HEADER DE NOVO PROTEIN 16-JAN-24 8VPS TITLE UIC-12-BPE EXTENSION OF UIC-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UIC-12-BPE; 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 SYNTHETIC CONSTRUCT, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.GANATRA REVDAT 3 04-SEP-24 8VPS 1 JRNL REVDAT 2 14-AUG-24 8VPS 1 JRNL REVDAT 1 07-AUG-24 8VPS 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. 1.00 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) : 1.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 5614 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.130 REMARK 3 R VALUE (WORKING SET) : 0.128 REMARK 3 FREE R VALUE : 0.146 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1039 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 19.9200 - 1.9100 0.99 1374 140 0.1049 0.1263 REMARK 3 2 1.9100 - 1.5200 0.99 1337 160 0.1310 0.1338 REMARK 3 3 1.5200 - 1.3300 0.98 1354 150 0.1485 0.1737 REMARK 3 4 1.3300 - 1.2100 0.96 1322 151 0.1427 0.1608 REMARK 3 5 1.2000 - 1.1200 0.99 1333 144 0.1591 0.1596 REMARK 3 6 1.1200 - 1.0500 0.93 1291 134 0.1691 0.2021 REMARK 3 7 1.0500 - 1.0000 1.00 1337 160 0.2249 0.2156 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) : 0.083 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.636 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.75 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.45 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 : 0.010 131 REMARK 3 ANGLE : 1.846 187 REMARK 3 CHIRALITY : 0.058 11 REMARK 3 PLANARITY : 0.008 22 REMARK 3 DIHEDRAL : 34.592 27 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 8VPS 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_1000280701. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-NOV-23 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 : SOLEIL REMARK 200 BEAMLINE : PROXIMA 2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.729317 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5614 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.000 REMARK 200 RESOLUTION RANGE LOW (A) : 19.920 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.04 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 (%): 37.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: DMF, WATER, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 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 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 25.65400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 4.98000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 25.65400 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 4.98000 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: 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 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 206 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 207 O HOH A 208 2.07 REMARK 500 REMARK 500 REMARK: NULL DBREF 8VPS A 1 14 PDB 8VPS 8VPS 1 14 SEQRES 1 A 14 I6W AIB ALA AIB LEU AIB ALA AIB LEU AIB GLN AIB LEU SEQRES 2 A 14 I77 HET I6W A 1 30 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 AIB A 12 13 HET I77 A 14 29 HET DMF A 101 12 HETNAM I6W ETHYL 5'-FORMYL[2,2'-BIPYRIDINE]-5-CARBOXYLATE HETNAM AIB ALPHA-AMINOISOBUTYRIC ACID HETNAM I77 5'-(HYDRAZINECARBONYL)[2,2'-BIPYRIDINE]-5-CARBOXAMIDE HETNAM DMF DIMETHYLFORMAMIDE FORMUL 1 I6W C14 H12 N2 O3 FORMUL 1 AIB 6(C4 H9 N O2) FORMUL 1 I77 C12 H11 N5 O2 FORMUL 2 DMF C3 H7 N O FORMUL 3 HOH *9(H2 O) HELIX 1 AA1 AIB A 2 GLN A 11 1 10 LINK C02 I6W A 1 N AIB A 2 1555 1555 1.42 LINK C AIB A 2 N ALA A 3 1555 1555 1.33 LINK C ALA A 3 N AIB A 4 1555 1555 1.33 LINK C AIB A 4 N LEU A 5 1555 1555 1.33 LINK C LEU A 5 N AIB A 6 1555 1555 1.33 LINK C AIB A 6 N ALA A 7 1555 1555 1.33 LINK C ALA A 7 N AIB A 8 1555 1555 1.33 LINK C AIB A 8 N ALEU A 9 1555 1555 1.33 LINK C AIB A 8 N BLEU A 9 1555 1555 1.32 LINK C ALEU A 9 N AIB A 10 1555 1555 1.33 LINK C BLEU A 9 N AIB A 10 1555 1555 1.33 LINK C AIB A 10 N GLN A 11 1555 1555 1.33 LINK C GLN A 11 N AIB A 12 1555 1555 1.33 LINK C AIB A 12 N LEU A 13 1555 1555 1.33 LINK C LEU A 13 N15 I77 A 14 1555 1555 1.43 CRYST1 51.308 9.960 19.974 90.00 94.02 90.00 C 1 2 1 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 0.019490 0.000000 0.001370 0.00000 SCALE2 0.000000 0.100402 0.000000 0.00000 SCALE3 0.000000 0.000000 0.050189 0.00000 HETATM 1 C05 I6W A 1 -7.269 6.331 14.381 1.00 8.35 C ANISOU 1 C05 I6W A 1 1057 1017 1096 169 35 -29 C HETATM 2 C08 I6W A 1 -6.657 5.120 14.438 1.00 8.06 C ANISOU 2 C08 I6W A 1 1110 876 1076 182 13 -123 C HETATM 3 C09 I6W A 1 -5.949 4.783 15.736 1.00 9.19 C ANISOU 3 C09 I6W A 1 1269 908 1317 276 -69 -97 C HETATM 4 N10 I6W A 1 -5.969 5.635 16.733 1.00 12.56 N ANISOU 4 N10 I6W A 1 1554 1522 1696 374 -396 -76 N HETATM 5 C02 I6W A 1 -8.728 6.014 10.890 1.00 7.90 C ANISOU 5 C02 I6W A 1 1133 871 996 -171 101 -61 C HETATM 6 C03 I6W A 1 -7.976 5.766 12.184 1.00 7.86 C ANISOU 6 C03 I6W A 1 1042 882 1063 -118 201 31 C HETATM 7 C04 I6W A 1 -7.963 6.672 13.219 1.00 8.26 C ANISOU 7 C04 I6W A 1 1034 995 1109 -47 56 -29 C HETATM 8 C06 I6W A 1 -7.330 4.559 12.290 1.00 8.09 C ANISOU 8 C06 I6W A 1 1061 765 1246 117 130 -106 C HETATM 9 C11 I6W A 1 -5.414 5.382 17.900 1.00 12.84 C ANISOU 9 C11 I6W A 1 1622 1668 1589 277 -325 -189 C HETATM 10 C12 I6W A 1 -4.828 4.163 18.096 1.00 11.35 C ANISOU 10 C12 I6W A 1 1573 1232 1508 294 -183 -41 C HETATM 11 C13 I6W A 1 -4.196 3.836 19.459 1.00 13.05 C ANISOU 11 C13 I6W A 1 1712 1611 1636 380 -227 -2 C HETATM 12 C15 I6W A 1 -3.419 2.262 21.011 1.00 18.85 C ANISOU 12 C15 I6W A 1 1842 3193 2125 710 -88 575 C HETATM 13 C16 I6W A 1 -3.015 0.777 21.119 1.00 21.42 C ANISOU 13 C16 I6W A 1 1924 3731 2485 774 78 372 C HETATM 14 C18 I6W A 1 -4.819 3.233 17.093 1.00 10.27 C ANISOU 14 C18 I6W A 1 1375 1028 1499 321 -61 174 C HETATM 15 C19 I6W A 1 -5.404 3.550 15.878 1.00 9.86 C ANISOU 15 C19 I6W A 1 1281 1096 1368 193 -139 -131 C HETATM 16 N07 I6W A 1 -6.683 4.261 13.414 1.00 9.69 N ANISOU 16 N07 I6W A 1 1148 1058 1476 255 35 80 N HETATM 17 O01 I6W A 1 -8.518 5.344 9.905 1.00 9.00 O ANISOU 17 O01 I6W A 1 1172 1188 1059 -117 154 -30 O HETATM 18 O14 I6W A 1 -3.922 2.485 19.682 1.00 15.24 O ANISOU 18 O14 I6W A 1 1794 2229 1767 414 -152 430 O HETATM 19 O17 I6W A 1 -4.012 4.656 20.277 1.00 14.79 O ANISOU 19 O17 I6W A 1 1794 2090 1734 311 -402 -305 O HETATM 20 H051 I6W A 1 -7.220 7.007 15.206 1.00 10.02 H HETATM 21 H041 I6W A 1 -8.494 7.655 13.131 1.00 9.91 H HETATM 22 H061 I6W A 1 -7.348 3.855 11.463 1.00 9.70 H HETATM 23 H111 I6W A 1 -5.423 6.112 18.675 1.00 15.41 H HETATM 24 H152 I6W A 1 -4.189 2.487 21.739 1.00 22.62 H HETATM 25 H151 I6W A 1 -2.555 2.892 21.188 1.00 22.62 H HETATM 26 H162 I6W A 1 -1.930 0.676 20.927 1.00 25.71 H HETATM 27 H163 I6W A 1 -3.578 0.187 20.372 1.00 25.71 H HETATM 28 H161 I6W A 1 -3.246 0.405 22.134 1.00 25.71 H HETATM 29 H181 I6W A 1 -4.358 2.257 17.247 1.00 12.32 H HETATM 30 H191 I6W A 1 -5.425 2.830 15.062 1.00 11.83 H HETATM 31 N AIB A 2 -9.734 7.017 10.900 1.00 8.05 N ANISOU 31 N AIB A 2 1203 932 922 -143 42 30 N HETATM 32 CA AIB A 2 -10.549 7.231 9.726 1.00 8.54 C ANISOU 32 CA AIB A 2 1201 1037 1006 -31 56 131 C HETATM 33 C AIB A 2 -9.739 7.365 8.439 1.00 9.21 C ANISOU 33 C AIB A 2 1243 1253 1004 -347 60 85 C HETATM 34 O AIB A 2 -10.058 6.832 7.378 1.00 9.63 O ANISOU 34 O AIB A 2 1305 1337 1018 -256 -17 38 O HETATM 35 CB1 AIB A 2 -11.553 6.088 9.573 1.00 8.39 C ANISOU 35 CB1 AIB A 2 1126 1046 1016 -51 147 -30 C HETATM 36 CB2 AIB A 2 -11.320 8.539 9.897 1.00 8.98 C ANISOU 36 CB2 AIB A 2 1218 1009 1185 -130 -148 64 C HETATM 37 H AIB A 2 -10.054 7.593 11.654 1.00 9.66 H HETATM 38 HB11 AIB A 2 -12.301 6.129 10.401 1.00 10.07 H HETATM 39 HB12 AIB A 2 -11.018 5.109 9.610 1.00 10.07 H HETATM 40 HB13 AIB A 2 -12.083 6.180 8.595 1.00 10.07 H HETATM 41 HB21 AIB A 2 -12.013 8.443 10.768 1.00 10.78 H HETATM 42 HB22 AIB A 2 -11.905 8.742 8.967 1.00 10.78 H HETATM 43 HB23 AIB A 2 -10.594 9.368 10.079 1.00 10.78 H