HEADER DE NOVO PROTEIN 01-DEC-23 8V5X TITLE UIC-1 MUTANT - UIC-1-L6A COMPND MOL_ID: 1; COMPND 2 MOLECULE: UIC-1-L6A; 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 8V5X 1 JRNL REVDAT 1 06-MAR-24 8V5X 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) : 17.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.440 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 6420 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.980 REMARK 3 FREE R VALUE TEST SET COUNT : 1192 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 17.5500 - 2.3300 0.96 1203 133 0.1270 0.1780 REMARK 3 2 2.3300 - 1.8500 0.99 1218 136 0.1343 0.1699 REMARK 3 3 1.8500 - 1.6200 0.98 1220 139 0.1511 0.2258 REMARK 3 4 1.6200 - 1.4700 0.93 1171 123 0.1953 0.2453 REMARK 3 5 1.4700 - 1.3600 0.96 1212 133 0.1946 0.2471 REMARK 3 6 1.3600 - 1.2800 0.97 1191 134 0.2294 0.2907 REMARK 3 7 1.2800 - 1.2200 0.98 1230 140 0.2460 0.2926 REMARK 3 8 1.2200 - 1.1600 0.96 1198 134 0.2637 0.2830 REMARK 3 9 1.1600 - 1.1200 0.91 1109 120 0.2912 0.3558 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) : 0.159 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.915 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.06 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.67 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 : 1.814 349 REMARK 3 CHIRALITY : 0.073 15 REMARK 3 PLANARITY : 0.010 43 REMARK 3 DIHEDRAL : 40.618 46 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 8V5X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-DEC-23. REMARK 100 THE DEPOSITION ID IS D_1000279597. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-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 : 6420 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.120 REMARK 200 RESOLUTION RANGE LOW (A) : 17.550 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.11910 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.6900 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 (%) : 94.6 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.75250 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.550 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 (%): 21.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: WATER, ACETONITRILE, 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 25.40050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 8.39600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 25.40050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 8.39600 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 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 202 LIES ON A SPECIAL POSITION. 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 10 H1 I77 A 11 1.19 REMARK 500 REMARK 500 REMARK: NULL DBREF 8V5X A 1 11 PDB 8V5X 8V5X 1 11 DBREF 8V5X B 1 11 PDB 8V5X 8V5X 1 11 SEQRES 1 A 11 I6W LEU AIB ALA AIB ALA AIB GLN AIB LEU I77 SEQRES 1 B 11 I6W LEU AIB ALA AIB ALA AIB GLN AIB 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 I77 A 11 58 HET I6W B 1 30 HET AIB B 3 13 HET AIB B 5 13 HET AIB B 7 13 HET AIB B 9 13 HET I77 B 11 57 HET CCN A 101 12 HET CCN B 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 CCN ACETONITRILE FORMUL 1 I6W 2(C14 H12 N2 O3) FORMUL 1 AIB 8(C4 H9 N O2) FORMUL 1 I77 2(C12 H11 N5 O2) FORMUL 3 CCN 2(C2 H3 N) FORMUL 5 HOH *6(H2 O) HELIX 1 AA1 LEU A 2 GLN A 8 1 7 HELIX 2 AA2 AIB B 3 LEU B 10 1 8 LINK C02 I6W A 1 N LEU A 2 1555 1555 1.43 LINK C LEU A 2 N AIB A 3 1555 1555 1.33 LINK C AIB A 3 N ALA A 4 1555 1555 1.34 LINK C ALA A 4 N AIB A 5 1555 1555 1.33 LINK C AIB A 5 N AALA A 6 1555 1555 1.33 LINK C AALA A 6 N AIB A 7 1555 1555 1.33 LINK C AIB A 7 N AGLN A 8 1555 1555 1.34 LINK C AIB A 7 N BGLN A 8 1555 1555 1.33 LINK C AGLN A 8 N AIB A 9 1555 1555 1.33 LINK C BGLN A 8 N AIB A 9 1555 1555 1.33 LINK C AIB A 9 N LEU A 10 1555 1555 1.34 LINK C LEU A 10 N15AI77 A 11 1555 1555 1.43 LINK C LEU A 10 N15BI77 A 11 1555 1555 1.42 LINK C02 I6W B 1 N LEU B 2 1555 1555 1.43 LINK C LEU B 2 N AIB B 3 1555 1555 1.33 LINK C AIB B 3 N ALA B 4 1555 1555 1.34 LINK C ALA B 4 N AIB B 5 1555 1555 1.34 LINK C AIB B 5 N ALA B 6 1555 1555 1.34 LINK C ALA B 6 N AIB B 7 1555 1555 1.32 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 1.34 LINK C LEU B 10 N15AI77 B 11 1555 1555 1.43 LINK C LEU B 10 N15BI77 B 11 1555 1555 1.43 CRYST1 50.801 16.792 20.200 90.00 103.99 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 0.019685 0.000000 0.004904 0.00000 SCALE2 0.000000 0.059552 0.000000 0.00000 SCALE3 0.000000 0.000000 0.051018 0.00000 HETATM 1 C05 I6W A 1 -1.153 2.177 11.538 1.00 9.90 C ANISOU 1 C05 I6W A 1 845 1770 1148 78 28 92 C HETATM 2 C08 I6W A 1 -1.083 3.531 11.583 1.00 10.27 C ANISOU 2 C08 I6W A 1 924 2111 867 -8 17 88 C HETATM 3 C09 I6W A 1 -2.368 4.319 11.509 1.00 9.94 C ANISOU 3 C09 I6W A 1 981 2001 796 -79 130 173 C HETATM 4 N10 I6W A 1 -3.511 3.681 11.415 1.00 9.89 N ANISOU 4 N10 I6W A 1 987 1816 953 52 69 171 N HETATM 5 C02 I6W A 1 2.468 1.251 11.735 1.00 10.09 C ANISOU 5 C02 I6W A 1 1101 1570 1163 -217 160 300 C HETATM 6 C03 I6W A 1 1.199 2.104 11.701 1.00 9.06 C ANISOU 6 C03 I6W A 1 953 1430 1060 63 98 444 C HETATM 7 C04 I6W A 1 0.014 1.422 11.591 1.00 9.34 C ANISOU 7 C04 I6W A 1 856 1625 1066 -58 72 155 C HETATM 8 C06 I6W A 1 1.229 3.485 11.715 1.00 10.99 C ANISOU 8 C06 I6W A 1 890 1986 1301 146 -21 504 C HETATM 9 C11 I6W A 1 -4.668 4.323 11.337 1.00 10.39 C ANISOU 9 C11 I6W A 1 1027 1976 944 -28 -101 515 C HETATM 10 C12 I6W A 1 -4.676 5.697 11.339 1.00 11.78 C ANISOU 10 C12 I6W A 1 1162 1988 1327 151 7 346 C HETATM 11 C13 I6W A 1 -5.993 6.490 11.234 1.00 12.59 C ANISOU 11 C13 I6W A 1 1236 2028 1520 87 59 547 C HETATM 12 C15 I6W A 1 -7.004 8.657 11.106 1.00 15.60 C ANISOU 12 C15 I6W A 1 1453 2396 2080 323 7 877 C HETATM 13 C16 I6W A 1 -6.588 10.137 11.283 1.00 15.77 C ANISOU 13 C16 I6W A 1 1639 2563 1790 276 -52 1020 C HETATM 14 C18 I6W A 1 -3.505 6.389 11.433 1.00 10.21 C ANISOU 14 C18 I6W A 1 1144 1432 1304 208 -150 181 C HETATM 15 C19 I6W A 1 -2.315 5.682 11.498 1.00 9.41 C ANISOU 15 C19 I6W A 1 1018 1462 1094 123 -142 208 C HETATM 16 N07 I6W A 1 0.080 4.165 11.659 1.00 11.23 N ANISOU 16 N07 I6W A 1 984 2017 1266 136 125 207 N HETATM 17 O01 I6W A 1 2.446 0.102 12.079 1.00 9.73 O ANISOU 17 O01 I6W A 1 1177 1306 1214 -233 90 210 O HETATM 18 O14 I6W A 1 -5.804 7.882 11.162 1.00 14.87 O ANISOU 18 O14 I6W A 1 1368 2298 1984 225 44 587 O HETATM 19 O17 I6W A 1 -7.038 5.975 11.164 1.00 14.11 O ANISOU 19 O17 I6W A 1 1166 1711 2483 80 136 599 O HETATM 20 H051 I6W A 1 -2.101 1.693 11.462 1.00 11.88 H HETATM 21 H041 I6W A 1 -0.013 0.303 11.545 1.00 11.21 H HETATM 22 H061 I6W A 1 2.177 4.013 11.772 1.00 13.19 H HETATM 23 H111 I6W A 1 -5.582 3.780 11.274 1.00 12.47 H HETATM 24 H152 I6W A 1 -7.492 8.520 10.149 1.00 18.72 H HETATM 25 H151 I6W A 1 -7.676 8.362 11.903 1.00 18.72 H HETATM 26 H162 I6W A 1 -7.491 10.774 11.294 1.00 18.92 H HETATM 27 H163 I6W A 1 -5.934 10.438 10.443 1.00 18.92 H HETATM 28 H161 I6W A 1 -6.041 10.254 12.237 1.00 18.92 H HETATM 29 H181 I6W A 1 -3.504 7.478 11.457 1.00 12.25 H HETATM 30 H191 I6W A 1 -1.360 6.203 11.541 1.00 11.29 H