HEADER DE NOVO PROTEIN 19-JAN-22 7TMK TITLE POROUS FRAMEWORK FORMED BY ASSEMBLY OF A BIPYRIDYL-CONJUGATED HELICAL TITLE 2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HELICAL PEPTIDE; COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS POROUS, FRAMEWORK, HELIX, 310, ALPHA, ASSEMBLY, BIPYRIDINE, UIC-1, DE KEYWDS 2 NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.I.NGUYEN REVDAT 4 15-NOV-23 7TMK 1 REMARK REVDAT 3 18-OCT-23 7TMK 1 REMARK REVDAT 2 27-APR-22 7TMK 1 JRNL REVDAT 1 20-APR-22 7TMK 0 JRNL AUTH S.L.HEINZ-KUNERT,A.PANDYA,V.T.DANG,P.N.TRAN,S.GHOSH, JRNL AUTH 2 D.MCELHENY,B.D.SANTARSIERO,Z.REN,A.I.NGUYEN JRNL TITL ASSEMBLY OF PI-STACKING HELICAL PEPTIDES INTO A POROUS AND JRNL TITL 2 MULTIVARIABLE PROTEOMIMETIC FRAMEWORK. JRNL REF J.AM.CHEM.SOC. V. 144 7001 2022 JRNL REFN ESSN 1520-5126 JRNL PMID 35390261 JRNL DOI 10.1021/JACS.2C02146 REMARK 2 REMARK 2 RESOLUTION. 0.83 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) : 0.83 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.980 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 17291 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.140 REMARK 3 R VALUE (WORKING SET) : 0.139 REMARK 3 FREE R VALUE : 0.157 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.890 REMARK 3 FREE R VALUE TEST SET COUNT : 889 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 8.8800 - 1.5100 0.99 2866 167 0.1077 0.1319 REMARK 3 2 1.5100 - 1.2000 1.00 2929 131 0.1209 0.1160 REMARK 3 3 1.2000 - 1.0500 0.99 2875 140 0.1318 0.1422 REMARK 3 4 1.0500 - 0.9500 0.99 2894 135 0.1589 0.2045 REMARK 3 5 0.9500 - 0.8800 0.99 2882 161 0.2032 0.2257 REMARK 3 6 0.8800 - 0.8300 0.99 2845 155 0.2450 0.2368 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) : 0.075 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.210 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 3.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 5.13 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 : 0.012 289 REMARK 3 ANGLE : 2.008 390 REMARK 3 CHIRALITY : 0.054 21 REMARK 3 PLANARITY : 0.007 45 REMARK 3 DIHEDRAL : 35.806 79 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 7TMK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JAN-22. REMARK 100 THE DEPOSITION ID IS D_1000262550. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUL-21 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 : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER D8 QUEST REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.711 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : BRUKER PHOTON II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : APEX 2 REMARK 200 DATA SCALING SOFTWARE : APEX 2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18180 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.830 REMARK 200 RESOLUTION RANGE LOW (A) : 8.880 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.0300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.83 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.86 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: 7TLS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: WATER AND ACETONITRILE, SLOW COOLING, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 H191 I6W C 102 O HOH C 207 1.08 REMARK 500 C19 I6W C 102 O HOH C 207 1.27 REMARK 500 C18 I6W C 102 O HOH C 207 1.67 REMARK 500 O HOH A 204 O HOH A 211 2.02 REMARK 500 O HOH A 201 O HOH A 209 2.17 REMARK 500 REMARK 500 REMARK: NULL DBREF 7TMK A 2 10 PDB 7TMK 7TMK 2 10 DBREF 7TMK C 2 10 PDB 7TMK 7TMK 2 10 SEQRES 1 A 9 LEU AIB ALA AIB LEU MET GLN AIB LEU SEQRES 1 C 9 LEU AIB ALA AIB LEU MET GLN AIB LEU HET AIB A 3 13 HET AIB A 5 13 HET AIB A 9 13 HET AIB C 3 13 HET AIB C 5 13 HET AIB C 9 13 HET I77 A 101 56 HET I6W A 102 60 HET CCN A 103 6 HET CCN A 104 6 HET I77 C 101 28 HET I6W C 102 60 HET CCN C 103 6 HETNAM AIB ALPHA-AMINOISOBUTYRIC ACID HETNAM I77 5'-(HYDRAZINECARBONYL)[2,2'-BIPYRIDINE]-5-CARBOXAMIDE HETNAM I6W ETHYL 5'-FORMYL[2,2'-BIPYRIDINE]-5-CARBOXYLATE HETNAM CCN ACETONITRILE FORMUL 1 AIB 6(C4 H9 N O2) FORMUL 3 I77 2(C12 H11 N5 O2) FORMUL 4 I6W 2(C14 H12 N2 O3) FORMUL 5 CCN 3(C2 H3 N) FORMUL 10 HOH *21(H2 O) HELIX 1 AA1 LEU A 2 GLN A 8 1 7 HELIX 2 AA2 AIB C 3 GLN C 8 1 6 LINK C LEU A 2 N AIB A 3 1555 1555 1.33 LINK N LEU A 2 C02AI6W A 102 1555 1555 1.42 LINK N LEU A 2 C02BI6W A 102 1555 1555 1.43 LINK C AIB 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 1.34 LINK C AIB A 9 N LEU A 10 1555 1555 1.34 LINK C LEU A 10 N15AI77 A 101 1555 1555 1.41 LINK C LEU A 10 N15BI77 A 101 1555 1555 1.43 LINK C LEU C 2 N AIB C 3 1555 1555 1.33 LINK N LEU C 2 C02AI6W C 102 1555 1555 1.42 LINK N LEU C 2 C02BI6W C 102 1555 1555 1.43 LINK C AIB C 3 N ALA C 4 1555 1555 1.33 LINK C ALA C 4 N AIB C 5 1555 1555 1.34 LINK C AIB C 5 N LEU C 6 1555 1555 1.34 LINK C GLN C 8 N AIB C 9 1555 1555 1.34 LINK C AIB C 9 N ALEU C 10 1555 1555 1.34 LINK C AIB C 9 N BLEU C 10 1555 1555 1.33 LINK C ALEU C 10 N15 I77 C 101 1555 1555 1.42 LINK C BLEU C 10 N15 I77 C 101 1555 1555 1.43 CRYST1 13.396 13.768 27.481 82.07 89.98 88.20 P 1 2 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 0.074649 -0.002347 0.000302 0.00000 SCALE2 0.000000 0.072668 -0.010131 0.00000 SCALE3 0.000000 0.000000 0.036741 0.00000