HEADER DE NOVO PROTEIN 26-FEB-23 8GBM 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 8GBM 1 COMPND SOURCE REMARK DBREF REVDAT 2 2 1 SEQRES HELIX LINK ATOM REVDAT 1 15-NOV-23 8GBM 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. 1.04 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) : 1.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 8046 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) : 0.170 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.040 REMARK 3 FREE R VALUE TEST SET COUNT : 808 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 15.2000 - 1.8900 1.00 1218 140 0.1376 0.1612 REMARK 3 2 1.8900 - 1.5000 1.00 1206 133 0.1501 0.1852 REMARK 3 3 1.5000 - 1.3100 1.00 1226 133 0.1865 0.2181 REMARK 3 4 1.3100 - 1.1900 1.00 1191 134 0.2377 0.2671 REMARK 3 5 1.1900 - 1.1100 1.00 1184 131 0.2736 0.3029 REMARK 3 6 1.1100 - 1.0400 0.98 1213 137 0.3977 0.3480 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) : 0.132 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.640 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.88 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.44 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 92 REMARK 3 ANGLE : 1.323 126 REMARK 3 CHIRALITY : 0.037 9 REMARK 3 PLANARITY : 0.015 15 REMARK 3 DIHEDRAL : 26.083 24 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 8GBM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1000272517. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUL-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) : 0.729405 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 : 8046 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.040 REMARK 200 RESOLUTION RANGE LOW (A) : 15.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 11.80 REMARK 200 R MERGE (I) : 0.13860 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.7900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.08 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.88400 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 (%): 48.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 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 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 27.41800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 27.41800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 5.00150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 15.81550 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 5.00150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 15.81550 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 27.41800 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 5.00150 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 15.81550 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 27.41800 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 5.00150 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 15.81550 REMARK 290 SMTRY3 8 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 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 PB A 201 PB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 NIO A 1 N REMARK 620 2 ACT A 202 O 72.3 REMARK 620 3 ACT A 202 OXT 61.8 10.6 REMARK 620 4 HOH A 304 O 76.1 4.6 14.8 REMARK 620 N 1 2 3 DBREF 8GBM A 2 10 PDB 8GBM 8GBM 2 10 SEQRES 1 A 11 NIO LEU AIB ALA AIB LEU CYS GLN AIB LEU I77 HET NIO A 1 12 HET AIB A 3 13 HET AIB A 5 13 HET AIB A 9 13 HET I77 A 11 29 HET PB A 201 1 HET ACT A 202 7 HETNAM NIO NICOTINIC ACID HETNAM AIB ALPHA-AMINOISOBUTYRIC ACID HETNAM I77 5'-(HYDRAZINECARBONYL)[2,2'-BIPYRIDINE]-5-CARBOXAMIDE HETNAM PB LEAD (II) ION HETNAM ACT ACETATE ION FORMUL 1 NIO C6 H5 N O2 FORMUL 1 AIB 3(C4 H9 N O2) FORMUL 1 I77 C12 H11 N5 O2 FORMUL 2 PB PB 2+ FORMUL 3 ACT C2 H3 O2 1- FORMUL 4 HOH *4(H2 O) HELIX 1 AA1 AIB A 3 LEU A 10 1 8 LINK C6 NIO 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 1.33 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 NIO A 1 PB PB A 201 1555 1655 2.63 LINK PB PB A 201 O ACT A 202 1555 1555 2.67 LINK PB PB A 201 OXT ACT A 202 1555 1555 2.33 LINK PB PB A 201 O HOH A 304 1555 1455 2.91 CRYST1 10.003 31.631 54.836 90.00 90.00 90.00 C 2 2 21 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 0.099970 0.000000 0.000000 0.00000 SCALE2 0.000000 0.031615 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018236 0.00000 HETATM 1 N NIO A 1 6.955 7.785 6.124 1.00 11.71 N ANISOU 1 N NIO A 1 1160 761 2530 -58 433 -246 N HETATM 2 C1 NIO A 1 6.279 7.454 7.222 1.00 11.16 C ANISOU 2 C1 NIO A 1 825 947 2470 69 130 -501 C HETATM 3 C2 NIO A 1 5.623 8.371 8.026 1.00 11.04 C ANISOU 3 C2 NIO A 1 754 979 2463 38 -15 -296 C HETATM 4 C3 NIO A 1 5.691 9.707 7.666 1.00 11.26 C ANISOU 4 C3 NIO A 1 824 976 2477 -155 -115 -216 C HETATM 5 C4 NIO A 1 6.388 10.069 6.537 1.00 11.52 C ANISOU 5 C4 NIO A 1 1137 713 2527 191 -4 -115 C HETATM 6 C5 NIO A 1 7.007 9.082 5.804 1.00 12.36 C ANISOU 6 C5 NIO A 1 963 1118 2616 -326 360 -84 C HETATM 7 C6 NIO A 1 4.867 7.933 9.225 1.00 10.60 C ANISOU 7 C6 NIO A 1 724 903 2399 -191 -53 -38 C HETATM 8 O2 NIO A 1 4.582 6.675 9.254 1.00 12.59 O ANISOU 8 O2 NIO A 1 1043 950 2791 -188 165 -69 O HETATM 9 H1 NIO A 1 6.244 6.557 7.462 1.00 13.48 H HETATM 10 H3 NIO A 1 5.268 10.354 8.183 1.00 13.59 H HETATM 11 H4 NIO A 1 6.440 10.960 6.275 1.00 13.90 H HETATM 12 H5 NIO A 1 7.487 9.330 5.047 1.00 14.91 H