HEADER DE NOVO PROTEIN 15-JAN-24 8VOG TITLE UIC-12-BIF EXTENSION OF UIC-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UIC-12-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 8VOG 1 JRNL REVDAT 2 14-AUG-24 8VOG 1 JRNL REVDAT 1 07-AUG-24 8VOG 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. 0.94 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) : 0.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.090 REMARK 3 COMPLETENESS FOR RANGE (%) : 83.9 REMARK 3 NUMBER OF REFLECTIONS : 11219 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.080 REMARK 3 R VALUE (WORKING SET) : 0.079 REMARK 3 FREE R VALUE : 0.090 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.880 REMARK 3 FREE R VALUE TEST SET COUNT : 2074 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 15.6800 - 2.3200 0.83 1250 132 0.0895 0.0979 REMARK 3 2 2.3200 - 1.8400 0.76 1131 127 0.0859 0.0956 REMARK 3 3 1.8400 - 1.6100 0.82 1255 129 0.0835 0.1061 REMARK 3 4 1.6100 - 1.4600 0.87 1270 140 0.0791 0.0761 REMARK 3 5 1.4600 - 1.3600 0.86 1333 156 0.0772 0.0768 REMARK 3 6 1.3600 - 1.2800 0.91 1343 145 0.0745 0.0781 REMARK 3 7 1.2800 - 1.2100 0.71 1091 121 0.0737 0.0927 REMARK 3 8 1.2100 - 1.1600 0.82 1235 134 0.0661 0.0764 REMARK 3 9 1.1600 - 1.1100 0.83 1203 144 0.0650 0.0899 REMARK 3 10 1.1100 - 1.0800 0.82 1279 121 0.0669 0.0837 REMARK 3 11 1.0800 - 1.0400 0.87 1268 152 0.0718 0.0767 REMARK 3 12 1.0400 - 1.0100 0.90 1405 139 0.0719 0.0924 REMARK 3 13 1.0100 - 0.9900 0.82 1188 135 0.0769 0.1025 REMARK 3 14 0.9900 - 0.9600 0.89 1372 158 0.0711 0.0866 REMARK 3 15 0.9600 - 0.9400 0.90 1297 141 0.0802 0.0904 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) : 0.046 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 7.156 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 4.65 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 7.60 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 : 0.008 274 REMARK 3 ANGLE : 1.801 385 REMARK 3 CHIRALITY : 0.038 20 REMARK 3 PLANARITY : 0.007 46 REMARK 3 DIHEDRAL : 30.887 74 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 8VOG 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_1000280626. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-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 : 11219 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.940 REMARK 200 RESOLUTION RANGE LOW (A) : 15.680 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.6 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.9300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.94 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.97 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 (%): 32.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83 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 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 C LEU A 13 H1 I77 A 14 1.51 REMARK 500 REMARK 500 REMARK: NULL DBREF 8VOG A 1 14 PDB 8VOG 8VOG 1 14 DBREF 8VOG B 1 14 PDB 8VOG 8VOG 1 14 SEQRES 1 A 14 Z7Z AIB ALA AIB LEU AIB ALA AIB LEU AIB GLN AIB LEU SEQRES 2 A 14 I77 SEQRES 1 B 14 Z7Z AIB ALA AIB LEU AIB ALA AIB LEU AIB GLN AIB LEU SEQRES 2 B 14 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 AIB A 12 13 HET I77 A 14 58 HET Z7Z B 1 23 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 AIB B 12 13 HET I77 B 14 29 HET CCN A 101 6 HET CCN A 102 6 HET CCN B 101 6 HET CCN B 102 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 12(C4 H9 N O2) FORMUL 1 I77 2(C12 H11 N5 O2) FORMUL 3 CCN 4(C2 H3 N) FORMUL 7 HOH *19(H2 O) HELIX 1 AA1 AIB A 2 LEU A 13 1 12 HELIX 2 AA2 ALA B 3 LEU B 13 1 11 LINK C1 Z7Z A 1 N AIB A 2 1555 1555 1.42 LINK C AIB A 2 N ALA A 3 1555 1555 1.34 LINK C ALA A 3 N AIB A 4 1555 1555 1.33 LINK C AIB A 4 N LEU A 5 1555 1555 1.34 LINK C LEU A 5 N AIB A 6 1555 1555 1.33 LINK C AIB A 6 N ALA A 7 1555 1555 1.34 LINK C ALA A 7 N AIB A 8 1555 1555 1.33 LINK C AIB A 8 N LEU A 9 1555 1555 1.34 LINK C LEU A 9 N AIB A 10 1555 1555 1.33 LINK C AIB A 10 N AGLN A 11 1555 1555 1.33 LINK C AIB A 10 N BGLN A 11 1555 1555 1.33 LINK C AGLN A 11 N AIB A 12 1555 1555 1.33 LINK C BGLN 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 N15AI77 A 14 1555 1555 1.43 LINK C LEU A 13 N15BI77 A 14 1555 1555 1.43 LINK C1 Z7Z B 1 N AIB B 2 1555 1555 1.41 LINK C AIB B 2 N ALA B 3 1555 1555 1.34 LINK C ALA B 3 N AIB B 4 1555 1555 1.33 LINK C AIB B 4 N LEU B 5 1555 1555 1.34 LINK C LEU B 5 N AIB B 6 1555 1555 1.34 LINK C AIB B 6 N ALA B 7 1555 1555 1.34 LINK C ALA B 7 N AIB B 8 1555 1555 1.34 LINK C AIB B 8 N LEU B 9 1555 1555 1.33 LINK C LEU B 9 N AIB B 10 1555 1555 1.33 LINK C AIB B 10 N AGLN B 11 1555 1555 1.34 LINK C AIB B 10 N BGLN B 11 1555 1555 1.33 LINK C AGLN B 11 N AIB B 12 1555 1555 1.33 LINK C BGLN B 11 N AIB B 12 1555 1555 1.33 LINK C AIB B 12 N LEU B 13 1555 1555 1.33 LINK C LEU B 13 N15 I77 B 14 1555 1555 1.43 CRYST1 10.240 15.760 31.197 95.87 97.00 90.09 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 0.097656 0.000153 0.012071 0.00000 SCALE2 0.000000 0.063452 0.006585 0.00000 SCALE3 0.000000 0.000000 0.032469 0.00000 HETATM 1 O1 Z7Z A 1 -5.425 8.421 14.781 1.00 3.43 O ANISOU 1 O1 Z7Z A 1 585 287 433 -103 -2 -33 O HETATM 2 C1 Z7Z A 1 -5.398 8.347 16.010 1.00 3.19 C ANISOU 2 C1 Z7Z A 1 541 204 467 -120 -32 -60 C HETATM 3 C2 Z7Z A 1 -6.606 8.649 16.846 1.00 3.38 C ANISOU 3 C2 Z7Z A 1 565 228 491 -162 -29 -31 C HETATM 4 C3 Z7Z A 1 -7.601 9.395 16.252 1.00 3.82 C ANISOU 4 C3 Z7Z A 1 610 341 500 -194 -17 -51 C HETATM 5 C4 Z7Z A 1 -8.738 9.727 16.961 1.00 3.77 C ANISOU 5 C4 Z7Z A 1 567 370 496 -127 -45 -24 C HETATM 6 C5 Z7Z A 1 -6.746 8.207 18.142 1.00 4.11 C ANISOU 6 C5 Z7Z A 1 736 273 554 -68 63 46 C HETATM 7 C6 Z7Z A 1 -7.894 8.531 18.854 1.00 4.18 C ANISOU 7 C6 Z7Z A 1 704 306 577 -77 90 59 C HETATM 8 C7 Z7Z A 1 -8.885 9.307 18.265 1.00 3.83 C ANISOU 8 C7 Z7Z A 1 592 320 544 -176 -1 -36 C HETATM 9 C8 Z7Z A 1 -10.100 9.729 19.064 1.00 4.11 C ANISOU 9 C8 Z7Z A 1 569 415 579 -167 46 -14 C HETATM 10 C9 Z7Z A 1 -10.653 10.990 18.842 1.00 4.24 C ANISOU 10 C9 Z7Z A 1 566 443 602 -131 -18 26 C HETATM 11 C10 Z7Z A 1 -10.611 8.922 20.054 1.00 5.09 C ANISOU 11 C10 Z7Z A 1 674 584 677 -85 123 83 C HETATM 12 C11 Z7Z A 1 -11.738 11.422 19.584 1.00 5.05 C ANISOU 12 C11 Z7Z A 1 663 553 704 -79 65 77 C HETATM 13 C12 Z7Z A 1 -11.695 9.359 20.801 1.00 5.64 C ANISOU 13 C12 Z7Z A 1 694 699 751 -76 107 141 C HETATM 14 C13 Z7Z A 1 -12.254 10.605 20.570 1.00 5.88 C ANISOU 14 C13 Z7Z A 1 748 727 760 -16 143 86 C HETATM 15 H31 Z7Z A 1 -7.490 9.723 15.225 1.00 4.58 H HETATM 16 H41 Z7Z A 1 -9.515 10.319 16.492 1.00 4.52 H HETATM 17 H51 Z7Z A 1 -5.967 7.612 18.603 1.00 4.94 H HETATM 18 H61 Z7Z A 1 -8.017 8.177 19.870 1.00 5.01 H HETATM 19 H91 Z7Z A 1 -10.230 11.636 18.082 1.00 5.09 H HETATM 20 H101 Z7Z A 1 -10.171 7.952 20.249 1.00 6.11 H HETATM 21 H111 Z7Z A 1 -12.178 12.393 19.392 1.00 6.06 H HETATM 22 H121 Z7Z A 1 -12.107 8.720 21.572 1.00 6.77 H HETATM 23 H131 Z7Z A 1 -13.097 10.939 21.163 1.00 7.06 H HETATM 24 N AIB A 2 -4.196 8.058 16.698 1.00 3.59 N ANISOU 24 N AIB A 2 666 285 413 -173 -21 -32 N HETATM 25 CA AIB A 2 -2.991 7.877 15.932 1.00 3.71 C ANISOU 25 CA AIB A 2 577 397 435 -220 -35 0 C HETATM 26 C AIB A 2 -3.185 6.823 14.823 1.00 2.90 C ANISOU 26 C AIB A 2 375 324 403 -109 -58 42 C HETATM 27 O AIB A 2 -2.784 6.992 13.675 1.00 3.11 O ANISOU 27 O AIB A 2 454 345 381 -138 -28 29 O HETATM 28 CB1 AIB A 2 -2.516 9.212 15.316 1.00 4.30 C ANISOU 28 CB1 AIB A 2 712 410 510 -291 -7 -59 C HETATM 29 CB2 AIB A 2 -1.897 7.333 16.860 1.00 4.32 C ANISOU 29 CB2 AIB A 2 577 628 438 -251 -84 33 C HETATM 30 H AIB A 2 -3.973 8.298 17.644 1.00 4.31 H HETATM 31 HB11 AIB A 2 -1.640 9.029 14.649 1.00 5.15 H HETATM 32 HB12 AIB A 2 -3.343 9.667 14.719 1.00 5.15 H HETATM 33 HB13 AIB A 2 -2.219 9.917 16.128 1.00 5.15 H HETATM 34 HB21 AIB A 2 -0.955 7.199 16.274 1.00 5.19 H HETATM 35 HB22 AIB A 2 -1.727 8.062 17.689 1.00 5.19 H HETATM 36 HB23 AIB A 2 -2.227 6.352 17.278 1.00 5.19 H