HEADER DE NOVO PROTEIN 20-MAR-23 8GL0 TITLE POROUS FRAMEWORK FORMED BY ASSEMBLY OF A BIPYRIDYL-CONJUGATED HELICAL TITLE 2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIPYRIDYL-CONJUGATED HELICAL PEPTIDE; 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 DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.S.HESS,A.I.NGUYEN REVDAT 2 25-SEP-24 8GL0 1 COMPND SOURCE REMARK DBREF REVDAT 2 2 1 SEQRES HELIX LINK ATOM REVDAT 1 15-NOV-23 8GL0 0 JRNL AUTH S.S.HESS,F.COPPOLA,V.T.DANG,P.N.TRAN,P.J.MICKEL,J.OKTAWIEC, JRNL AUTH 2 Z.REN,P.KRAL,A.I.NGUYEN JRNL TITL NONCOVALENT PEPTIDE ASSEMBLY ENABLES CRYSTALLINE, JRNL TITL 2 PERMUTABLE, AND REACTIVE THIOL FRAMEWORKS. JRNL REF J.AM.CHEM.SOC. V. 145 19588 2023 JRNL REFN ESSN 1520-5126 JRNL PMID 37639365 JRNL DOI 10.1021/JACS.3C03645 REMARK 2 REMARK 2 RESOLUTION. 1.02 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 1.02 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.460 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 16428 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.124 REMARK 3 R VALUE (WORKING SET) : 0.121 REMARK 3 FREE R VALUE : 0.151 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1641 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 17.6400 - 2.3300 0.95 1221 138 0.1041 0.1544 REMARK 3 2 2.3300 - 1.8500 0.97 1260 139 0.1079 0.1107 REMARK 3 3 1.8500 - 1.6200 0.98 1204 133 0.1121 0.1411 REMARK 3 4 1.6200 - 1.4700 0.98 1257 139 0.1181 0.1331 REMARK 3 5 1.4700 - 1.3700 0.95 1245 134 0.1138 0.1567 REMARK 3 6 1.3700 - 1.2900 0.95 1181 136 0.1213 0.1744 REMARK 3 7 1.2800 - 1.2200 0.96 1248 139 0.1160 0.1674 REMARK 3 8 1.2200 - 1.1700 0.96 1241 137 0.1395 0.1424 REMARK 3 9 1.1700 - 1.1200 0.98 1209 129 0.1565 0.1386 REMARK 3 10 1.1200 - 1.0800 0.98 1292 146 0.1635 0.2028 REMARK 3 11 1.0800 - 1.0500 0.98 1260 140 0.1932 0.2282 REMARK 3 12 1.0500 - 1.0200 0.95 1169 131 0.2111 0.2454 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.085 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.754 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 6.93 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 8.29 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 : 0.012 249 REMARK 3 ANGLE : 1.908 339 REMARK 3 CHIRALITY : 0.074 23 REMARK 3 PLANARITY : 0.011 42 REMARK 3 DIHEDRAL : 35.774 43 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 8GL0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-MAR-23. REMARK 100 THE DEPOSITION ID IS D_1000273111. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-NOV-21 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) : 0.688800 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 : 16428 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.020 REMARK 200 RESOLUTION RANGE LOW (A) : 17.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.08232 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.4500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.02 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.06 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.44070 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 (%): 46.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 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: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 24.27250 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 O16 I77 B 11 O HOH B 301 1.98 REMARK 500 REMARK 500 REMARK: NULL DBREF 8GL0 A 2 10 PDB 8GL0 8GL0 2 10 DBREF 8GL0 B 2 10 PDB 8GL0 8GL0 2 10 SEQRES 1 A 11 I6W LEU AIB ALA CYS LEU CYS GLN AIB LEU I77 SEQRES 1 B 11 I6W LEU AIB ALA CYS LEU CYS GLN AIB LEU I77 HET I6W A 1 30 HET AIB A 3 13 HET AIB A 9 13 HET I77 A 11 29 HET I6W B 1 30 HET AIB B 3 13 HET AIB B 9 13 HET I77 B 11 58 HET CCN A 201 6 HET CCN B 201 6 HET CCN B 202 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 2(C14 H12 N2 O3) FORMUL 1 AIB 4(C4 H9 N O2) FORMUL 1 I77 2(C12 H11 N5 O2) FORMUL 3 CCN 3(C2 H3 N) FORMUL 6 HOH *7(H2 O) HELIX 1 AA1 LEU A 2 LEU A 10 1 9 HELIX 2 AA2 AIB B 3 LEU B 10 1 8 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 1.34 LINK C GLN 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 N15 I77 A 11 1555 1555 1.41 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 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 1.42 LINK C LEU B 10 N15BI77 B 11 1555 1555 1.43 CRYST1 10.069 48.545 17.730 90.00 95.79 90.00 P 1 21 1 4 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 0.099315 0.000000 0.010071 0.00000 SCALE2 0.000000 0.020599 0.000000 0.00000 SCALE3 0.000000 0.000000 0.056691 0.00000 HETATM 1 C05 I6W A 1 4.377 -5.109 3.673 1.00 4.34 C ANISOU 1 C05 I6W A 1 468 325 856 76 185 83 C HETATM 2 C08 I6W A 1 4.366 -4.994 2.341 1.00 5.64 C ANISOU 2 C08 I6W A 1 420 486 1237 12 210 12 C HETATM 3 C09 I6W A 1 4.517 -6.298 1.601 1.00 6.89 C ANISOU 3 C09 I6W A 1 631 549 1439 -20 250 -55 C HETATM 4 N10 I6W A 1 4.601 -7.459 2.242 1.00 8.34 N ANISOU 4 N10 I6W A 1 952 584 1635 -35 260 -164 N HETATM 5 C02 I6W A 1 4.137 -1.564 4.779 1.00 6.81 C ANISOU 5 C02 I6W A 1 947 372 1270 14 300 60 C HETATM 6 C03 I6W A 1 4.235 -2.736 3.816 1.00 5.73 C ANISOU 6 C03 I6W A 1 657 407 1114 23 182 35 C HETATM 7 C04 I6W A 1 4.282 -3.966 4.427 1.00 5.65 C ANISOU 7 C04 I6W A 1 760 366 1020 46 215 57 C HETATM 8 C06 I6W A 1 4.263 -2.640 2.438 1.00 5.93 C ANISOU 8 C06 I6W A 1 514 502 1236 51 192 74 C HETATM 9 C11 I6W A 1 4.812 -8.602 1.611 1.00 8.18 C ANISOU 9 C11 I6W A 1 950 618 1542 70 369 -140 C HETATM 10 C12 I6W A 1 4.930 -8.562 0.243 1.00 10.66 C ANISOU 10 C12 I6W A 1 1890 740 1420 22 486 -264 C HETATM 11 C13 I6W A 1 5.200 -9.862 -0.529 1.00 13.93 C ANISOU 11 C13 I6W A 1 2688 1031 1573 102 827 -280 C HETATM 12 C15 I6W A 1 6.313 -12.010 -0.378 1.00 13.35 C ANISOU 12 C15 I6W A 1 2370 966 1737 220 633 -364 C HETATM 13 C16 I6W A 1 7.202 -12.714 0.680 1.00 12.61 C ANISOU 13 C16 I6W A 1 1948 1013 1831 364 298 -289 C HETATM 14 C18 I6W A 1 4.853 -7.392 -0.441 1.00 11.52 C ANISOU 14 C18 I6W A 1 2383 699 1295 83 310 -102 C HETATM 15 C19 I6W A 1 4.645 -6.225 0.258 1.00 9.47 C ANISOU 15 C19 I6W A 1 1798 617 1184 -16 320 -44 C HETATM 16 N07 I6W A 1 4.348 -3.786 1.735 1.00 7.24 N ANISOU 16 N07 I6W A 1 806 573 1370 14 256 81 N HETATM 17 O01 I6W A 1 4.128 -1.745 5.964 1.00 7.80 O ANISOU 17 O01 I6W A 1 1420 401 1144 3 282 39 O HETATM 18 O14 I6W A 1 5.622 -10.936 0.281 1.00 12.88 O ANISOU 18 O14 I6W A 1 2197 953 1745 162 737 -339 O HETATM 19 O17 I6W A 1 5.143 -9.905 -1.698 1.00 17.78 O ANISOU 19 O17 I6W A 1 3742 1274 1741 64 713 -380 O HETATM 20 H051 I6W A 1 4.458 -6.067 4.139 1.00 5.22 H HETATM 21 H041 I6W A 1 4.242 -4.036 5.544 1.00 6.78 H HETATM 22 H061 I6W A 1 4.218 -1.676 1.940 1.00 7.12 H HETATM 23 H111 I6W A 1 4.887 -9.520 2.145 1.00 9.83 H HETATM 24 H152 I6W A 1 5.598 -12.714 -0.785 1.00 16.03 H HETATM 25 H151 I6W A 1 6.931 -11.616 -1.175 1.00 16.03 H HETATM 26 H162 I6W A 1 7.612 -13.648 0.252 1.00 15.14 H HETATM 27 H163 I6W A 1 6.594 -12.952 1.572 1.00 15.14 H HETATM 28 H161 I6W A 1 8.033 -12.043 0.967 1.00 15.14 H HETATM 29 H181 I6W A 1 4.953 -7.376 -1.526 1.00 13.83 H HETATM 30 H191 I6W A 1 4.586 -5.268 -0.257 1.00 11.37 H