HEADER DE NOVO PROTEIN 16-JAN-24 8VPE TITLE UIC-10-BIF EXTENSION OF UIC-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UIC-10-BIF; 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 SYNTHETIC CONSTRUCT, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.GANATRA REVDAT 3 04-SEP-24 8VPE 1 JRNL REVDAT 2 14-AUG-24 8VPE 1 JRNL REVDAT 1 07-AUG-24 8VPE 0 JRNL AUTH P.GANATRA,D.F.WANG,V.GANATRA,V.T.DANG,A.I.NGUYEN JRNL TITL DIVERSE PROTEOMIMETIC FRAMEWORKS VIA RATIONAL DESIGN OF JRNL TITL 2 PI-STACKING PEPTIDE TECTONS. JRNL REF J.AM.CHEM.SOC. V. 146 22236 2024 JRNL REFN ESSN 1520-5126 JRNL PMID 39096501 JRNL DOI 10.1021/JACS.4C03094 REMARK 2 REMARK 2 RESOLUTION. 0.91 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.91 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 13878 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.097 REMARK 3 R VALUE (WORKING SET) : 0.095 REMARK 3 FREE R VALUE : 0.111 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.930 REMARK 3 FREE R VALUE TEST SET COUNT : 2520 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 16.8400 - 2.3800 1.00 1290 143 0.0976 0.1317 REMARK 3 2 2.3800 - 1.8900 0.98 1241 136 0.0819 0.0849 REMARK 3 3 1.8900 - 1.6500 1.00 1301 138 0.0881 0.0864 REMARK 3 4 1.6500 - 1.5000 1.00 1258 134 0.0912 0.1007 REMARK 3 5 1.5000 - 1.3900 1.00 1289 142 0.0914 0.1237 REMARK 3 6 1.3900 - 1.3100 1.00 1259 143 0.0961 0.1236 REMARK 3 7 1.3100 - 1.2500 1.00 1306 142 0.0930 0.1044 REMARK 3 8 1.2500 - 1.1900 0.97 1197 132 0.0853 0.0997 REMARK 3 9 1.1900 - 1.1500 0.99 1307 142 0.0862 0.1065 REMARK 3 10 1.1500 - 1.1100 1.00 1285 141 0.0877 0.0924 REMARK 3 11 1.1100 - 1.0700 0.99 1226 127 0.1017 0.1102 REMARK 3 12 1.0700 - 1.0400 1.00 1334 142 0.1058 0.1259 REMARK 3 13 1.0400 - 1.0100 1.00 1273 148 0.1072 0.0942 REMARK 3 14 1.0100 - 0.9900 1.00 1231 137 0.1089 0.1254 REMARK 3 15 0.9900 - 0.9700 1.00 1280 140 0.1150 0.1356 REMARK 3 16 0.9700 - 0.9500 1.00 1301 149 0.1186 0.1261 REMARK 3 17 0.9500 - 0.9300 1.00 1283 146 0.1318 0.1651 REMARK 3 18 0.9300 - 0.9100 0.95 1194 138 0.1449 0.1768 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.041 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 9.922 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 6.92 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 8.48 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 : 0.012 256 REMARK 3 ANGLE : 1.938 352 REMARK 3 CHIRALITY : 0.079 23 REMARK 3 PLANARITY : 0.016 40 REMARK 3 DIHEDRAL : 29.061 71 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 8VPE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1000280602. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-OCT-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.6199 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13878 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.910 REMARK 200 RESOLUTION RANGE LOW (A) : 16.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 12.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.6900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.91 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.94 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: ACETONITRILE, WATER, SLOW COOLING, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 5.38200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 23.72750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.01000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 23.72750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 5.38200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 18.01000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 DBREF 8VPE A 1 12 PDB 8VPE 8VPE 1 12 DBREF 8VPE B 1 12 PDB 8VPE 8VPE 1 12 SEQRES 1 A 12 Z7Z AIB LEU AIB ALA AIB LEU AIB GLN AIB LEU I77 SEQRES 1 B 12 Z7Z AIB LEU AIB ALA AIB LEU AIB GLN AIB LEU I77 HET Z7Z A 1 23 HET AIB A 2 13 HET AIB A 4 13 HET AIB A 6 13 HET AIB A 8 13 HET AIB A 10 13 HET I77 A 12 29 HET Z7Z B 1 23 HET AIB B 2 13 HET AIB B 4 13 HET AIB B 6 13 HET AIB B 8 14 HET AIB B 10 13 HET I77 B 12 29 HET CCN A 101 6 HET CCN A 102 6 HET CCN A 103 6 HET CCN B 101 6 HET CCN B 102 12 HET CCN B 103 6 HET CCN B 104 6 HETNAM Z7Z BIPHENYL-4-CARBOXYLIC ACID HETNAM AIB ALPHA-AMINOISOBUTYRIC ACID HETNAM I77 5'-(HYDRAZINECARBONYL)[2,2'-BIPYRIDINE]-5-CARBOXAMIDE HETNAM CCN ACETONITRILE FORMUL 1 Z7Z 2(C13 H10 O2) FORMUL 1 AIB 10(C4 H9 N O2) FORMUL 1 I77 2(C12 H11 N5 O2) FORMUL 3 CCN 7(C2 H3 N) FORMUL 10 HOH *11(H2 O) HELIX 1 AA1 AIB A 2 LEU A 11 1 10 HELIX 2 AA2 LEU B 3 LEU B 11 1 9 LINK C1 Z7Z A 1 N AIB A 2 1555 1555 1.42 LINK C AIB A 2 N LEU A 3 1555 1555 1.33 LINK C LEU A 3 N AIB A 4 1555 1555 1.33 LINK C AIB A 4 N ALA A 5 1555 1555 1.34 LINK C ALA A 5 N AIB A 6 1555 1555 1.33 LINK C AIB A 6 N LEU A 7 1555 1555 1.33 LINK C LEU A 7 N AIB A 8 1555 1555 1.33 LINK C AIB A 8 N GLN A 9 1555 1555 1.34 LINK C GLN A 9 N AIB A 10 1555 1555 1.33 LINK C AIB A 10 N LEU A 11 1555 1555 1.34 LINK C LEU A 11 N15 I77 A 12 1555 1555 1.41 LINK C1 Z7Z B 1 N AIB B 2 1555 1555 1.42 LINK C AIB B 2 N ALEU B 3 1555 1555 1.33 LINK C AIB B 2 N BLEU B 3 1555 1555 1.33 LINK C ALEU B 3 N AIB B 4 1555 1555 1.33 LINK C BLEU B 3 N AIB B 4 1555 1555 1.33 LINK C AIB B 4 N ALA B 5 1555 1555 1.33 LINK C ALA B 5 N AIB B 6 1555 1555 1.33 LINK C AIB B 6 N ALEU B 7 1555 1555 1.32 LINK C AIB B 6 N BLEU B 7 1555 1555 1.34 LINK C ALEU B 7 N AIB B 8 1555 1555 1.33 LINK C BLEU B 7 N AIB B 8 1555 1555 1.33 LINK C AIB B 8 N AGLN B 9 1555 1555 1.34 LINK C AIB B 8 N BGLN B 9 1555 1555 1.32 LINK C AGLN B 9 N AIB B 10 1555 1555 1.33 LINK C BGLN B 9 N AIB B 10 1555 1555 1.33 LINK C AIB B 10 N ALEU B 11 1555 1555 1.33 LINK C AIB B 10 N BLEU B 11 1555 1555 1.33 LINK C ALEU B 11 N15 I77 B 12 1555 1555 1.43 LINK C BLEU B 11 N15 I77 B 12 1555 1555 1.43 CRYST1 10.764 36.020 47.455 90.00 90.00 90.00 P 21 21 21 8 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 0.092902 0.000000 0.000000 0.00000 SCALE2 0.000000 0.027762 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021073 0.00000 HETATM 1 O1 Z7Z A 1 -2.212 -15.486 5.482 1.00 5.50 O ANISOU 1 O1 Z7Z A 1 608 917 563 -126 8 -7 O HETATM 2 C1 Z7Z A 1 -2.596 -16.654 5.546 1.00 5.45 C ANISOU 2 C1 Z7Z A 1 536 981 552 -73 -4 23 C HETATM 3 C2 Z7Z A 1 -2.050 -17.753 4.682 1.00 5.16 C ANISOU 3 C2 Z7Z A 1 513 986 462 -114 -50 27 C HETATM 4 C3 Z7Z A 1 -1.471 -17.400 3.482 1.00 5.36 C ANISOU 4 C3 Z7Z A 1 591 986 461 -103 -40 49 C HETATM 5 C4 Z7Z A 1 -1.032 -18.392 2.613 1.00 5.41 C ANISOU 5 C4 Z7Z A 1 622 1027 407 -75 -40 83 C HETATM 6 C5 Z7Z A 1 -2.157 -19.079 5.053 1.00 5.19 C ANISOU 6 C5 Z7Z A 1 605 963 405 -91 -58 53 C HETATM 7 C6 Z7Z A 1 -1.725 -20.064 4.181 1.00 5.40 C ANISOU 7 C6 Z7Z A 1 685 965 402 -61 -39 45 C HETATM 8 C7 Z7Z A 1 -1.166 -19.729 2.949 1.00 5.23 C ANISOU 8 C7 Z7Z A 1 592 1025 371 -41 -63 28 C HETATM 9 C8 Z7Z A 1 -0.786 -20.819 1.973 1.00 5.88 C ANISOU 9 C8 Z7Z A 1 789 1054 393 6 -41 33 C HETATM 10 C9 Z7Z A 1 -0.947 -20.585 0.604 1.00 6.03 C ANISOU 10 C9 Z7Z A 1 746 1150 396 -16 3 31 C HETATM 11 C10 Z7Z A 1 -0.414 -22.080 2.401 1.00 7.42 C ANISOU 11 C10 Z7Z A 1 1296 1075 447 12 -97 -1 C HETATM 12 C11 Z7Z A 1 -0.674 -21.584 -0.316 1.00 7.07 C ANISOU 12 C11 Z7Z A 1 1052 1225 408 40 -16 -17 C HETATM 13 C12 Z7Z A 1 -0.137 -23.082 1.478 1.00 8.72 C ANISOU 13 C12 Z7Z A 1 1752 1091 471 114 -53 -36 C HETATM 14 C13 Z7Z A 1 -0.264 -22.829 0.123 1.00 8.25 C ANISOU 14 C13 Z7Z A 1 1471 1181 484 139 -16 -48 C HETATM 15 H31 Z7Z A 1 -1.360 -16.355 3.217 1.00 6.45 H HETATM 16 H41 Z7Z A 1 -0.582 -18.118 1.667 1.00 6.50 H HETATM 17 H51 Z7Z A 1 -2.574 -19.345 6.016 1.00 6.24 H HETATM 18 H61 Z7Z A 1 -1.823 -21.106 4.459 1.00 6.49 H HETATM 19 H91 Z7Z A 1 -1.287 -19.616 0.260 1.00 7.25 H HETATM 20 H101 Z7Z A 1 -0.339 -22.289 3.461 1.00 8.91 H HETATM 21 H111 Z7Z A 1 -0.781 -21.390 -1.376 1.00 8.49 H HETATM 22 H121 Z7Z A 1 0.178 -24.060 1.820 1.00 10.47 H HETATM 23 H131 Z7Z A 1 -0.043 -23.609 -0.595 1.00 9.91 H HETATM 24 N AIB A 2 -3.821 -16.983 6.184 1.00 5.95 N ANISOU 24 N AIB A 2 537 1015 710 -109 50 -40 N HETATM 25 CA AIB A 2 -4.661 -15.965 6.766 1.00 6.62 C ANISOU 25 CA AIB A 2 533 1075 908 -47 98 -75 C HETATM 26 C AIB A 2 -3.854 -15.021 7.675 1.00 6.32 C ANISOU 26 C AIB A 2 580 1036 784 -52 232 -122 C HETATM 27 O AIB A 2 -3.921 -13.795 7.604 1.00 6.96 O ANISOU 27 O AIB A 2 772 1019 853 -70 214 -112 O HETATM 28 CB1 AIB A 2 -5.379 -15.147 5.677 1.00 7.42 C ANISOU 28 CB1 AIB A 2 689 1104 1027 -6 -70 -61 C HETATM 29 CB2 AIB A 2 -5.721 -16.659 7.637 1.00 7.61 C ANISOU 29 CB2 AIB A 2 655 1170 1067 -78 207 -106 C HETATM 30 H AIB A 2 -4.292 -17.866 6.190 1.00 7.15 H HETATM 31 HB11 AIB A 2 -6.012 -14.361 6.153 1.00 8.92 H HETATM 32 HB12 AIB A 2 -4.626 -14.661 5.013 1.00 8.92 H HETATM 33 HB13 AIB A 2 -6.027 -15.821 5.067 1.00 8.92 H HETATM 34 HB21 AIB A 2 -6.395 -15.884 8.077 1.00 9.14 H HETATM 35 HB22 AIB A 2 -6.313 -17.361 7.002 1.00 9.14 H HETATM 36 HB23 AIB A 2 -5.209 -17.224 8.453 1.00 9.14 H