HEADER DE NOVO PROTEIN 24-JAN-24 8VSF TITLE UIC-13-BPE EXTENSION OF UIC-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UIC-13-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 8VSF 1 JRNL REVDAT 2 14-AUG-24 8VSF 1 JRNL REVDAT 1 07-AUG-24 8VSF 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. 1.11 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) : 1.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 7064 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.241 REMARK 3 R VALUE (WORKING SET) : 0.240 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.160 REMARK 3 FREE R VALUE TEST SET COUNT : 1257 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 16.6900 - 2.3100 1.00 1245 138 0.2005 0.2045 REMARK 3 2 2.3000 - 1.8300 1.00 1227 136 0.2267 0.2449 REMARK 3 3 1.8300 - 1.6000 1.00 1260 144 0.2568 0.2589 REMARK 3 4 1.6000 - 1.4500 0.99 1236 148 0.2887 0.2759 REMARK 3 5 1.4500 - 1.3500 0.99 1244 137 0.2961 0.3786 REMARK 3 6 1.3500 - 1.2700 0.99 1195 131 0.3324 0.3628 REMARK 3 7 1.2700 - 1.2100 0.99 1258 143 0.3417 0.3549 REMARK 3 8 1.2100 - 1.1500 1.00 1235 142 0.4062 0.4059 REMARK 3 9 1.1500 - 1.1100 0.99 1221 138 0.4461 0.4405 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) : 0.175 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 44.070 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.07 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.42 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 : 0.014 125 REMARK 3 ANGLE : 1.906 177 REMARK 3 CHIRALITY : 0.049 10 REMARK 3 PLANARITY : 0.015 20 REMARK 3 DIHEDRAL : 28.786 34 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 8VSF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1000281150. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-APR-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) : 0.619920 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 : 7064 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.110 REMARK 200 RESOLUTION RANGE LOW (A) : 16.690 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 24.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.5400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.11 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.15 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 (%): 58.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.99 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 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 4.48550 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 30.08150 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 30.08150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 6.72825 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 30.08150 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 30.08150 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 2.24275 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 30.08150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.08150 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 6.72825 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 30.08150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 30.08150 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 2.24275 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 4.48550 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 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 201 O HOH A 204 2.04 REMARK 500 REMARK 500 REMARK: NULL DBREF 8VSF A 1 15 PDB 8VSF 8VSF 1 15 SEQRES 1 A 15 I6W ALA AIB ALA AIB LEU AIB ALA AIB LEU AIB GLN AIB SEQRES 2 A 15 LEU I77 HET I6W A 1 30 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 AIB A 13 13 HET I77 A 15 29 HET CCN A 101 6 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 CCN ACETONITRILE FORMUL 1 I6W C14 H12 N2 O3 FORMUL 1 AIB 6(C4 H9 N O2) FORMUL 1 I77 C12 H11 N5 O2 FORMUL 2 CCN C2 H3 N FORMUL 3 HOH *7(H2 O) HELIX 1 AA1 ALA A 2 LEU A 14 1 13 LINK C02 I6W A 1 N ALA A 2 1555 1555 1.34 LINK C ALA A 2 N AIB A 3 1555 1555 1.34 LINK C AIB A 3 N ALA A 4 1555 1555 1.32 LINK C ALA A 4 N AIB A 5 1555 1555 1.33 LINK C AIB A 5 N LEU A 6 1555 1555 1.32 LINK C LEU A 6 N AIB A 7 1555 1555 1.34 LINK C AIB A 7 N ALA A 8 1555 1555 1.33 LINK C ALA A 8 N AIB A 9 1555 1555 1.32 LINK C AIB A 9 N LEU A 10 1555 1555 1.33 LINK C LEU A 10 N AIB A 11 1555 1555 1.33 LINK C AIB A 11 N GLN A 12 1555 1555 1.33 LINK C GLN A 12 N AIB A 13 1555 1555 1.33 LINK C AIB A 13 N LEU A 14 1555 1555 1.34 LINK C LEU A 14 N15 I77 A 15 1555 1555 1.43 CRYST1 60.163 60.163 8.971 90.00 90.00 90.00 P 43 21 2 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 0.016622 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016622 0.000000 0.00000 SCALE3 0.000000 0.000000 0.111470 0.00000 HETATM 1 C05 I6W A 1 3.977 -8.899 -1.246 1.00 46.98 C ANISOU 1 C05 I6W A 1 3922 3732 10195 -693 -871 -673 C HETATM 2 C08 I6W A 1 5.143 -9.122 -0.583 1.00 50.84 C ANISOU 2 C08 I6W A 1 3986 3880 11449 -520 -1393 478 C HETATM 3 C09 I6W A 1 5.973 -7.914 -0.212 1.00 57.52 C ANISOU 3 C09 I6W A 1 4438 4149 13267 -270 -2332 -908 C HETATM 4 N10 I6W A 1 5.476 -6.729 -0.450 1.00 59.42 N ANISOU 4 N10 I6W A 1 4629 4453 13495 -394 -2022 -1479 N HETATM 5 C02 I6W A 1 2.951 -12.377 -2.052 1.00 30.20 C ANISOU 5 C02 I6W A 1 3573 3942 3959 -479 -215 227 C HETATM 6 C03 I6W A 1 3.716 -11.245 -1.406 1.00 27.23 C ANISOU 6 C03 I6W A 1 3747 3624 2976 -823 346 878 C HETATM 7 C04 I6W A 1 3.208 -9.990 -1.664 1.00 38.28 C ANISOU 7 C04 I6W A 1 3738 3704 7103 -908 -1065 -744 C HETATM 8 C06 I6W A 1 4.921 -11.413 -0.764 1.00 26.36 C ANISOU 8 C06 I6W A 1 3731 3520 2764 -673 -784 714 C HETATM 9 C11 I6W A 1 6.154 -5.630 -0.220 1.00 59.42 C ANISOU 9 C11 I6W A 1 4692 4448 13436 -432 -2127 -1370 C HETATM 10 C12 I6W A 1 7.443 -5.709 0.268 1.00 58.24 C ANISOU 10 C12 I6W A 1 4739 4554 12837 -468 -2842 -704 C HETATM 11 C13 I6W A 1 8.239 -4.403 0.523 1.00 54.77 C ANISOU 11 C13 I6W A 1 4749 4770 11291 -1011 -2435 -902 C HETATM 12 C15 I6W A 1 8.692 -2.723 2.062 1.00 56.75 C ANISOU 12 C15 I6W A 1 5314 4922 11325 -872 -1088 935 C HETATM 13 C16 I6W A 1 8.145 -1.457 2.770 1.00 53.01 C ANISOU 13 C16 I6W A 1 5388 4912 9843 -567 -965 2199 C HETATM 14 C18 I6W A 1 8.024 -6.930 0.495 1.00 59.32 C ANISOU 14 C18 I6W A 1 4741 4504 13295 -229 -2441 -1622 C HETATM 15 C19 I6W A 1 7.263 -8.067 0.234 1.00 58.96 C ANISOU 15 C19 I6W A 1 4520 4293 13591 -105 -2139 -1656 C HETATM 16 N07 I6W A 1 5.609 -10.352 -0.390 1.00 33.58 N ANISOU 16 N07 I6W A 1 3850 3794 5115 -324 -1187 1462 N HETATM 17 O01 I6W A 1 1.680 -12.448 -2.076 1.00 24.83 O ANISOU 17 O01 I6W A 1 3978 4080 1378 -207 -290 38 O HETATM 18 O14 I6W A 1 7.676 -3.320 1.245 1.00 51.77 O ANISOU 18 O14 I6W A 1 4996 4846 9830 -983 -2162 -970 O HETATM 19 O17 I6W A 1 9.325 -4.326 0.088 1.00 53.28 O ANISOU 19 O17 I6W A 1 4810 4993 10440 -1185 -1626 -188 O HETATM 20 H051 I6W A 1 3.652 -7.901 -1.446 1.00 56.58 H HETATM 21 H041 I6W A 1 2.225 -9.851 -2.183 1.00 46.14 H HETATM 22 H061 I6W A 1 5.302 -12.411 -0.566 1.00 31.83 H HETATM 23 H111 I6W A 1 5.711 -4.680 -0.408 1.00 71.50 H HETATM 24 H152 I6W A 1 9.533 -2.447 1.439 1.00 68.30 H HETATM 25 H151 I6W A 1 9.013 -3.438 2.810 1.00 68.30 H HETATM 26 H162 I6W A 1 8.941 -1.011 3.395 1.00 63.82 H HETATM 27 H163 I6W A 1 7.286 -1.735 3.409 1.00 63.82 H HETATM 28 H161 I6W A 1 7.817 -0.723 2.010 1.00 63.82 H HETATM 29 H181 I6W A 1 9.046 -7.009 0.866 1.00 71.39 H HETATM 30 H191 I6W A 1 7.683 -9.060 0.382 1.00 70.96 H