HEADER DE NOVO PROTEIN 23-SEP-19 6UF8 TITLE S2 SYMMETRIC PEPTIDE DESIGN NUMBER 6, LONDON BRIDGE COMPND MOL_ID: 1; COMPND 2 MOLECULE: S2-6, LONDON BRIDGE; 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 2 23-OCT-24 6UF8 1 REMARK REVDAT 1 02-DEC-20 6UF8 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. 0.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16-3549 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 10290 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.146 REMARK 3 R VALUE (WORKING SET) : 0.146 REMARK 3 FREE R VALUE : 0.148 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1019 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 16.3600 - 1.5300 0.98 1360 154 0.1750 0.1744 REMARK 3 2 1.5300 - 1.2100 0.99 1363 137 0.1121 0.1281 REMARK 3 3 1.2100 - 1.0600 0.99 1386 154 0.0951 0.0986 REMARK 3 4 1.0600 - 0.9600 0.99 1379 153 0.1062 0.0908 REMARK 3 5 0.9600 - 0.9000 1.00 1369 153 0.1313 0.1327 REMARK 3 6 0.9000 - 0.8400 0.98 1340 149 0.1592 0.1596 REMARK 3 7 0.8400 - 0.8000 0.78 1074 119 0.2833 0.3138 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.059 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 11.265 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.92 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.27 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 : 0.008 63 REMARK 3 ANGLE : 1.413 85 REMARK 3 CHIRALITY : 0.067 8 REMARK 3 PLANARITY : 0.020 11 REMARK 3 DIHEDRAL : 28.527 29 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 6UF8 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_1000244518. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-OCT-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 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-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8856 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 20170923 REMARK 200 DATA SCALING SOFTWARE : XSCALE 20170923 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10306 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.800 REMARK 200 RESOLUTION RANGE LOW (A) : 18.930 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 5.695 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.8800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.82 REMARK 200 COMPLETENESS FOR SHELL (%) : 60.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.21 REMARK 200 R MERGE FOR SHELL (I) : 0.28000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.540 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 (%): 34.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M PHOSPHATE/CITRATE PH 4.2, 40% REMARK 280 (V/V) PEG 300, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H -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 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 -X+2/3,-Y+1/3,-Z+1/3 REMARK 290 11555 Y+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 12555 X-Y+2/3,X+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 -X+1/3,-Y+2/3,-Z+2/3 REMARK 290 17555 Y+1/3,-X+Y+2/3,-Z+2/3 REMARK 290 18555 X-Y+1/3,X+2/3,-Z+2/3 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 SMTRY1 7 1.000000 0.000000 0.000000 16.36000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 9.44545 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 8.48000 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 16.36000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 9.44545 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 8.48000 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 16.36000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 9.44545 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 8.48000 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 16.36000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 9.44545 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 8.48000 REMARK 290 SMTRY1 11 0.500000 0.866025 0.000000 16.36000 REMARK 290 SMTRY2 11 -0.866025 0.500000 0.000000 9.44545 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 8.48000 REMARK 290 SMTRY1 12 0.500000 -0.866025 0.000000 16.36000 REMARK 290 SMTRY2 12 0.866025 0.500000 0.000000 9.44545 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 8.48000 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 18.89090 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 16.96000 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 18.89090 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 16.96000 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 18.89090 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 16.96000 REMARK 290 SMTRY1 16 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 18.89090 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 16.96000 REMARK 290 SMTRY1 17 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 17 -0.866025 0.500000 0.000000 18.89090 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 16.96000 REMARK 290 SMTRY1 18 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 0.866025 0.500000 0.000000 18.89090 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 16.96000 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 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 16.36000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 9.44545 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 8.48000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 112 LIES ON A SPECIAL POSITION. 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 ALA A 7 REMARK 465 DSG A 8 REMARK 465 LYS A 9 REMARK 465 HIS A 10 REMARK 465 DPR A 11 REMARK 465 GLU A 12 REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 112 DISTANCE = 5.82 ANGSTROMS DBREF 6UF8 A 1 12 PDB 6UF8 6UF8 1 12 SEQRES 1 A 12 DAL ASN DLY DHI PRO DGL ALA DSG LYS HIS DPR GLU HET DAL A 1 10 HET DLY A 3 40 HET DHI A 4 18 HET DGL A 6 26 HETNAM DAL D-ALANINE HETNAM DLY D-LYSINE HETNAM DHI D-HISTIDINE HETNAM DGL D-GLUTAMIC ACID FORMUL 1 DAL C3 H7 N O2 FORMUL 1 DLY C6 H14 N2 O2 FORMUL 1 DHI C6 H10 N3 O2 1+ FORMUL 1 DGL C5 H9 N O4 FORMUL 2 HOH *12(H2 O) LINK C DAL A 1 N ASN A 2 1555 1555 1.34 LINK N DAL A 1 C DGL A 6 1555 10555 1.34 LINK C ASN A 2 N DLY A 3 1555 1555 1.33 LINK C DLY A 3 N DHI A 4 1555 1555 1.34 LINK C DHI A 4 N PRO A 5 1555 1555 1.35 LINK C PRO A 5 N DGL A 6 1555 1555 1.34 CRYST1 32.720 32.720 25.440 90.00 90.00 120.00 H -3 18 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 0.030562 0.017645 0.000000 0.00000 SCALE2 0.000000 0.035290 0.000000 0.00000 SCALE3 0.000000 0.000000 0.039308 0.00000 HETATM 1 N DAL A 1 9.484 3.355 4.557 1.00 6.11 N ANISOU 1 N DAL A 1 861 1010 448 -90 -112 -122 N HETATM 2 CA DAL A 1 8.163 2.742 4.600 1.00 6.13 C ANISOU 2 CA DAL A 1 868 981 478 -89 -155 -96 C HETATM 3 CB DAL A 1 7.549 2.920 5.973 1.00 6.88 C ANISOU 3 CB DAL A 1 923 1133 558 -140 -80 -160 C HETATM 4 C DAL A 1 8.267 1.262 4.255 1.00 6.35 C ANISOU 4 C DAL A 1 955 982 475 -48 -132 -48 C HETATM 5 O DAL A 1 9.297 0.621 4.450 1.00 8.42 O ANISOU 5 O DAL A 1 1036 1062 1101 44 -253 -47 O HETATM 6 H1 DAL A 1 9.634 3.748 5.375 1.00 6.47 H HETATM 7 HA DAL A 1 7.587 3.184 3.933 1.00 6.30 H HETATM 8 HB1 DAL A 1 8.174 2.622 6.652 1.00 10.63 H HETATM 9 HB2 DAL A 1 7.342 3.858 6.117 1.00 9.82 H HETATM 10 HB3 DAL A 1 6.732 2.397 6.035 1.00 8.30 H