HEADER DE NOVO PROTEIN 20-MAR-23 8GKX 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 8GKX 1 COMPND SOURCE REMARK DBREF REVDAT 2 2 1 SEQRES HELIX LINK ATOM REVDAT 1 15-NOV-23 8GKX 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. 0.81 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) : 0.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 3 NUMBER OF REFLECTIONS : 32406 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.127 REMARK 3 R VALUE (WORKING SET) : 0.126 REMARK 3 FREE R VALUE : 0.138 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.830 REMARK 3 FREE R VALUE TEST SET COUNT : 3184 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 17.9300 - 2.3000 0.99 1332 160 0.1099 0.1378 REMARK 3 2 2.3000 - 1.8300 0.99 1340 141 0.0980 0.1057 REMARK 3 3 1.8300 - 1.6000 0.89 1217 127 0.1130 0.1352 REMARK 3 4 1.6000 - 1.4500 0.96 1241 147 0.1091 0.0958 REMARK 3 5 1.4500 - 1.3500 0.97 1375 141 0.1132 0.1219 REMARK 3 6 1.3500 - 1.2700 0.98 1267 137 0.0969 0.0947 REMARK 3 7 1.2700 - 1.2000 0.96 1341 150 0.0933 0.1005 REMARK 3 8 1.2000 - 1.1500 0.97 1343 142 0.0939 0.0964 REMARK 3 9 1.1500 - 1.1100 0.97 1269 147 0.0940 0.1101 REMARK 3 10 1.1100 - 1.0700 0.98 1340 151 0.0976 0.1028 REMARK 3 11 1.0700 - 1.0400 0.96 1305 129 0.1071 0.1144 REMARK 3 12 1.0400 - 1.0100 0.86 1117 135 0.1221 0.1402 REMARK 3 13 1.0100 - 0.9800 0.90 1285 144 0.1299 0.1503 REMARK 3 14 0.9800 - 0.9600 0.92 1259 130 0.1497 0.1655 REMARK 3 15 0.9600 - 0.9300 0.94 1236 134 0.1491 0.1756 REMARK 3 16 0.9300 - 0.9100 0.93 1274 113 0.1648 0.1762 REMARK 3 17 0.9100 - 0.9000 0.93 1286 144 0.2009 0.1900 REMARK 3 18 0.9000 - 0.8800 0.92 1247 147 0.2219 0.2796 REMARK 3 19 0.8800 - 0.8600 0.91 1204 135 0.2394 0.2557 REMARK 3 20 0.8600 - 0.8500 0.91 1192 121 0.2478 0.2360 REMARK 3 21 0.8500 - 0.8300 0.91 1305 116 0.2725 0.3353 REMARK 3 22 0.8300 - 0.8200 0.90 1243 128 0.2952 0.2866 REMARK 3 23 0.8200 - 0.8100 0.89 1204 165 0.3450 0.3581 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) : 0.081 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.618 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 4.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 5.03 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 : 0.012 222 REMARK 3 ANGLE : 1.913 309 REMARK 3 CHIRALITY : 0.046 19 REMARK 3 PLANARITY : 0.013 37 REMARK 3 DIHEDRAL : 36.702 38 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 8GKX 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_1000273085. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-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 : 32406 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.810 REMARK 200 RESOLUTION RANGE LOW (A) : 17.930 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.11080 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.2600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.81 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.84 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.55700 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 (%): 46.68 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 24.07050 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 C LEU B 10 H1 I77 B 11 1.49 REMARK 500 REMARK 500 REMARK: NULL DBREF 8GKX A 2 10 PDB 8GKX 8GKX 2 10 DBREF 8GKX B 2 10 PDB 8GKX 8GKX 2 10 SEQRES 1 A 11 I6W LEU AIB ALA AIB LEU HIS GLN AIB LEU I77 SEQRES 1 B 11 I6W LEU AIB ALA AIB LEU HIS GLN AIB LEU I77 HET I6W A 1 30 HET AIB A 3 13 HET AIB A 5 13 HET AIB A 9 13 HET I77 A 11 29 HET I6W B 1 30 HET AIB B 3 13 HET AIB B 5 13 HET AIB B 9 13 HET I77 B 11 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 6(C4 H9 N O2) FORMUL 1 I77 2(C12 H11 N5 O2) FORMUL 3 HOH *19(H2 O) HELIX 1 AA1 AIB A 3 LEU A 10 1 8 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 1.34 LINK C AIB A 3 N ALA A 4 1555 1555 1.33 LINK C ALA A 4 N AIB A 5 1555 1555 1.33 LINK C AIB A 5 N LEU A 6 1555 1555 1.33 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 ALA B 4 N AIB B 5 1555 1555 1.33 LINK C AIB B 5 N LEU B 6 1555 1555 1.34 LINK C AGLN B 8 N AIB B 9 1555 1555 1.33 LINK C BGLN 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 N15 I77 B 11 1555 1555 1.41 CRYST1 10.158 48.141 17.967 90.00 93.77 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 0.098445 0.000000 0.006483 0.00000 SCALE2 0.000000 0.020772 0.000000 0.00000 SCALE3 0.000000 0.000000 0.055778 0.00000 HETATM 1 C05 I6W A 1 4.554 -3.846 1.710 1.00 3.02 C ANISOU 1 C05 I6W A 1 288 237 622 85 -106 7 C HETATM 2 C08 I6W A 1 4.497 -5.040 2.394 1.00 2.98 C ANISOU 2 C08 I6W A 1 279 244 608 33 -34 10 C HETATM 3 C09 I6W A 1 4.513 -6.365 1.688 1.00 3.23 C ANISOU 3 C09 I6W A 1 359 272 597 41 -111 10 C HETATM 4 N10 I6W A 1 4.673 -7.509 2.360 1.00 3.91 N ANISOU 4 N10 I6W A 1 441 294 751 54 -122 27 N HETATM 5 C02 I6W A 1 4.663 -1.554 4.739 1.00 3.12 C ANISOU 5 C02 I6W A 1 354 234 596 47 -59 42 C HETATM 6 C03 I6W A 1 4.599 -2.745 3.802 1.00 2.90 C ANISOU 6 C03 I6W A 1 296 244 563 100 -25 16 C HETATM 7 C04 I6W A 1 4.583 -2.642 2.423 1.00 2.95 C ANISOU 7 C04 I6W A 1 290 238 594 89 -61 24 C HETATM 8 C06 I6W A 1 4.578 -3.976 4.402 1.00 3.56 C ANISOU 8 C06 I6W A 1 464 245 645 113 -54 0 C HETATM 9 C11 I6W A 1 4.766 -8.674 1.725 1.00 3.54 C ANISOU 9 C11 I6W A 1 372 288 686 39 -93 -6 C HETATM 10 C12 I6W A 1 4.690 -8.681 0.344 1.00 3.82 C ANISOU 10 C12 I6W A 1 494 281 676 3 -103 -67 C HETATM 11 C13 I6W A 1 4.834 -9.962 -0.464 1.00 4.51 C ANISOU 11 C13 I6W A 1 666 306 743 78 -168 -90 C HETATM 12 C15 I6W A 1 5.721 -12.124 -0.528 1.00 5.36 C ANISOU 12 C15 I6W A 1 774 364 899 149 -101 -96 C HETATM 13 C16 I6W A 1 6.293 -13.214 0.386 1.00 6.27 C ANISOU 13 C16 I6W A 1 1014 407 961 270 18 -9 C HETATM 14 C18 I6W A 1 4.531 -7.520 -0.344 1.00 4.40 C ANISOU 14 C18 I6W A 1 772 271 631 17 -124 -50 C HETATM 15 C19 I6W A 1 4.442 -6.328 0.334 1.00 3.65 C ANISOU 15 C19 I6W A 1 611 255 522 39 -149 -8 C HETATM 16 N07 I6W A 1 4.546 -5.096 3.716 1.00 3.36 N ANISOU 16 N07 I6W A 1 439 248 588 111 -46 26 N HETATM 17 O01 I6W A 1 4.719 -1.715 5.933 1.00 3.49 O ANISOU 17 O01 I6W A 1 461 267 596 62 -91 32 O HETATM 18 O14 I6W A 1 5.429 -10.980 0.271 1.00 4.32 O ANISOU 18 O14 I6W A 1 528 312 801 65 -155 -112 O HETATM 19 O17 I6W A 1 4.582 -10.056 -1.613 1.00 5.92 O ANISOU 19 O17 I6W A 1 1065 348 835 99 -286 -116 O HETATM 20 H051 I6W A 1 4.576 -3.839 0.643 1.00 3.62 H HETATM 21 H041 I6W A 1 4.592 -1.649 1.905 1.00 3.54 H HETATM 22 H061 I6W A 1 4.589 -4.028 5.486 1.00 4.28 H HETATM 23 H111 I6W A 1 4.897 -9.581 2.268 1.00 4.25 H HETATM 24 H152 I6W A 1 4.814 -12.482 -1.000 1.00 6.43 H HETATM 25 H151 I6W A 1 6.448 -11.864 -1.287 1.00 6.43 H HETATM 26 H162 I6W A 1 6.414 -14.151 -0.190 1.00 7.52 H HETATM 27 H163 I6W A 1 7.277 -12.890 0.774 1.00 7.52 H HETATM 28 H161 I6W A 1 5.601 -13.387 1.231 1.00 7.52 H HETATM 29 H181 I6W A 1 4.475 -7.532 -1.433 1.00 5.29 H HETATM 30 H191 I6W A 1 4.318 -5.386 -0.197 1.00 4.38 H