HEADER DE NOVO PROTEIN 19-SEP-19 6UDW TITLE S2 SYMMETRIC PEPTIDE DESIGN NUMBER 3 CRYSTAL FORM 2, LURCH COMPND MOL_ID: 1; COMPND 2 MOLECULE: S2-3, LURCH CRYSTAL FORM 2; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 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 02-DEC-20 6UDW 1 JRNL REVDAT 1 23-SEP-20 6UDW 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 : PHENIX V1.16 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) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 12.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.7 REMARK 3 NUMBER OF REFLECTIONS : 5277 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.111 REMARK 3 R VALUE (WORKING SET) : 0.111 REMARK 3 FREE R VALUE : 0.113 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 528 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 12.1000 - 1.7500 0.94 1244 138 0.1047 0.0952 REMARK 3 2 1.7500 - 1.3900 0.92 1225 137 0.1064 0.1241 REMARK 3 3 1.3900 - 1.2100 0.89 1203 134 0.1132 0.1095 REMARK 3 4 1.2100 - 1.1000 0.83 1077 119 0.1371 0.1656 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) : 0.040 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 47.267 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 4.32 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 : 0.011 85 REMARK 3 ANGLE : 1.468 115 REMARK 3 CHIRALITY : 0.169 12 REMARK 3 PLANARITY : 0.008 17 REMARK 3 DIHEDRAL : 13.700 37 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 6UDW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-SEP-19. REMARK 100 THE DEPOSITION ID IS D_1000244448. 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 : 4.5 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) : 0.9792 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 : 5289 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 17.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.6 REMARK 200 DATA REDUNDANCY : 3.528 REMARK 200 R MERGE (I) : 0.10700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.7800 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 (%) : 72.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.11 REMARK 200 R MERGE FOR SHELL (I) : 0.13200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.150 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING REMARK 200 SOFTWARE USED: SHELXD 2013/2 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 20.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM SULFATE, 0.1 M SODIUM REMARK 280 ACETATE, PH 4.5, 50% (W/V) PEG 400, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P -1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -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 -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 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6UDR RELATED DB: PDB REMARK 900 ALTERNATE CRYSTAL FORM DBREF 6UDW A 1 10 PDB 6UDW 6UDW 1 10 SEQRES 1 A 10 DGN THR ARG PRO ASP GLN DTH DAR DPR DAS HET DGN A 1 17 HET DTH A 7 14 HET DAR A 8 24 HET DPR A 9 14 HET DAS A 10 12 HETNAM DGN D-GLUTAMINE HETNAM DTH D-THREONINE HETNAM DAR D-ARGININE HETNAM DPR D-PROLINE HETNAM DAS D-ASPARTIC ACID FORMUL 1 DGN C5 H10 N2 O3 FORMUL 1 DTH C4 H9 N O3 FORMUL 1 DAR C6 H15 N4 O2 1+ FORMUL 1 DPR C5 H9 N O2 FORMUL 1 DAS C4 H7 N O4 FORMUL 2 HOH *20(H2 O) HELIX 1 AA1 ARG A 3 DTH A 7 5 5 LINK C DGN A 1 N THR A 2 1555 1555 1.34 LINK N DGN A 1 C DAS A 10 1555 1555 1.34 LINK C GLN A 6 N DTH A 7 1555 1555 1.34 LINK C DTH A 7 N DAR A 8 1555 1555 1.34 LINK C DAR A 8 N DPR A 9 1555 1555 1.33 LINK C DPR A 9 N DAS A 10 1555 1555 1.33 CRYST1 14.010 15.480 18.720 105.15 99.96 99.47 P -1 2 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 0.071378 0.011909 0.016849 0.00000 SCALE2 0.000000 0.065492 0.020466 0.00000 SCALE3 0.000000 0.000000 0.056822 0.00000 HETATM 1 N DGN A 1 4.733 3.594 4.789 1.00 2.94 N ANISOU 1 N DGN A 1 357 286 474 44 -28 -162 N HETATM 2 CA DGN A 1 4.260 3.883 3.444 1.00 3.07 C ANISOU 2 CA DGN A 1 417 303 447 78 -66 -197 C HETATM 3 C DGN A 1 4.138 5.384 3.213 1.00 2.86 C ANISOU 3 C DGN A 1 381 284 420 71 -46 -180 C HETATM 4 O DGN A 1 3.981 5.841 2.078 1.00 3.36 O ANISOU 4 O DGN A 1 503 361 412 87 -58 -145 O HETATM 5 CB DGN A 1 5.134 3.234 2.388 1.00 3.55 C ANISOU 5 CB DGN A 1 505 363 480 139 -91 -215 C HETATM 6 CG DGN A 1 5.122 1.723 2.508 1.00 4.28 C ANISOU 6 CG DGN A 1 626 450 549 178 -121 -255 C HETATM 7 CD DGN A 1 5.945 1.081 1.395 1.00 4.69 C ANISOU 7 CD DGN A 1 640 542 602 192 -174 -307 C HETATM 8 OE1 DGN A 1 7.070 1.466 1.154 1.00 5.35 O ANISOU 8 OE1 DGN A 1 690 646 698 208 -110 -366 O HETATM 9 NE2 DGN A 1 5.383 0.083 0.734 1.00 5.21 N ANISOU 9 NE2 DGN A 1 749 584 648 173 -147 -337 N HETATM 10 H1 DGN A 1 5.645 3.711 4.782 1.00 3.54 H HETATM 11 HA DGN A 1 3.357 3.499 3.357 1.00 3.70 H HETATM 12 HB2 DGN A 1 6.051 3.563 2.486 1.00 4.27 H HETATM 13 HB3 DGN A 1 4.808 3.492 1.501 1.00 4.27 H HETATM 14 HG2 DGN A 1 5.492 1.460 3.377 1.00 5.14 H HETATM 15 HG3 DGN A 1 4.197 1.399 2.460 1.00 5.14 H HETATM 16 HE21 DGN A 1 5.815 -0.306 0.071 1.00 6.27 H HETATM 17 HE22 DGN A 1 4.574 -0.197 0.956 1.00 6.27 H