HEADER DE NOVO PROTEIN 16-MAR-23 8GK2 TITLE POROUS FRAMEWORK FORMED BY ASSEMBLY OF A BIPYRIDYL-CONJUGATED HELICAL TITLE 2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEU-AIB-ALA-SER-LEU-ALA-CYS-AIB-LEU; 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 1 15-NOV-23 8GK2 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. 0.89 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) : 0.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.72 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 11349 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.070 REMARK 3 FREE R VALUE TEST SET COUNT : 1143 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 16.7200 - 1.7800 0.99 1291 154 0.1594 0.1910 REMARK 3 2 1.7800 - 1.4100 1.00 1276 141 0.1723 0.2068 REMARK 3 3 1.4100 - 1.2300 1.00 1308 142 0.1634 0.1850 REMARK 3 4 1.2300 - 1.1200 1.00 1302 151 0.1669 0.1933 REMARK 3 5 1.1200 - 1.0400 0.99 1268 138 0.1837 0.2128 REMARK 3 6 1.0400 - 0.9800 0.99 1314 147 0.1990 0.2179 REMARK 3 7 0.9800 - 0.9300 0.97 1234 135 0.1958 0.2370 REMARK 3 8 0.9300 - 0.8900 0.91 1213 135 0.2395 0.2300 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) : 0.064 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.499 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 7.34 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 7.33 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 : 0.014 108 REMARK 3 ANGLE : 1.967 146 REMARK 3 CHIRALITY : 0.061 10 REMARK 3 PLANARITY : 0.009 18 REMARK 3 DIHEDRAL : 31.242 16 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 8GK2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-MAR-23. REMARK 100 THE DEPOSITION ID IS D_1000273065. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-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) : 0.619840 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 : 11349 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.890 REMARK 200 RESOLUTION RANGE LOW (A) : 16.720 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 11.90 REMARK 200 R MERGE (I) : 0.17230 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.2900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.89 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.92 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.80580 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 (%): 45.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: WATER/ACETONTRILE, SLOW COOLING, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 2 21 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,-Z+1/2 REMARK 290 4555 -X+1/2,-Y,Z+1/2 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 4.22450 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 27.54350 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 4.22450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 27.54350 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 204 LIES ON A SPECIAL POSITION. REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 204 DISTANCE = 6.21 ANGSTROMS REMARK 525 HOH A 205 DISTANCE = 10.15 ANGSTROMS REMARK 525 HOH A 206 DISTANCE = 10.78 ANGSTROMS REMARK 525 HOH A 207 DISTANCE = 11.82 ANGSTROMS REMARK 525 HOH A 208 DISTANCE = 12.27 ANGSTROMS 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 AG A 104 AG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 8 O REMARK 620 2 CYS A 8 SG 88.1 REMARK 620 3 NIO A 101 N 86.2 13.3 REMARK 620 4 HOH A 203 O 139.2 99.9 92.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 AG A 107 AG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 I77 A 102 N07 REMARK 620 2 I77 A 102 N10 64.3 REMARK 620 3 NO3 A 103 O3 67.6 16.7 REMARK 620 4 HOH A 208 O 116.5 152.4 135.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 AG A 107 AG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 I77 A 102 N07 REMARK 620 2 I77 A 102 N10 80.4 REMARK 620 3 HOH A 202 O 142.0 115.9 REMARK 620 4 HOH A 204 O 137.6 125.8 62.0 REMARK 620 N 1 2 3 DBREF 8GK2 A 2 10 PDB 8GK2 8GK2 2 10 SEQRES 1 A 9 LEU AIB ALA SER LEU ALA CYS AIB LEU HET AIB A 3 13 HET AIB A 9 13 HET NIO A 101 12 HET I77 A 102 58 HET NO3 A 103 4 HET AG A 104 1 HET AG A 105 1 HET AG A 106 1 HET AG A 107 2 HETNAM AIB ALPHA-AMINOISOBUTYRIC ACID HETNAM NIO NICOTINIC ACID HETNAM I77 5'-(HYDRAZINECARBONYL)[2,2'-BIPYRIDINE]-5-CARBOXAMIDE HETNAM NO3 NITRATE ION HETNAM AG SILVER ION FORMUL 1 AIB 2(C4 H9 N O2) FORMUL 2 NIO C6 H5 N O2 FORMUL 3 I77 C12 H11 N5 O2 FORMUL 4 NO3 N O3 1- FORMUL 5 AG 4(AG 1+) FORMUL 9 HOH *8(H2 O) HELIX 1 AA1 LEU A 2 LEU A 10 1 9 LINK C LEU A 2 N AIB A 3 1555 1555 1.34 LINK N LEU A 2 C6 NIO A 101 1555 1555 1.43 LINK C AIB A 3 N ALA A 4 1555 1555 1.33 LINK C CYS 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 N15AI77 A 102 1555 1555 1.43 LINK C LEU A 10 N15BI77 A 102 1555 1555 1.43 LINK O CYS A 8 AG AG A 104 1555 1555 2.68 LINK SG CYS A 8 AG AG A 104 1555 1555 2.39 LINK SG CYS A 8 AG AG A 105 1555 1555 2.42 LINK SG CYS A 8 AG AG A 106 1555 1555 2.34 LINK N NIO A 101 AG AG A 104 1555 1545 2.20 LINK N07AI77 A 102 AG A AG A 107 1555 1555 2.55 LINK N07BI77 A 102 AG B AG A 107 1555 1555 2.31 LINK N10AI77 A 102 AG A AG A 107 1555 1555 2.40 LINK N10BI77 A 102 AG B AG A 107 1555 1555 2.31 LINK O3 NO3 A 103 AG A AG A 107 1555 1445 2.51 LINK AG AG A 104 O HOH A 203 1555 1555 2.52 LINK AG B AG A 107 O HOH A 202 1555 1665 2.29 LINK AG B AG A 107 O HOH A 204 1555 1665 2.45 LINK AG A AG A 107 O HOH A 208 1555 2475 2.41 CRYST1 8.449 16.716 55.087 90.00 90.00 90.00 P 21 2 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 0.118357 0.000000 0.000000 0.00000 SCALE2 0.000000 0.059823 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018153 0.00000