HEADER DE NOVO PROTEIN 16-JAN-24 8VPD TITLE UIC-11-BIF EXTENSION OF UIC-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UIC-11-BIF; 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 8VPD 1 JRNL REVDAT 2 14-AUG-24 8VPD 1 JRNL REVDAT 1 07-AUG-24 8VPD 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. 1.20 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.430 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 3163 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.820 REMARK 3 FREE R VALUE TEST SET COUNT : 559 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 14.5300 - 1.9100 0.98 1319 146 0.1558 0.1887 REMARK 3 2 1.9000 - 1.5100 0.97 1283 139 0.2354 0.2278 REMARK 3 3 1.5100 - 1.3200 0.98 1336 142 0.2791 0.2837 REMARK 3 4 1.3200 - 1.2000 0.88 1197 132 0.3523 0.4123 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) : 0.167 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.074 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.21 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.32 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 : 0.010 118 REMARK 3 ANGLE : 1.815 167 REMARK 3 CHIRALITY : 0.045 11 REMARK 3 PLANARITY : 0.008 19 REMARK 3 DIHEDRAL : 30.803 22 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 8VPD 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_1000280608. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-SEP-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) : 0.688839 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 : 3163 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 14.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.2600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.24 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 (%): 36.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 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: 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 19.24250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 4.39700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 19.24250 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 4.39700 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 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 209 DISTANCE = 7.43 ANGSTROMS REMARK 525 HOH A 210 DISTANCE = 9.66 ANGSTROMS DBREF 8VPD A 1 13 PDB 8VPD 8VPD 1 13 SEQRES 1 A 13 Z7Z ALA AIB LEU AIB ALA AIB LEU AIB GLN AIB LEU I77 HET Z7Z A 1 23 HET AIB A 3 13 HET AIB A 5 13 HET AIB A 7 13 HET AIB A 9 13 HET AIB A 11 13 HET I77 A 13 29 HET CCN A 101 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 C13 H10 O2 FORMUL 1 AIB 5(C4 H9 N O2) FORMUL 1 I77 C12 H11 N5 O2 FORMUL 2 CCN C2 H3 N FORMUL 3 HOH *10(H2 O) HELIX 1 AA1 ALA A 2 LEU A 12 1 11 LINK C1 Z7Z A 1 N ALA A 2 1555 1555 1.42 LINK C ALA A 2 N AIB A 3 1555 1555 1.33 LINK C AIB A 3 N ALEU A 4 1555 1555 1.33 LINK C AIB A 3 N BLEU A 4 1555 1555 1.33 LINK C ALEU A 4 N AIB A 5 1555 1555 1.33 LINK C BLEU A 4 N AIB A 5 1555 1555 1.33 LINK C AIB A 5 N ALA A 6 1555 1555 1.32 LINK C ALA A 6 N AIB A 7 1555 1555 1.33 LINK C AIB A 7 N LEU A 8 1555 1555 1.32 LINK C LEU A 8 N AIB A 9 1555 1555 1.33 LINK C AIB A 9 N GLN A 10 1555 1555 1.32 LINK C GLN A 10 N AIB A 11 1555 1555 1.33 LINK C AIB A 11 N LEU A 12 1555 1555 1.33 LINK C LEU A 12 N15 I77 A 13 1555 1555 1.42 CRYST1 38.485 8.794 31.786 90.00 113.90 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 0.025984 0.000000 0.011515 0.00000 SCALE2 0.000000 0.113714 0.000000 0.00000 SCALE3 0.000000 0.000000 0.034411 0.00000 HETATM 1 O1 Z7Z A 1 11.112 -2.923 3.935 1.00 11.02 O ANISOU 1 O1 Z7Z A 1 765 862 2561 -20 392 -199 O HETATM 2 C1 Z7Z A 1 12.290 -3.315 4.054 1.00 10.43 C ANISOU 2 C1 Z7Z A 1 794 714 2455 -30 319 -334 C HETATM 3 C2 Z7Z A 1 13.196 -3.239 2.852 1.00 10.32 C ANISOU 3 C2 Z7Z A 1 791 661 2468 7 288 -178 C HETATM 4 C3 Z7Z A 1 12.846 -2.481 1.754 1.00 11.68 C ANISOU 4 C3 Z7Z A 1 819 1084 2533 23 262 -115 C HETATM 5 C4 Z7Z A 1 13.671 -2.427 0.653 1.00 11.96 C ANISOU 5 C4 Z7Z A 1 793 1243 2510 34 277 -61 C HETATM 6 C5 Z7Z A 1 14.379 -3.941 2.858 1.00 10.55 C ANISOU 6 C5 Z7Z A 1 800 769 2439 91 232 -174 C HETATM 7 C6 Z7Z A 1 15.198 -3.885 1.756 1.00 10.84 C ANISOU 7 C6 Z7Z A 1 786 962 2370 154 234 -134 C HETATM 8 C7 Z7Z A 1 14.845 -3.129 0.656 1.00 11.13 C ANISOU 8 C7 Z7Z A 1 805 993 2429 97 231 -98 C HETATM 9 C8 Z7Z A 1 15.754 -3.051 -0.550 1.00 10.17 C ANISOU 9 C8 Z7Z A 1 827 725 2311 36 272 -75 C HETATM 10 C9 Z7Z A 1 17.127 -3.052 -0.374 1.00 9.99 C ANISOU 10 C9 Z7Z A 1 833 692 2271 -55 316 -108 C HETATM 11 C10 Z7Z A 1 15.176 -2.965 -1.804 1.00 10.73 C ANISOU 11 C10 Z7Z A 1 854 972 2252 -102 279 -172 C HETATM 12 C11 Z7Z A 1 17.950 -2.961 -1.481 1.00 10.48 C ANISOU 12 C11 Z7Z A 1 844 901 2237 -121 338 -298 C HETATM 13 C12 Z7Z A 1 16.022 -2.868 -2.902 1.00 10.59 C ANISOU 13 C12 Z7Z A 1 870 929 2223 -151 284 -213 C HETATM 14 C13 Z7Z A 1 17.398 -2.891 -2.741 1.00 9.90 C ANISOU 14 C13 Z7Z A 1 858 656 2248 -75 302 -234 C HETATM 15 H31 Z7Z A 1 11.916 -1.926 1.757 1.00 14.03 H HETATM 16 H41 Z7Z A 1 13.393 -1.833 -0.209 1.00 14.38 H HETATM 17 H51 Z7Z A 1 14.661 -4.532 3.720 1.00 12.68 H HETATM 18 H61 Z7Z A 1 16.128 -4.439 1.751 1.00 13.02 H HETATM 19 H91 Z7Z A 1 17.551 -3.122 0.619 1.00 12.01 H HETATM 20 H101 Z7Z A 1 14.100 -2.973 -1.926 1.00 12.90 H HETATM 21 H111 Z7Z A 1 19.026 -2.945 -1.358 1.00 12.59 H HETATM 22 H121 Z7Z A 1 15.600 -2.773 -3.895 1.00 12.72 H HETATM 23 H131 Z7Z A 1 18.043 -2.855 -3.610 1.00 11.90 H