HEADER DE NOVO PROTEIN 24-FEB-23 8GBA 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 8GBA 1 COMPND SOURCE REMARK DBREF REVDAT 2 2 1 SEQRES HELIX LINK ATOM REVDAT 1 15-NOV-23 8GBA 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. 0.89 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) : 28.63 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 11662 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.085 REMARK 3 R VALUE (WORKING SET) : 0.083 REMARK 3 FREE R VALUE : 0.097 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1171 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 28.6300 - 1.7800 0.99 1350 144 0.1002 0.1246 REMARK 3 2 1.7800 - 1.4100 1.00 1326 147 0.0844 0.0800 REMARK 3 3 1.4100 - 1.2300 0.99 1349 151 0.0818 0.0939 REMARK 3 4 1.2300 - 1.1200 0.99 1359 152 0.0651 0.0706 REMARK 3 5 1.1200 - 1.0400 0.99 1290 151 0.0655 0.0706 REMARK 3 6 1.0400 - 0.9800 1.00 1361 152 0.0689 0.0963 REMARK 3 7 0.9800 - 0.9300 0.97 1296 148 0.0810 0.0912 REMARK 3 8 0.9300 - 0.8900 0.84 1160 126 0.0956 0.1385 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) : 0.043 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 8.622 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 3.52 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 4.94 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 99 REMARK 3 ANGLE : 1.912 138 REMARK 3 CHIRALITY : 0.045 12 REMARK 3 PLANARITY : 0.007 17 REMARK 3 DIHEDRAL : 20.586 27 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 8GBA 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_1000272504. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-MAR-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) : 0.619920 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 : 11662 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.890 REMARK 200 RESOLUTION RANGE LOW (A) : 28.630 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : 12.40 REMARK 200 R MERGE (I) : 0.09684 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.2600 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) : 0.20030 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 (%): 47.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 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 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 4.23850 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 28.62850 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 4.23850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.62850 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 C LEU A 10 H1 I77 A 11 1.19 REMARK 500 SG CYS A 8 O HOH A 206 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 212 DISTANCE = 6.38 ANGSTROMS DBREF 8GBA A 2 10 PDB 8GBA 8GBA 2 10 SEQRES 1 A 11 NIO LEU AIB ALA SER LEU ALA CYS AIB LEU I77 HET NIO A 1 12 HET AIB A 3 13 HET AIB A 9 14 HET I77 A 11 30 HETNAM NIO NICOTINIC ACID HETNAM AIB ALPHA-AMINOISOBUTYRIC ACID HETNAM I77 5'-(HYDRAZINECARBONYL)[2,2'-BIPYRIDINE]-5-CARBOXAMIDE FORMUL 1 NIO C6 H5 N O2 FORMUL 1 AIB 2(C4 H9 N O2) FORMUL 1 I77 C12 H11 N5 O2 FORMUL 2 HOH *12(H2 O) HELIX 1 AA1 AIB A 3 LEU A 10 1 8 LINK C6 NIO A 1 N LEU A 2 1555 1555 1.40 LINK C LEU A 2 N AAIB A 3 1555 1555 1.34 LINK C AAIB A 3 N ALA A 4 1555 1555 1.34 LINK C ACYS A 8 N AIB A 9 1555 1555 1.33 LINK C CCYS 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 1.42 CRYST1 8.477 16.637 57.257 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 0.117966 0.000000 0.000000 0.00000 SCALE2 0.000000 0.060107 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017465 0.00000 HETATM 1 N NIO A 1 -5.252 -0.949 4.864 1.00 3.91 N ANISOU 1 N NIO A 1 485 544 458 106 -25 -70 N HETATM 2 C1 NIO A 1 -4.971 -0.224 5.940 1.00 2.85 C ANISOU 2 C1 NIO A 1 370 297 417 -54 -17 -20 C HETATM 3 C2 NIO A 1 -5.411 -0.546 7.212 1.00 2.13 C ANISOU 3 C2 NIO A 1 238 184 389 27 -19 16 C HETATM 4 C3 NIO A 1 -6.185 -1.691 7.370 1.00 2.61 C ANISOU 4 C3 NIO A 1 343 225 424 -14 -75 -17 C HETATM 5 C4 NIO A 1 -6.486 -2.453 6.263 1.00 3.05 C ANISOU 5 C4 NIO A 1 410 249 499 -19 -141 -105 C HETATM 6 C5 NIO A 1 -5.992 -2.049 5.038 1.00 3.98 C ANISOU 6 C5 NIO A 1 556 459 496 174 -142 -188 C HETATM 7 C6 NIO A 1 -5.067 0.332 8.348 1.00 1.82 C ANISOU 7 C6 NIO A 1 219 117 357 8 -21 37 C HETATM 8 O1 NIO A 1 -5.020 1.584 8.207 1.00 2.25 O ANISOU 8 O1 NIO A 1 330 131 392 -36 -11 52 O HETATM 9 H1 NIO A 1 -4.458 0.544 5.832 1.00 3.42 H HETATM 10 H3 NIO A 1 -6.502 -1.934 8.210 1.00 3.13 H HETATM 11 H4 NIO A 1 -6.996 -3.227 6.340 1.00 3.65 H HETATM 12 H5 NIO A 1 -6.191 -2.567 4.292 1.00 4.77 H