HEADER DE NOVO PROTEIN 30-NOV-23 8V59 TITLE UIC-1 MUTANT - UIC-1-B5I COMPND MOL_ID: 1; COMPND 2 MOLECULE: UIC-1-B5I; 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 S.L.HEINZ-KUNERT REVDAT 2 20-MAR-24 8V59 1 JRNL REVDAT 1 06-MAR-24 8V59 0 JRNL AUTH S.L.HEINZ-KUNERT,A.PANDYA,V.T.DANG,J.OKTAWIEC,A.I.NGUYEN JRNL TITL PORE RESTRUCTURING OF PEPTIDE FRAMEWORKS BY MUTATIONS AT JRNL TITL 2 DISTAL PACKING RESIDUES. JRNL REF BIOMACROMOLECULES V. 25 2016 2024 JRNL REFN ESSN 1526-4602 JRNL PMID 38362872 JRNL DOI 10.1021/ACS.BIOMAC.3C01418 REMARK 2 REMARK 2 RESOLUTION. 1.12 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) : 1.12 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 6964 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.133 REMARK 3 R VALUE (WORKING SET) : 0.131 REMARK 3 FREE R VALUE : 0.154 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.890 REMARK 3 FREE R VALUE TEST SET COUNT : 1264 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 15.8700 - 2.3300 0.95 1269 130 0.1305 0.1633 REMARK 3 2 2.3300 - 1.8500 0.98 1306 137 0.1250 0.1311 REMARK 3 3 1.8500 - 1.6200 0.99 1290 145 0.1305 0.1282 REMARK 3 4 1.6100 - 1.4700 0.94 1216 140 0.1426 0.1272 REMARK 3 5 1.4700 - 1.3600 0.99 1333 144 0.1286 0.1722 REMARK 3 6 1.3600 - 1.2800 0.99 1259 144 0.1289 0.1646 REMARK 3 7 1.2800 - 1.2200 0.99 1363 147 0.1300 0.1585 REMARK 3 8 1.2200 - 1.1600 0.99 1260 138 0.1310 0.2224 REMARK 3 9 1.1600 - 1.1200 0.91 1218 139 0.1473 0.1891 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) : 0.098 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.310 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 7.41 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.50 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 : 0.010 254 REMARK 3 ANGLE : 1.708 352 REMARK 3 CHIRALITY : 0.049 26 REMARK 3 PLANARITY : 0.010 41 REMARK 3 DIHEDRAL : 38.944 44 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 8V59 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-DEC-23. REMARK 100 THE DEPOSITION ID IS D_1000279560. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-OCT-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) : 0.61992 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 : 6964 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.120 REMARK 200 RESOLUTION RANGE LOW (A) : 15.870 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.16830 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.1500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.12 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.34390 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.030 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 (%): 21.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: WATER, METHANOL, 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 27.00600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 5.15800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 27.00600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 5.15800 REMARK 290 SMTRY3 4 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 DBREF 8V59 A 1 11 PDB 8V59 8V59 1 11 DBREF 8V59 B 1 11 PDB 8V59 8V59 1 11 SEQRES 1 A 11 I6W LEU AIB ALA ILE LEU AIB GLN AIB LEU I77 SEQRES 1 B 11 I6W LEU AIB ALA ILE LEU AIB GLN AIB LEU I77 HET I6W A 1 30 HET AIB A 3 13 HET AIB A 7 13 HET AIB A 9 13 HET I77 A 11 58 HET I6W B 1 30 HET AIB B 3 13 HET AIB B 7 13 HET AIB B 9 13 HET I77 B 11 29 HET MOH 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 MOH METHANOL FORMUL 1 I6W 2(C14 H12 N2 O3) FORMUL 1 AIB 6(C4 H9 N O2) FORMUL 1 I77 2(C12 H11 N5 O2) FORMUL 3 MOH C H4 O FORMUL 4 HOH *7(H2 O) HELIX 1 AA1 LEU A 2 AIB A 7 1 6 HELIX 2 AA2 GLN A 8 LEU A 10 5 3 HELIX 3 AA3 AIB B 3 GLN B 8 1 6 LINK C02 I6W A 1 N LEU A 2 1555 1555 1.42 LINK C LEU A 2 N AIB A 3 1555 1555 1.33 LINK C AIB A 3 N ALA A 4 1555 1555 1.33 LINK C LEU A 6 N AIB A 7 1555 1555 1.33 LINK C AIB A 7 N GLN A 8 1555 1555 1.33 LINK C GLN A 8 N AIB A 9 1555 1555 1.33 LINK C AIB A 9 N ALEU A 10 1555 1555 1.34 LINK C AIB A 9 N BLEU A 10 1555 1555 1.33 LINK C ALEU A 10 N15AI77 A 11 1555 1555 1.42 LINK C BLEU A 10 N15BI77 A 11 1555 1555 1.43 LINK C02 I6W B 1 N LEU B 2 1555 1555 1.42 LINK C LEU B 2 N AIB B 3 1555 1555 1.33 LINK C AIB B 3 N ALA B 4 1555 1555 1.33 LINK C LEU B 6 N AIB B 7 1555 1555 1.33 LINK C AIB B 7 N GLN B 8 1555 1555 1.33 LINK C GLN B 8 N AIB B 9 1555 1555 1.33 LINK C AIB B 9 N LEU B 10 1555 1555 1.33 LINK C LEU B 10 N15 I77 B 11 1555 1555 1.42 CRYST1 54.012 10.316 32.278 90.00 100.50 90.00 C 1 2 1 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 0.018514 0.000000 0.003431 0.00000 SCALE2 0.000000 0.096937 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031508 0.00000 HETATM 1 C05 I6W A 1 -8.613 2.057 24.542 1.00 6.32 C ANISOU 1 C05 I6W A 1 384 1021 996 -40 182 32 C HETATM 2 C08 I6W A 1 -7.294 2.014 24.174 1.00 6.46 C ANISOU 2 C08 I6W A 1 400 1050 1003 -127 77 -92 C HETATM 3 C09 I6W A 1 -6.213 1.918 25.209 1.00 7.38 C ANISOU 3 C09 I6W A 1 512 1205 1088 -158 -22 2 C HETATM 4 N10 I6W A 1 -6.549 1.732 26.452 1.00 12.21 N ANISOU 4 N10 I6W A 1 698 2722 1219 -154 -38 2 N HETATM 5 C02 I6W A 1 -10.129 2.004 21.071 1.00 5.49 C ANISOU 5 C02 I6W A 1 316 847 922 -36 178 126 C HETATM 6 C03 I6W A 1 -9.155 2.014 22.234 1.00 5.44 C ANISOU 6 C03 I6W A 1 324 797 944 -28 149 49 C HETATM 7 C04 I6W A 1 -9.594 2.068 23.540 1.00 6.44 C ANISOU 7 C04 I6W A 1 341 1093 1013 0 171 97 C HETATM 8 C06 I6W A 1 -7.810 1.973 21.936 1.00 5.36 C ANISOU 8 C06 I6W A 1 292 827 917 3 98 45 C HETATM 9 C11 I6W A 1 -5.608 1.574 27.368 1.00 12.97 C ANISOU 9 C11 I6W A 1 743 2889 1298 -117 -69 204 C HETATM 10 C12 I6W A 1 -4.263 1.558 27.021 1.00 10.49 C ANISOU 10 C12 I6W A 1 664 1884 1438 -220 -177 60 C HETATM 11 C13 I6W A 1 -3.171 1.356 28.093 1.00 12.40 C ANISOU 11 C13 I6W A 1 835 2312 1566 -202 -191 142 C HETATM 12 C15 I6W A 1 -2.734 0.849 30.361 1.00 18.78 C ANISOU 12 C15 I6W A 1 1214 4296 1626 -311 -246 293 C HETATM 13 C16 I6W A 1 -3.544 0.263 31.546 1.00 20.91 C ANISOU 13 C16 I6W A 1 1301 4739 1903 -283 -247 445 C HETATM 14 C18 I6W A 1 -3.884 1.707 25.740 1.00 8.90 C ANISOU 14 C18 I6W A 1 619 1462 1300 -98 -168 151 C HETATM 15 C19 I6W A 1 -4.895 1.865 24.811 1.00 7.32 C ANISOU 15 C19 I6W A 1 530 1137 1115 -81 -104 131 C HETATM 16 N07 I6W A 1 -6.900 1.951 22.904 1.00 6.45 N ANISOU 16 N07 I6W A 1 343 1117 990 -32 63 3 N HETATM 17 O01 I6W A 1 -9.839 2.353 19.952 1.00 5.90 O ANISOU 17 O01 I6W A 1 352 1026 865 -32 238 1 O HETATM 18 O14 I6W A 1 -3.668 1.378 29.396 1.00 16.15 O ANISOU 18 O14 I6W A 1 1033 3620 1482 -370 -206 198 O HETATM 19 O17 I6W A 1 -2.032 1.156 27.848 1.00 12.57 O ANISOU 19 O17 I6W A 1 891 2157 1728 -238 -335 224 O HETATM 20 H051 I6W A 1 -8.889 2.082 25.573 1.00 7.59 H HETATM 21 H041 I6W A 1 -10.685 2.117 23.788 1.00 7.73 H HETATM 22 H061 I6W A 1 -7.491 1.959 20.898 1.00 6.43 H HETATM 23 H111 I6W A 1 -5.885 1.456 28.389 1.00 15.57 H HETATM 24 H152 I6W A 1 -2.087 1.642 30.716 1.00 22.54 H HETATM 25 H151 I6W A 1 -2.138 0.069 29.904 1.00 22.54 H HETATM 26 H162 I6W A 1 -3.115 0.625 32.500 1.00 25.09 H HETATM 27 H163 I6W A 1 -3.495 -0.841 31.515 1.00 25.09 H HETATM 28 H161 I6W A 1 -4.598 0.589 31.469 1.00 25.09 H HETATM 29 H181 I6W A 1 -2.834 1.704 25.448 1.00 10.68 H HETATM 30 H191 I6W A 1 -4.648 1.948 23.754 1.00 8.79 H