HEADER DE NOVO PROTEIN 17-MAY-23 8SW2 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; 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 8SW2 1 COMPND SOURCE REMARK DBREF REVDAT 2 2 1 SEQRES HELIX LINK ATOM REVDAT 1 15-NOV-23 8SW2 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. 1.20 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 12.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.410 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 3040 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.030 REMARK 3 FREE R VALUE TEST SET COUNT : 305 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 12.8500 - 1.5100 1.00 1420 158 0.1720 0.1793 REMARK 3 2 1.5100 - 1.2000 1.00 1315 147 0.2151 0.2383 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) : 0.115 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.548 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 6.65 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.73 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 96 REMARK 3 ANGLE : 1.913 128 REMARK 3 CHIRALITY : 0.068 10 REMARK 3 PLANARITY : 0.011 15 REMARK 3 DIHEDRAL : 23.375 23 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 8SW2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-MAY-23. REMARK 100 THE DEPOSITION ID IS D_1000274576. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54184 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : RIGAKU HYPIX-3000 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO REMARK 200 DATA SCALING SOFTWARE : CRYSALISPRO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3040 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 12.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 11.40 REMARK 200 R MERGE (I) : 0.13790 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 58.1700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.24 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.22680 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 (%): 50.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 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 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 4.26350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.45400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 8.30150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.45400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 4.26350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 8.30150 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: 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 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 H181 I77 A 11 HG HG A 204 1.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HG A 203 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 NIO A 1 N REMARK 620 2 CYS A 8 O 20.4 REMARK 620 3 CYS A 8 SG 25.0 9.9 REMARK 620 4 HOH A 301 O 22.0 15.1 8.4 REMARK 620 5 HOH A 304 O 33.4 13.6 10.6 18.8 REMARK 620 6 HOH A 305 O 32.4 17.1 7.8 12.1 10.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HG A 202 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 8 SG REMARK 620 2 ACT A 201 O 97.9 REMARK 620 3 ACT A 201 OXT 68.1 48.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HG A 204 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 I77 A 11 N07 REMARK 620 2 I77 A 11 N10 79.4 REMARK 620 3 HOH A 302 O 78.4 89.1 REMARK 620 N 1 2 DBREF 8SW2 A 2 10 PDB 8SW2 8SW2 2 10 SEQRES 1 A 11 NIO LEU AIB ALA SER LEU ALA CYS AIB LEU I77 HET NIO A 1 24 HET AIB A 3 13 HET AIB A 9 13 HET I77 A 11 29 HET ACT A 201 7 HET HG A 202 1 HET HG A 203 1 HET HG A 204 3 HETNAM NIO NICOTINIC ACID HETNAM AIB ALPHA-AMINOISOBUTYRIC ACID HETNAM I77 5'-(HYDRAZINECARBONYL)[2,2'-BIPYRIDINE]-5-CARBOXAMIDE HETNAM ACT ACETATE ION HETNAM HG MERCURY (II) ION FORMUL 1 NIO C6 H5 N O2 FORMUL 1 AIB 2(C4 H9 N O2) FORMUL 1 I77 C12 H11 N5 O2 FORMUL 2 ACT C2 H3 O2 1- FORMUL 3 HG 3(HG 2+) FORMUL 6 HOH *5(H2 O) HELIX 1 AA1 AIB A 3 LEU A 10 1 8 LINK C6 ANIO A 1 N LEU A 2 1555 1555 1.43 LINK C6 BNIO A 1 N LEU A 2 1555 1555 1.43 LINK C LEU A 2 N AIB A 3 1555 1555 1.32 LINK C AIB A 3 N ALA A 4 1555 1555 1.34 LINK C CYS 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 N ANIO A 1 HG HG A 203 1555 1565 2.10 LINK SG CYS A 8 HG HG A 202 1555 1555 2.36 LINK O CYS A 8 HG HG A 203 1555 1555 2.44 LINK SG CYS A 8 HG HG A 203 1555 1555 2.35 LINK N07 I77 A 11 HG A HG A 204 1555 1555 2.40 LINK N10 I77 A 11 HG A HG A 204 1555 1555 2.13 LINK O ACT A 201 HG HG A 202 1555 1555 2.87 LINK OXT ACT A 201 HG HG A 202 1555 1555 2.67 LINK HG HG A 203 O HOH A 301 1555 1655 2.98 LINK HG HG A 203 O HOH A 304 1555 1555 2.80 LINK HG HG A 203 O HOH A 305 1555 1555 2.68 LINK HG A HG A 204 O HOH A 302 1555 1555 2.29 LINK HG B HG A 204 O HOH A 303 1555 1445 3.05 CRYST1 8.527 16.603 60.908 90.00 90.00 90.00 P 21 21 21 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 0.117275 0.000000 0.000000 0.00000 SCALE2 0.000000 0.060230 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016418 0.00000 HETATM 1 N ANIO A 1 0.217 15.013 -8.076 0.61 10.43 N ANISOU 1 N ANIO A 1 1697 1195 1071 830 53 33 N HETATM 2 N BNIO A 1 -0.073 12.589 -9.659 0.39 8.89 N ANISOU 2 N BNIO A 1 1778 596 1005 -10 500 160 N HETATM 3 C1 ANIO A 1 0.068 14.183 -7.045 0.61 10.43 C ANISOU 3 C1 ANIO A 1 1873 1006 1084 743 60 -14 C HETATM 4 C1 BNIO A 1 -0.312 12.010 -8.480 0.39 8.23 C ANISOU 4 C1 BNIO A 1 1306 827 993 -52 532 276 C HETATM 5 C2 ANIO A 1 -0.192 12.826 -7.180 0.61 8.35 C ANISOU 5 C2 ANIO A 1 1095 914 1165 -160 33 -118 C HETATM 6 C2 BNIO A 1 -0.174 12.661 -7.262 0.39 6.81 C ANISOU 6 C2 BNIO A 1 924 708 956 439 243 81 C HETATM 7 C3 ANIO A 1 -0.312 12.320 -8.468 0.61 5.96 C ANISOU 7 C3 ANIO A 1 977 341 946 106 20 -217 C HETATM 8 C3 BNIO A 1 0.228 13.990 -7.283 0.39 9.00 C ANISOU 8 C3 BNIO A 1 1560 873 986 636 163 97 C HETATM 9 C4 ANIO A 1 -0.169 13.167 -9.550 0.61 10.67 C ANISOU 9 C4 ANIO A 1 1971 922 1162 -486 31 -307 C HETATM 10 C4 BNIO A 1 0.475 14.603 -8.494 0.39 8.72 C ANISOU 10 C4 BNIO A 1 1354 973 988 282 650 129 C HETATM 11 C5 ANIO A 1 0.090 14.499 -9.305 0.61 6.59 C ANISOU 11 C5 ANIO A 1 686 785 1034 420 -109 70 C HETATM 12 C5 BNIO A 1 0.311 13.869 -9.647 0.39 7.52 C ANISOU 12 C5 BNIO A 1 1354 507 997 -31 401 194 C HETATM 13 C6 ANIO A 1 -0.351 11.955 -5.981 0.61 3.66 C ANISOU 13 C6 ANIO A 1 241 253 895 8 85 170 C HETATM 14 C6 BNIO A 1 -0.450 11.947 -5.991 0.39 3.32 C ANISOU 14 C6 BNIO A 1 186 226 851 0 42 83 C HETATM 15 O1 ANIO A 1 -0.474 10.740 -6.111 0.61 6.98 O ANISOU 15 O1 ANIO A 1 683 908 1061 234 7 132 O HETATM 16 O1 BNIO A 1 -0.300 10.734 -5.916 0.39 6.20 O ANISOU 16 O1 BNIO A 1 750 724 883 -433 -93 3 O HETATM 17 H1 ANIO A 1 0.142 14.532 -6.186 0.61 12.62 H HETATM 18 H1 BNIO A 1 -0.587 11.122 -8.475 0.39 9.97 H HETATM 19 H3 ANIO A 1 -0.487 11.416 -8.601 0.61 7.25 H HETATM 20 H3 BNIO A 1 0.331 14.462 -6.488 0.39 10.90 H HETATM 21 H4 ANIO A 1 -0.246 12.847 -10.420 0.61 12.91 H HETATM 22 H4 BNIO A 1 0.747 15.491 -8.531 0.39 10.57 H HETATM 23 H5 ANIO A 1 0.182 15.071 -10.032 0.61 8.01 H HETATM 24 H5 BNIO A 1 0.476 14.286 -10.461 0.39 9.13 H