HEADER DE NOVO PROTEIN 14-MAR-23 8GIV 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 8GIV 1 COMPND REMARK DBREF SEQRES REVDAT 2 2 1 HET HETNAM FORMUL LINK REVDAT 2 3 1 ATOM REVDAT 1 15-NOV-23 8GIV 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 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.V.AFONINE REMARK 1 TITL TOWARDS AUTOMATED CRYSTALLOGRAPHIC STRUCTURE REFINEMENT WITH REMARK 1 TITL 2 PHENIX.REFINE. REMARK 1 REF ACTA CRYSTALLOGR., SECT. D: V. 68 352 2012 REMARK 1 REF 2 BIOL. CRYSTALLOGR. REMARK 1 REFN ISSN 0907-4449 REMARK 2 REMARK 2 RESOLUTION. 0.99 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) : 0.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.67 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 18314 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1829 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 18.6700 - 2.3300 0.96 1287 135 0.2208 0.2557 REMARK 3 2 2.3300 - 1.8500 0.98 1274 142 0.1998 0.1769 REMARK 3 3 1.8500 - 1.6100 0.97 1307 145 0.1931 0.1663 REMARK 3 4 1.6100 - 1.4700 0.98 1269 149 0.1879 0.2646 REMARK 3 5 1.4700 - 1.3600 0.96 1276 137 0.1929 0.2138 REMARK 3 6 1.3600 - 1.2800 0.97 1230 146 0.1949 0.2265 REMARK 3 7 1.2800 - 1.2200 0.98 1306 150 0.1868 0.1916 REMARK 3 8 1.2200 - 1.1600 0.99 1346 153 0.1878 0.2035 REMARK 3 9 1.1600 - 1.1200 0.98 1264 135 0.1888 0.2524 REMARK 3 10 1.1200 - 1.0800 0.97 1291 139 0.1821 0.1959 REMARK 3 11 1.0800 - 1.0500 0.98 1288 146 0.1867 0.2353 REMARK 3 12 1.0500 - 1.0200 0.95 1284 137 0.1787 0.2024 REMARK 3 13 1.0200 - 0.9900 0.87 1063 115 0.2135 0.2449 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) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.609 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 5.77 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 8.84 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 : 0.008 192 REMARK 3 ANGLE : 1.714 270 REMARK 3 CHIRALITY : 0.035 19 REMARK 3 PLANARITY : 0.007 32 REMARK 3 DIHEDRAL : 28.474 37 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 8GIV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-MAR-23. REMARK 100 THE DEPOSITION ID IS D_1000272638. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-SEP-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) : 0.688839 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 : 18314 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.990 REMARK 200 RESOLUTION RANGE LOW (A) : 18.670 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.06039 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.2600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.03 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.14680 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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 (%): 29.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.75 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 4.94300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.93150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 4.94300 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 15.93150 REMARK 290 SMTRY3 4 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 DBREF 8GIV A 1 11 PDB 8GIV 8GIV 1 11 DBREF 8GIV B 1 11 PDB 8GIV 8GIV 1 11 SEQRES 1 A 11 BEZ LEU AIB ALA AIB LEU CYS GLN AIB LEU I77 SEQRES 1 B 11 BEZ LEU AIB ALA AIB LEU CYS GLN AIB LEU I77 HET BEZ A 1 13 HET AIB A 3 13 HET AIB A 5 13 HET AIB A 9 13 HET I77 A 11 29 HET BEZ B 1 13 HET AIB B 3 13 HET AIB B 5 26 HET AIB B 9 13 HET I77 B 11 29 HETNAM BEZ BENZOIC ACID HETNAM AIB ALPHA-AMINOISOBUTYRIC ACID HETNAM I77 5'-(HYDRAZINECARBONYL)[2,2'-BIPYRIDINE]-5-CARBOXAMIDE FORMUL 1 BEZ 2(C7 H6 O2) FORMUL 1 AIB 6(C4 H9 N O2) FORMUL 1 I77 2(C12 H11 N5 O2) FORMUL 3 HOH *7(H2 O) HELIX 1 AA1 LEU A 2 LEU A 10 1 9 HELIX 2 AA2 LEU B 2 LEU B 10 1 9 LINK C BEZ A 1 N LEU A 2 1555 1555 1.42 LINK C LEU A 2 N AAIB A 3 1555 1555 1.33 LINK C AAIB 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 1.32 LINK C AIB A 9 N LEU A 10 1555 1555 1.33 LINK C LEU A 10 N15 I77 A 11 1555 1555 1.42 LINK C BEZ B 1 N LEU B 2 1555 1555 1.42 LINK C LEU B 2 N AAIB B 3 1555 1555 1.33 LINK C AAIB B 3 N ALA B 4 1555 1555 1.33 LINK C ALA B 4 N AAIB B 5 1555 1555 1.33 LINK C ALA B 4 N BAIB B 5 1555 1555 1.33 LINK C AAIB B 5 N LEU B 6 1555 1555 1.33 LINK C BAIB B 5 N LEU B 6 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 N15 I77 B 11 1555 1555 1.42 CRYST1 9.886 31.863 56.051 90.00 92.36 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 0.101153 0.000000 0.004165 0.00000 SCALE2 0.000000 0.031384 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017856 0.00000 HETATM 1 C BEZ A 1 -0.988 -7.366 23.264 1.00 6.07 C ANISOU 1 C BEZ A 1 923 285 1098 34 26 -69 C HETATM 2 O1 BEZ A 1 -0.692 -6.155 23.314 1.00 7.05 O ANISOU 2 O1 BEZ A 1 1095 352 1232 -161 46 -65 O HETATM 3 C1 BEZ A 1 -1.794 -7.907 22.123 1.00 6.28 C ANISOU 3 C1 BEZ A 1 961 295 1131 -62 57 -42 C HETATM 4 C2 BEZ A 1 -2.292 -6.959 21.245 1.00 6.73 C ANISOU 4 C2 BEZ A 1 1044 324 1190 -120 -52 36 C HETATM 5 C3 BEZ A 1 -3.040 -7.348 20.143 1.00 8.40 C ANISOU 5 C3 BEZ A 1 1536 415 1242 -44 -169 90 C HETATM 6 C4 BEZ A 1 -3.287 -8.691 19.914 1.00 7.66 C ANISOU 6 C4 BEZ A 1 1339 388 1184 -17 -202 116 C HETATM 7 C5 BEZ A 1 -2.777 -9.648 20.790 1.00 6.88 C ANISOU 7 C5 BEZ A 1 1158 325 1133 -146 -35 3 C HETATM 8 C6 BEZ A 1 -2.020 -9.253 21.900 1.00 6.23 C ANISOU 8 C6 BEZ A 1 975 285 1108 -68 -9 -33 C HETATM 9 H2 BEZ A 1 -2.094 -5.901 21.419 1.00 8.09 H HETATM 10 H3 BEZ A 1 -3.434 -6.597 19.459 1.00 10.09 H HETATM 11 H4 BEZ A 1 -3.879 -8.999 19.052 1.00 9.20 H HETATM 12 H5 BEZ A 1 -2.968 -10.706 20.611 1.00 8.27 H HETATM 13 H6 BEZ A 1 -1.613 -9.999 22.583 1.00 7.49 H