HEADER DE NOVO PROTEIN 17-APR-26 12TI TITLE HELLOB-GGSSTSAA-A6DPP - DE NOVO PEPTIDE WITH TERTIARY STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HELLOB-GGSSTSAA-A6DPP- DE NOVO PEPTIDE WITH TERTIARY COMPND 3 STRUCTURE; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS SYNTHETIC CONSTRUCT, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.GANATRA REVDAT 1 28-OCT-26 12TI 0 JRNL AUTH P.GANATRA,D.F.WANG,S.NICHOLS,V.T.DANG,J.S.BRUNZELLE,P.JANA, JRNL AUTH 2 A.I.NGUYEN JRNL TITL POROUS FRAMEWORK ASSEMBLY CREATES FUNCTIONAL TERTIARY FOLDS JRNL TITL 2 IN SMALL PEPTIDES JRNL REF J.AM.CHEM.SOC. 2026 JRNL REFN ESSN 1520-5126 REMARK 2 REMARK 2 RESOLUTION. 0.91 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 0.91 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 10122 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.170 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.050 REMARK 3 FREE R VALUE TEST SET COUNT : 1870 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 19.5300 - 2.1400 0.98 1278 146 0.1209 0.1333 REMARK 3 2 2.1400 - 1.7000 0.99 1316 149 0.1400 0.1372 REMARK 3 3 1.7000 - 1.4800 0.98 1275 142 0.1434 0.1715 REMARK 3 4 1.4800 - 1.3500 0.98 1286 141 0.1628 0.1684 REMARK 3 5 1.3500 - 1.2500 0.99 1327 145 0.1494 0.1555 REMARK 3 6 1.2500 - 1.1800 0.99 1267 143 0.1746 0.1668 REMARK 3 7 1.1800 - 1.1200 0.98 1284 147 0.1546 0.1807 REMARK 3 8 1.1200 - 1.0700 0.98 1297 144 0.1811 0.2228 REMARK 3 9 1.0700 - 1.0300 0.99 1233 136 0.2274 0.2512 REMARK 3 10 1.0300 - 0.9900 0.98 1331 151 0.2506 0.2078 REMARK 3 11 0.9900 - 0.9600 0.99 1307 142 0.2725 0.2538 REMARK 3 12 0.9600 - 0.9300 0.98 1239 140 0.3161 0.3303 REMARK 3 13 0.9300 - 0.9100 0.97 1298 144 0.3286 0.3852 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.102 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.992 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.05 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.96 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 : 0.006 172 REMARK 3 ANGLE : 1.535 242 REMARK 3 CHIRALITY : 0.063 19 REMARK 3 PLANARITY : 0.004 29 REMARK 3 DIHEDRAL : 22.439 31 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 12TI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-APR-26. REMARK 100 THE DEPOSITION ID IS D_1000307225. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-MAY-25 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 : MAX IV REMARK 200 BEAMLINE : BIOMAX REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.68879 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10122 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.910 REMARK 200 RESOLUTION RANGE LOW (A) : 19.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.6200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.91 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.94 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: ACETONITRILE, WATER, SLOW COOLING, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Z REMARK 290 4555 -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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 18.96050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 4.59350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 18.96050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 4.59350 REMARK 290 SMTRY3 4 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 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 O HOH A 203 O HOH A 212 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE1 GLN A 10 F2 TFA A 101 1565 1.83 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 214 DISTANCE = 6.70 ANGSTROMS REMARK 525 HOH A 215 DISTANCE = 7.90 ANGSTROMS REMARK 525 HOH A 216 DISTANCE = 9.23 ANGSTROMS DBREF 12TI A 1 21 PDB 12TI 12TI 1 21 SEQRES 1 A 21 Z7Z ALA AIB LEU AIB DPP AIB LEU AIB GLN AIB LEU GLY SEQRES 2 A 21 GLY SER SER THR SER ALA ALA NH2 HET Z7Z A 1 46 HET AIB A 3 13 HET AIB A 5 13 HET DPP A 6 12 HET AIB A 7 13 HET AIB A 9 13 HET AIB A 11 13 HET NH2 A 21 3 HET TFA A 101 7 HETNAM Z7Z BIPHENYL-4-CARBOXYLIC ACID HETNAM AIB ALPHA-AMINOISOBUTYRIC ACID HETNAM DPP DIAMINOPROPANOIC ACID HETNAM NH2 AMINO GROUP HETNAM TFA TRIFLUOROACETIC ACID FORMUL 1 Z7Z C13 H10 O2 FORMUL 1 AIB 5(C4 H9 N O2) FORMUL 1 DPP C3 H8 N2 O2 FORMUL 1 NH2 H2 N FORMUL 2 TFA C2 H F3 O2 FORMUL 3 HOH *16(H2 O) HELIX 1 AA1 ALA A 2 LEU A 12 1 11 LINK C1 AZ7Z A 1 N ALA A 2 1555 1555 1.42 LINK C1 BZ7Z A 1 N ALA A 2 1555 1555 1.43 LINK C ALA A 2 N AIB A 3 1555 1555 1.33 LINK C AIB A 3 N LEU A 4 1555 1555 1.33 LINK C LEU A 4 N AIB A 5 1555 1555 1.33 LINK C AIB A 5 N DPP A 6 1555 1555 1.33 LINK C DPP A 6 N AIB A 7 1555 1555 1.33 LINK C AIB A 7 N ALEU A 8 1555 1555 1.32 LINK C AIB A 7 N BLEU A 8 1555 1555 1.33 LINK C ALEU A 8 N AIB A 9 1555 1555 1.33 LINK C BLEU A 8 N AIB A 9 1555 1555 1.33 LINK C AIB A 9 N GLN A 10 1555 1555 1.33 LINK C GLN A 10 N AIB A 11 1555 1555 1.33 LINK C AIB A 11 N LEU A 12 1555 1555 1.34 LINK C ALA A 20 N NH2 A 21 1555 1555 1.42 CRYST1 37.921 9.187 39.679 90.00 100.20 90.00 C 1 2 1 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 0.026371 0.000000 0.004745 0.00000 SCALE2 0.000000 0.108849 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025607 0.00000 CONECT 1 3 CONECT 2 4 CONECT 3 1 5 47 CONECT 4 2 6 47 CONECT 5 3 7 11 CONECT 6 4 8 12 CONECT 7 5 9 29 CONECT 8 6 10 30 CONECT 9 7 15 31 CONECT 10 8 16 32 CONECT 11 5 13 33 CONECT 12 6 14 34 CONECT 13 11 15 35 CONECT 14 12 16 36 CONECT 15 9 13 17 CONECT 16 10 14 18 CONECT 17 15 19 21 CONECT 18 16 20 22 CONECT 19 17 23 37 CONECT 20 18 24 38 CONECT 21 17 25 39 CONECT 22 18 26 40 CONECT 23 19 27 41 CONECT 24 20 28 42 CONECT 25 21 27 43 CONECT 26 22 28 44 CONECT 27 23 25 45 CONECT 28 24 26 46 CONECT 29 7 CONECT 30 8 CONECT 31 9 CONECT 32 10 CONECT 33 11 CONECT 34 12 CONECT 35 13 CONECT 36 14 CONECT 37 19 CONECT 38 20 CONECT 39 21 CONECT 40 22 CONECT 41 23 CONECT 42 24 CONECT 43 25 CONECT 44 26 CONECT 45 27 CONECT 46 28 CONECT 47 3 4 CONECT 49 57 CONECT 57 49 58 63 CONECT 58 57 59 61 62 CONECT 59 58 60 70 CONECT 60 59 CONECT 61 58 64 65 66 CONECT 62 58 67 68 69 CONECT 63 57 CONECT 64 61 CONECT 65 61 CONECT 66 61 CONECT 67 62 CONECT 68 62 CONECT 69 62 CONECT 70 59 CONECT 72 89 CONECT 89 72 90 95 CONECT 90 89 91 93 94 CONECT 91 90 92 102 CONECT 92 91 CONECT 93 90 96 97 98 CONECT 94 90 99 100 101 CONECT 95 89 CONECT 96 93 CONECT 97 93 CONECT 98 93 CONECT 99 94 CONECT 100 94 CONECT 101 94 CONECT 102 91 103 108 CONECT 103 102 104 106 109 CONECT 104 103 105 114 CONECT 105 104 CONECT 106 103 107 110 111 CONECT 107 106 112 113 CONECT 108 102 CONECT 109 103 CONECT 110 106 CONECT 111 106 CONECT 112 107 CONECT 113 107 CONECT 114 104 115 120 CONECT 115 114 116 118 119 CONECT 116 115 117 127 128 CONECT 117 116 CONECT 118 115 121 122 123 CONECT 119 115 124 125 126 CONECT 120 114 CONECT 121 118 CONECT 122 118 CONECT 123 118 CONECT 124 119 CONECT 125 119 CONECT 126 119 CONECT 127 116 CONECT 128 116 CONECT 131 165 CONECT 132 165 CONECT 165 131 132 166 171 CONECT 166 165 167 169 170 CONECT 167 166 168 178 CONECT 168 167 CONECT 169 166 172 173 174 CONECT 170 166 175 176 177 CONECT 171 165 CONECT 172 169 CONECT 173 169 CONECT 174 169 CONECT 175 170 CONECT 176 170 CONECT 177 170 CONECT 178 167 CONECT 180 195 CONECT 195 180 196 201 CONECT 196 195 197 199 200 CONECT 197 196 198 208 CONECT 198 197 CONECT 199 196 202 203 204 CONECT 200 196 205 206 207 CONECT 201 195 CONECT 202 199 CONECT 203 199 CONECT 204 199 CONECT 205 200 CONECT 206 200 CONECT 207 200 CONECT 208 197 CONECT 318 326 CONECT 326 318 327 328 CONECT 327 326 CONECT 328 326 CONECT 330 331 332 336 CONECT 331 330 333 334 335 CONECT 332 330 CONECT 333 331 CONECT 334 331 CONECT 335 331 CONECT 336 330 MASTER 243 0 9 1 0 0 0 6 155 1 145 2 END