A 13 N DAS A 14 1555 1555 1.33 CISPEP 1 DIL A 7 DPR A 8 0 9.98 CRYST1 42.640 42.640 12.965 90.00 90.00 120.00 P -3 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 0.023452 0.013540 0.000000 0.00000 SCALE2 0.000000 0.027080 0.000000 0.00000 SCALE3 0.000000 0.000000 0.077131 0.00000