HEADER DE NOVO PROTEIN 17-JAN-24 8VPX TITLE UIC-10-BPE EXTENSION OF UIC-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UIC-10-BPE; 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 8VPX 1 JRNL REVDAT 2 14-AUG-24 8VPX 1 JRNL REVDAT 1 07-AUG-24 8VPX 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. 1.45 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.22 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.140 REMARK 3 COMPLETENESS FOR RANGE (%) : 78.3 REMARK 3 NUMBER OF REFLECTIONS : 2572 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) : 0.123 REMARK 3 FREE R VALUE : 0.181 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 505 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 17.2200 - 2.3000 0.85 1237 139 0.1174 0.1504 REMARK 3 2 2.3000 - 1.8300 0.74 1064 119 0.1398 0.2264 REMARK 3 3 1.8300 - 1.6000 0.87 1243 138 0.1103 0.2244 REMARK 3 4 1.6000 - 1.4510 0.67 950 109 0.1511 0.2333 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) : 0.000 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.032 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.98 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 : 0.009 214 REMARK 3 ANGLE : 1.641 304 REMARK 3 CHIRALITY : 0.061 16 REMARK 3 PLANARITY : 0.005 34 REMARK 3 DIHEDRAL : 39.161 42 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 8VPX 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_1000280537. 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 : 2572 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.451 REMARK 200 RESOLUTION RANGE LOW (A) : 17.220 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 80.2 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.5600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 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 (%): 40.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: METHANOL, ACETONITRILE, WATER, SLOW REMARK 280 COOLING, 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 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 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 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 102 O HOH A 103 1.91 REMARK 500 REMARK 500 REMARK: NULL DBREF 8VPX A 1 12 PDB 8VPX 8VPX 1 12 DBREF 8VPX B 1 12 PDB 8VPX 8VPX 1 12 SEQRES 1 A 12 I6W AIB LEU AIB ALA AIB LEU AIB GLN AIB LEU I77 SEQRES 1 B 12 I6W AIB LEU AIB ALA AIB LEU AIB GLN AIB LEU 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 I77 A 12 29 HET I6W B 1 30 HET AIB B 2 13 HET AIB B 4 13 HET AIB B 6 13 HET AIB B 8 13 HET AIB B 10 13 HET I77 B 12 29 HETNAM I6W ETHYL 5'-FORMYL[2,2'-BIPYRIDINE]-5-CARBOXYLATE HETNAM AIB ALPHA-AMINOISOBUTYRIC ACID HETNAM I77 5'-(HYDRAZINECARBONYL)[2,2'-BIPYRIDINE]-5-CARBOXAMIDE FORMUL 1 I6W 2(C14 H12 N2 O3) FORMUL 1 AIB 10(C4 H9 N O2) FORMUL 1 I77 2(C12 H11 N5 O2) FORMUL 3 HOH *9(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 C02 I6W 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 1.33 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 1.33 LINK C GLN A 9 N AIB A 10 1555 1555 1.32 LINK C AIB A 10 N LEU A 11 1555 1555 1.32 LINK C LEU A 11 N15 I77 A 12 1555 1555 1.43 LINK C02 I6W B 1 N AIB B 2 1555 1555 1.43 LINK C AIB B 2 N LEU B 3 1555 1555 1.33 LINK C LEU 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 1.32 LINK C AIB B 6 N LEU B 7 1555 1555 1.33 LINK C LEU B 7 N AIB B 8 1555 1555 1.33 LINK C AIB B 8 N GLN B 9 1555 1555 1.33 LINK C GLN B 9 N AIB B 10 1555 1555 1.33 LINK C AIB B 10 N LEU B 11 1555 1555 1.34 LINK C LEU B 11 N15 I77 B 12 1555 1555 1.42 CRYST1 10.305 17.610 26.616 99.46 99.72 95.85 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 0.097040 0.009943 0.018788 0.00000 SCALE2 0.000000 0.057083 0.010756 0.00000 SCALE3 0.000000 0.000000 0.038789 0.00000 HETATM 1 C05 I6W A 1 3.108 12.416 3.544 1.00 9.04 C ANISOU 1 C05 I6W A 1 945 990 1497 -331 188 -559 C HETATM 2 C08 I6W A 1 3.012 13.758 3.649 1.00 10.35 C ANISOU 2 C08 I6W A 1 1030 1408 1493 -364 249 -381 C HETATM 3 C09 I6W A 1 2.924 14.513 2.342 1.00 12.43 C ANISOU 3 C09 I6W A 1 1744 1481 1499 -570 245 -451 C HETATM 4 N10 I6W A 1 3.030 13.852 1.208 1.00 13.93 N ANISOU 4 N10 I6W A 1 1978 1647 1669 -341 335 -373 N HETATM 5 C02 I6W A 1 3.291 11.463 7.160 1.00 11.19 C ANISOU 5 C02 I6W A 1 1792 809 1650 -497 519 -174 C HETATM 6 C03 I6W A 1 3.170 12.321 5.911 1.00 10.50 C ANISOU 6 C03 I6W A 1 1453 909 1626 -534 513 -342 C HETATM 7 C04 I6W A 1 3.215 11.661 4.705 1.00 9.26 C ANISOU 7 C04 I6W A 1 1120 953 1446 -181 473 -578 C HETATM 8 C06 I6W A 1 3.073 13.699 5.976 1.00 10.22 C ANISOU 8 C06 I6W A 1 1082 1259 1541 -545 404 -285 C HETATM 9 C11 I6W A 1 2.960 14.472 0.040 1.00 16.69 C ANISOU 9 C11 I6W A 1 3078 1557 1708 -258 404 -300 C HETATM 10 C12 I6W A 1 2.788 15.850 0.001 1.00 21.81 C ANISOU 10 C12 I6W A 1 4747 1774 1767 -125 415 -131 C HETATM 11 C13 I6W A 1 2.706 16.649 -1.335 1.00 30.03 C ANISOU 11 C13 I6W A 1 7202 2237 1971 261 619 130 C HETATM 12 C15 I6W A 1 2.631 18.817 -2.381 1.00 37.89 C ANISOU 12 C15 I6W A 1 8866 3036 2496 265 454 452 C HETATM 13 C16 I6W A 1 2.362 20.308 -2.032 1.00 39.55 C ANISOU 13 C16 I6W A 1 9078 3390 2557 208 412 542 C HETATM 14 C18 I6W A 1 2.681 16.561 1.173 1.00 19.32 C ANISOU 14 C18 I6W A 1 3955 1603 1782 -582 336 -337 C HETATM 15 C19 I6W A 1 2.759 15.877 2.378 1.00 14.55 C ANISOU 15 C19 I6W A 1 2524 1376 1627 -917 133 -390 C HETATM 16 N07 I6W A 1 2.996 14.377 4.836 1.00 11.83 N ANISOU 16 N07 I6W A 1 1413 1496 1588 -514 124 -241 N HETATM 17 O01 I6W A 1 3.034 10.287 7.131 1.00 13.04 O ANISOU 17 O01 I6W A 1 2131 1034 1789 -728 374 -182 O HETATM 18 O14 I6W A 1 2.506 18.050 -1.175 1.00 35.09 O ANISOU 18 O14 I6W A 1 8348 2684 2300 464 516 322 O HETATM 19 O17 I6W A 1 2.812 16.136 -2.391 1.00 31.12 O ANISOU 19 O17 I6W A 1 7465 2200 2160 354 842 -134 O HETATM 20 H051 I6W A 1 3.103 11.944 2.586 1.00 11.35 H HETATM 21 H041 I6W A 1 3.335 10.548 4.661 1.00 11.63 H HETATM 22 H061 I6W A 1 3.062 14.213 6.933 1.00 12.77 H HETATM 23 H111 I6W A 1 3.036 13.917 -0.866 1.00 20.54 H HETATM 24 H152 I6W A 1 1.907 18.475 -3.110 1.00 45.98 H HETATM 25 H151 I6W A 1 3.631 18.709 -2.782 1.00 45.98 H HETATM 26 H162 I6W A 1 1.451 20.382 -1.409 1.00 47.97 H HETATM 27 H163 I6W A 1 2.219 20.885 -2.964 1.00 47.97 H HETATM 28 H161 I6W A 1 3.225 20.717 -1.474 1.00 47.97 H HETATM 29 H181 I6W A 1 2.539 17.641 1.157 1.00 23.70 H HETATM 30 H191 I6W A 1 2.691 16.406 3.326 1.00 17.97 H HETATM 31 N AIB A 2 3.866 12.066 8.315 1.00 11.92 N ANISOU 31 N AIB A 2 2032 747 1749 -371 489 71 N HETATM 32 CA AIB A 2 4.239 11.245 9.448 1.00 14.49 C ANISOU 32 CA AIB A 2 2496 970 2039 -473 607 169 C HETATM 33 C AIB A 2 3.138 10.274 9.914 1.00 15.71 C ANISOU 33 C AIB A 2 2770 1033 2166 -433 624 232 C HETATM 34 O AIB A 2 3.293 9.047 10.002 1.00 15.81 O ANISOU 34 O AIB A 2 2869 1016 2122 -434 590 188 O HETATM 35 CB1 AIB A 2 5.494 10.423 9.118 1.00 15.32 C ANISOU 35 CB1 AIB A 2 2372 1114 2337 -764 201 273 C HETATM 36 CB2 AIB A 2 4.567 12.157 10.639 1.00 15.37 C ANISOU 36 CB2 AIB A 2 2779 1157 1905 -535 617 287 C HETATM 37 H AIB A 2 2.939 12.424 8.436 1.00 14.81 H HETATM 38 HB11 AIB A 2 5.767 9.785 9.993 1.00 18.90 H HETATM 39 HB12 AIB A 2 5.294 9.769 8.236 1.00 18.90 H HETATM 40 HB13 AIB A 2 6.342 11.108 8.884 1.00 18.90 H HETATM 41 HB21 AIB A 2 5.107 11.563 11.415 1.00 18.96 H HETATM 42 HB22 AIB A 2 5.212 12.998 10.287 1.00 18.96 H HETATM 43 HB23 AIB A 2 3.615 12.560 11.063 1.00 18.96 H