HEADER DE NOVO PROTEIN 19-JAN-22 7TME 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; 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 7TME 1 REMARK REVDAT 3 25-OCT-23 7TME 1 REMARK REVDAT 2 09-AUG-23 7TME 1 JRNL REVDAT 1 25-JAN-23 7TME 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. 0.80 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) : 0.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 12.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.440 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 20050 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.108 REMARK 3 R VALUE (WORKING SET) : 0.106 REMARK 3 FREE R VALUE : 0.125 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 2003 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 12.1400 - 1.9300 0.99 1296 144 0.1077 0.1641 REMARK 3 2 1.9200 - 1.5300 0.95 1277 140 0.1125 0.1068 REMARK 3 3 1.5300 - 1.3400 0.99 1321 146 0.1184 0.1183 REMARK 3 4 1.3400 - 1.2100 0.99 1289 146 0.0985 0.1078 REMARK 3 5 1.2100 - 1.1300 0.99 1305 141 0.0922 0.0974 REMARK 3 6 1.1300 - 1.0600 0.99 1342 142 0.0831 0.1084 REMARK 3 7 1.0600 - 1.0100 0.95 1276 146 0.0939 0.1129 REMARK 3 8 1.0100 - 0.9600 0.95 1225 141 0.0946 0.1180 REMARK 3 9 0.9600 - 0.9300 0.97 1339 154 0.0991 0.1071 REMARK 3 10 0.9300 - 0.8900 0.97 1264 137 0.1053 0.1258 REMARK 3 11 0.8900 - 0.8700 0.98 1293 140 0.1122 0.1133 REMARK 3 12 0.8700 - 0.8400 0.98 1266 145 0.1340 0.1350 REMARK 3 13 0.8400 - 0.8200 0.98 1343 149 0.1401 0.1485 REMARK 3 14 0.8200 - 0.8000 0.94 1211 132 0.1550 0.1403 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) : 0.031 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 12.037 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 4.63 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 8.29 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 : 0.010 172 REMARK 3 ANGLE : 1.810 234 REMARK 3 CHIRALITY : 0.033 14 REMARK 3 PLANARITY : 0.009 29 REMARK 3 DIHEDRAL : 48.667 29 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 7TME 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_1000262541. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-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) : 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) : 0.688 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 : 20050 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.800 REMARK 200 RESOLUTION RANGE LOW (A) : 12.140 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.5500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.83 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 : 9.960 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 (%): 54.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: ACETONITRILE AND WATER, SLOW COOLING, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 6.76350 REMARK 290 SMTRY3 2 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 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 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 O17 I6W A 102 O HOH A 201 2.02 REMARK 500 O HOH A 214 O HOH A 216 2.11 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 216 DISTANCE = 6.74 ANGSTROMS DBREF 7TME A 2 10 PDB 7TME 7TME 2 10 SEQRES 1 A 9 LEU AIB ALA ASP LEU AIB GLN AIB LEU HET AIB A 3 13 HET AIB A 7 13 HET AIB A 9 13 HET I77 A 101 56 HET I6W A 102 60 HET CCN A 103 6 HET CCN A 104 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 3(C4 H9 N O2) FORMUL 2 I77 C12 H11 N5 O2 FORMUL 3 I6W C14 H12 N2 O3 FORMUL 4 CCN 2(C2 H3 N) FORMUL 6 HOH *16(H2 O) HELIX 1 AA1 LEU A 2 GLN A 8 1 7 LINK C ALEU A 2 N AIB A 3 1555 1555 1.33 LINK C BLEU A 2 N AIB A 3 1555 1555 1.33 LINK N ALEU A 2 C02AI6W A 102 1555 1555 1.43 LINK N BLEU A 2 C02BI6W A 102 1555 1555 1.42 LINK C AIB A 3 N ALA A 4 1555 1555 1.33 LINK C LEU A 6 N AIB A 7 1555 1555 1.34 LINK C AIB A 7 N GLN A 8 1555 1555 1.34 LINK C GLN A 8 N AIB A 9 1555 1555 1.34 LINK C AIB A 9 N ALEU A 10 1555 1555 1.33 LINK C AIB A 9 N BLEU A 10 1555 1555 1.34 LINK C ALEU A 10 N15AI77 A 101 1555 1555 1.41 LINK C BLEU A 10 N15BI77 A 101 1555 1555 1.43 CRYST1 13.561 13.527 27.851 90.00 98.82 90.00 P 1 21 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 0.073741 0.000000 0.011443 0.00000 SCALE2 0.000000 0.073926 0.000000 0.00000 SCALE3 0.000000 0.000000 0.036335 0.00000