HEADER DE NOVO PROTEIN 22-APR-26 12YG TITLE HELLOB-GGFFAA-A6DPP - DE NOVO PEPTIDE WITH TERTIARY STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HELLOB-GGFFAA-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 12YG 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. 1.13 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) : 1.13 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 4908 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.148 REMARK 3 R VALUE (WORKING SET) : 0.144 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 892 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 17.9900 - 2.0500 0.99 1372 156 0.1353 0.1786 REMARK 3 2 2.0500 - 1.6300 0.99 1358 147 0.1404 0.1652 REMARK 3 3 1.6300 - 1.4200 0.98 1354 150 0.1516 0.1752 REMARK 3 4 1.4200 - 1.2900 0.97 1293 146 0.1334 0.1899 REMARK 3 5 1.2900 - 1.2000 0.98 1373 153 0.1636 0.2088 REMARK 3 6 1.2000 - 1.1300 0.93 1277 140 0.1900 0.2306 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) : 0.109 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.558 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.19 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 : 0.009 197 REMARK 3 ANGLE : 1.777 280 REMARK 3 CHIRALITY : 0.111 19 REMARK 3 PLANARITY : 0.004 36 REMARK 3 DIHEDRAL : 24.071 54 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 12YG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-APR-26. REMARK 100 THE DEPOSITION ID IS D_1000307303. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAR-26 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-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978720 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4908 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.130 REMARK 200 RESOLUTION RANGE LOW (A) : 17.990 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.5600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.13 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.17 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 (%): 29.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.75 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 18.89250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 4.63900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 18.89250 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 4.63900 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 202 O HOH A 203 1.96 REMARK 500 REMARK 500 REMARK: NULL DBREF 12YG A 1 19 PDB 12YG 12YG 1 19 SEQRES 1 A 19 Z7Z ALA AIB LEU AIB DPP AIB LEU AIB GLN AIB LEU GLY SEQRES 2 A 19 GLY PHE PHE ALA ALA NH2 HET Z7Z A 1 46 HET AIB A 3 13 HET AIB A 5 13 HET DPP A 6 36 HET AIB A 7 13 HET AIB A 9 13 HET AIB A 11 13 HET NH2 A 19 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 *4(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 ADPP A 6 1555 1555 1.33 LINK C AIB A 5 N BDPP A 6 1555 1555 1.33 LINK C AIB A 5 N CDPP A 6 1555 1555 1.33 LINK C ADPP A 6 N AIB A 7 1555 1555 1.33 LINK C BDPP A 6 N AIB A 7 1555 1555 1.33 LINK C CDPP A 6 N AIB A 7 1555 1555 1.33 LINK C AIB A 7 N ALEU A 8 1555 1555 1.33 LINK C AIB A 7 N BLEU A 8 1555 1555 1.32 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 AGLN A 10 1555 1555 1.32 LINK C AIB A 9 N BGLN A 10 1555 1555 1.34 LINK C AGLN A 10 N AIB A 11 1555 1555 1.33 LINK C BGLN A 10 N AIB A 11 1555 1555 1.32 LINK C AIB A 11 N LEU A 12 1555 1555 1.34 LINK C ALA A 18 N NH2 A 19 1555 1555 1.41 CRYST1 37.785 9.278 38.829 90.00 112.10 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 0.026466 0.000000 0.010747 0.00000 SCALE2 0.000000 0.107782 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027796 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 92 102 103 CONECT 91 104 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 91 105 120 CONECT 103 91 106 121 CONECT 104 91 107 122 CONECT 105 102 108 114 123 CONECT 106 103 109 115 124 CONECT 107 104 110 116 125 CONECT 108 105 111 138 CONECT 109 106 112 138 CONECT 110 107 113 138 CONECT 111 108 CONECT 112 109 CONECT 113 110 CONECT 114 105 117 126 129 CONECT 115 106 118 127 130 CONECT 116 107 119 128 131 CONECT 117 114 132 135 CONECT 118 115 133 136 CONECT 119 116 134 137 CONECT 120 102 CONECT 121 103 CONECT 122 104 CONECT 123 105 CONECT 124 106 CONECT 125 107 CONECT 126 114 CONECT 127 115 CONECT 128 116 CONECT 129 114 CONECT 130 115 CONECT 131 116 CONECT 132 117 CONECT 133 118 CONECT 134 119 CONECT 135 117 CONECT 136 118 CONECT 137 119 CONECT 138 108 109 110 139 CONECT 138 144 CONECT 139 138 140 142 143 CONECT 140 139 141 151 152 CONECT 141 140 CONECT 142 139 145 146 147 CONECT 143 139 148 149 150 CONECT 144 138 CONECT 145 142 CONECT 146 142 CONECT 147 142 CONECT 148 143 CONECT 149 143 CONECT 150 143 CONECT 151 140 CONECT 152 140 CONECT 155 189 CONECT 156 189 CONECT 189 155 156 190 195 CONECT 190 189 191 193 194 CONECT 191 190 192 202 203 CONECT 192 191 CONECT 193 190 196 197 198 CONECT 194 190 199 200 201 CONECT 195 189 CONECT 196 193 CONECT 197 193 CONECT 198 193 CONECT 199 194 CONECT 200 194 CONECT 201 194 CONECT 202 191 CONECT 203 191 CONECT 206 236 CONECT 207 236 CONECT 236 206 207 237 242 CONECT 237 236 238 240 241 CONECT 238 237 239 249 CONECT 239 238 CONECT 240 237 243 244 245 CONECT 241 237 246 247 248 CONECT 242 236 CONECT 243 240 CONECT 244 240 CONECT 245 240 CONECT 246 241 CONECT 247 241 CONECT 248 241 CONECT 249 238 CONECT 354 362 CONECT 362 354 363 364 CONECT 363 362 CONECT 364 362 CONECT 366 367 368 372 CONECT 367 366 369 370 371 CONECT 368 366 CONECT 369 367 CONECT 370 367 CONECT 371 367 CONECT 372 366 MASTER 202 0 9 1 0 0 0 6 140 1 173 2 END