HEADER DE NOVO PROTEIN 24-SEP-19 6UF9 TITLE S4 SYMMETRIC PEPTIDE DESIGN NUMBER 1, TIM APO FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: S4-1, TIM APO-FORM; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: THE ASYMMETRIC UNIT CONTAINS HALF OF THE MOLECULE. THE COMPND 6 SECOND HALF IS GENERATED BY A CRYSTALLOGRAPHIC SYMMETRY OPERATOR. SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 OTHER_DETAILS: AB INITIO DESIGN KEYWDS CYCLIC PEPTIDE, CENTROSYMMETRIC MACROCYCLE, L- AND D-AMINO ACIDS, DE KEYWDS 2 NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR V.K.MULLIGAN,C.S.KANG,I.ANTSELOVICH,M.R.SAWAYA,T.O.YEATES,D.BAKER REVDAT 1 02-DEC-20 6UF9 0 JRNL AUTH V.K.MULLIGAN,C.S.KANG,M.R.SAWAYA,S.RETTIE,X.LI, JRNL AUTH 2 I.ANTSELOVICH,T.W.CRAVEN,A.M.WATKINS,J.W.LABONTE,F.DIMAIO, JRNL AUTH 3 T.O.YEATES,D.BAKER JRNL TITL COMPUTATIONAL DESIGN OF MIXED CHIRALITY PEPTIDE MACROCYCLES JRNL TITL 2 WITH INTERNAL SYMMETRY. JRNL REF PROTEIN SCI. V. 29 2433 2020 JRNL REFN ESSN 1469-896X JRNL PMID 33058266 JRNL DOI 10.1002/PRO.3974 REMARK 2 REMARK 2 RESOLUTION. 1.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0253 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 4233 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.128 REMARK 3 FREE R VALUE : 0.173 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.017 REMARK 3 FREE R VALUE TEST SET COUNT : 424 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.13 REMARK 3 REFLECTION IN BIN (WORKING SET) : 269 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.71 REMARK 3 BIN R VALUE (WORKING SET) : 0.2470 REMARK 3 BIN FREE R VALUE SET COUNT : 30 REMARK 3 BIN FREE R VALUE : 0.3210 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 102 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 17 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.47 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.93 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.21400 REMARK 3 B22 (A**2) : -0.02100 REMARK 3 B33 (A**2) : -0.19300 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.038 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.040 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.028 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.347 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.987 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.979 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 146 ; 0.012 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 150 ; 0.002 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 201 ; 1.994 ; 1.659 REMARK 3 BOND ANGLES OTHERS (DEGREES): 355 ; 0.767 ; 1.606 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 19 ; 4.809 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 4 ;41.051 ;27.500 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 21 ;20.887 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 15 ; 0.152 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 156 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 24 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 32 ; 0.254 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 40 ; 0.314 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 56 ; 0.207 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 17 ; 0.148 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 57 ; 1.363 ; 1.039 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 57 ; 1.361 ; 1.038 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 70 ; 1.809 ; 1.570 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 71 ; 1.798 ; 1.567 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 89 ; 4.291 ; 1.717 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 82 ; 4.035 ; 1.622 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 126 ; 5.627 ; 2.419 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 115 ; 5.062 ; 2.202 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 296 ; 4.235 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 6UF9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-SEP-19. REMARK 100 THE DEPOSITION ID IS D_1000244519. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-MAR-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 20180126 REMARK 200 DATA SCALING SOFTWARE : XSCALE 20180126 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4233 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 19.838 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 10.31 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.0100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.13 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 7.19 REMARK 200 R MERGE FOR SHELL (I) : 0.51100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.830 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING 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 (%): 25.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.15 M AMMONIUM SULFATE, 0.1 M CITRIC REMARK 280 ACID, PH 5, PH 5.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 13.88500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 14.17500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 13.88500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 14.17500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 2680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 400 REMARK 400 COMPOUND REMARK 400 THE ASYMMETRIC UNIT CONTAINS HALF OF THE MOLECULE. THE SECOND HALF REMARK 400 IS GENERATED BY A CRYSTALLOGRAPHIC SYMMETRY OPERATOR. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 LYS A 13 REMARK 465 LEU A 14 REMARK 465 DGN A 15 REMARK 465 DGL A 16 REMARK 465 AIB A 17 REMARK 465 HIS A 18 REMARK 465 DLY A 19 REMARK 465 DLE A 20 REMARK 465 GLN A 21 REMARK 465 GLU A 22 REMARK 465 AIB A 23 REMARK 465 DHI A 24 DBREF 6UF9 A 1 24 PDB 6UF9 6UF9 1 24 SEQRES 1 A 24 LYS LEU DGN DGL AIB HIS DLY DLE GLN GLU AIB DHI LYS SEQRES 2 A 24 LEU DGN DGL AIB HIS DLY DLE GLN GLU AIB DHI HET DGN A 3 17 HET DGL A 4 25 HET AIB A 5 13 HET DLY A 7 39 HET DLE A 8 19 HET AIB A 11 13 HET DHI A 12 18 HET SO4 A 101 5 HET SO4 A 102 5 HETNAM DGN D-GLUTAMINE HETNAM DGL D-GLUTAMIC ACID HETNAM AIB ALPHA-AMINOISOBUTYRIC ACID HETNAM DLY D-LYSINE HETNAM DLE D-LEUCINE HETNAM DHI D-HISTIDINE HETNAM SO4 SULFATE ION FORMUL 1 DGN C5 H10 N2 O3 FORMUL 1 DGL C5 H9 N O4 FORMUL 1 AIB 2(C4 H9 N O2) FORMUL 1 DLY C6 H14 N2 O2 FORMUL 1 DLE C6 H13 N O2 FORMUL 1 DHI C6 H10 N3 O2 1+ FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 HOH *17(H2 O) LINK N LYS A 1 C DHI A 12 1555 2555 1.35 LINK C LEU A 2 N DGN A 3 1555 1555 1.34 LINK C DGN A 3 N DGL A 4 1555 1555 1.34 LINK C DGL A 4 N AIB A 5 1555 1555 1.35 LINK C AIB A 5 N HIS A 6 1555 1555 1.33 LINK C HIS A 6 N DLY A 7 1555 1555 1.33 LINK C DLY A 7 N DLE A 8 1555 1555 1.34 LINK C DLE A 8 N GLN A 9 1555 1555 1.34 LINK C GLU A 10 N AIB A 11 1555 1555 1.34 LINK C AIB A 11 N DHI A 12 1555 1555 1.34 CRYST1 27.770 28.350 12.220 90.00 90.00 90.00 P 21 21 2 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 0.036010 0.000000 0.000000 0.00000 SCALE2 0.000000 0.035273 0.000000 0.00000 SCALE3 0.000000 0.000000 0.081833 0.00000