HEADER DE NOVO PROTEIN 28-APR-26 13BO TITLE HELLOB-GGSSTMAA-A6DPP - DE NOVO PEPTIDE WITH TERTIARY STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HELLOB-GGSSTMAA-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 13BO 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. 1.15 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) : 1.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 5141 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.152 REMARK 3 R VALUE (WORKING SET) : 0.150 REMARK 3 FREE R VALUE : 0.174 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.060 REMARK 3 FREE R VALUE TEST SET COUNT : 943 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 39.9100 - 2.2000 0.99 1205 140 0.1329 0.1534 REMARK 3 2 2.2000 - 1.7500 1.00 1230 144 0.1290 0.1419 REMARK 3 3 1.7500 - 1.5300 1.00 1219 128 0.1566 0.1914 REMARK 3 4 1.5300 - 1.3900 0.99 1220 133 0.1609 0.2247 REMARK 3 5 1.3900 - 1.2900 1.00 1215 143 0.1702 0.1759 REMARK 3 6 1.2900 - 1.2100 0.99 1235 139 0.2095 0.2602 REMARK 3 7 1.2100 - 1.1500 0.92 1110 116 0.2153 0.2646 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) : 0.103 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.992 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.13 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.97 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 : 0.009 190 REMARK 3 ANGLE : 1.566 268 REMARK 3 CHIRALITY : 0.077 21 REMARK 3 PLANARITY : 0.006 33 REMARK 3 DIHEDRAL : 21.482 35 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 13BO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-MAY-26. REMARK 100 THE DEPOSITION ID IS D_1000307260. 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) : 0.688802 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 : 5141 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.150 REMARK 200 RESOLUTION RANGE LOW (A) : 39.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.6100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.19 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 (%): 32.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: METHANOL, 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 18.82900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 4.61950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 18.82900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 4.61950 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 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 1.90 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 208 DISTANCE = 8.67 ANGSTROMS DBREF 13BO A 1 21 PDB 13BO 13BO 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 MET ALA ALA NH2 HET Z7Z A 1 46 HET AIB A 3 13 HET AIB A 5 13 HET DPP A 6 24 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 *8(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 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 AIB A 7 N ALEU A 8 1555 1555 1.33 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 1.32 LINK C GLN A 10 N AIB A 11 1555 1555 1.33 LINK C AIB A 11 N LEU A 12 1555 1555 1.33 LINK C ALA A 20 N NH2 A 21 1555 1555 1.42 CRYST1 37.658 9.239 40.742 90.00 101.60 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 0.026555 0.000000 0.005451 0.00000 SCALE2 0.000000 0.108237 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025056 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 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 91 104 114 CONECT 103 91 105 115 CONECT 104 102 106 110 116 CONECT 105 103 107 111 117 CONECT 106 104 108 126 CONECT 107 105 109 126 CONECT 108 106 CONECT 109 107 CONECT 110 104 112 118 120 CONECT 111 105 113 119 121 CONECT 112 110 122 124 CONECT 113 111 123 125 CONECT 114 102 CONECT 115 103 CONECT 116 104 CONECT 117 105 CONECT 118 110 CONECT 119 111 CONECT 120 110 CONECT 121 111 CONECT 122 112 CONECT 123 113 CONECT 124 112 CONECT 125 113 CONECT 126 106 107 127 132 CONECT 127 126 128 130 131 CONECT 128 127 129 139 140 CONECT 129 128 CONECT 130 127 133 134 135 CONECT 131 127 136 137 138 CONECT 132 126 CONECT 133 130 CONECT 134 130 CONECT 135 130 CONECT 136 131 CONECT 137 131 CONECT 138 131 CONECT 139 128 CONECT 140 128 CONECT 143 177 CONECT 144 177 CONECT 177 143 144 178 183 CONECT 178 177 179 181 182 CONECT 179 178 180 190 CONECT 180 179 CONECT 181 178 184 185 186 CONECT 182 178 187 188 189 CONECT 183 177 CONECT 184 181 CONECT 185 181 CONECT 186 181 CONECT 187 182 CONECT 188 182 CONECT 189 182 CONECT 190 179 CONECT 192 207 CONECT 207 192 208 213 CONECT 208 207 209 211 212 CONECT 209 208 210 220 CONECT 210 209 CONECT 211 208 214 215 216 CONECT 212 208 217 218 219 CONECT 213 207 CONECT 214 211 CONECT 215 211 CONECT 216 211 CONECT 217 212 CONECT 218 212 CONECT 219 212 CONECT 220 209 CONECT 353 361 CONECT 361 353 362 363 CONECT 362 361 CONECT 363 361 CONECT 365 366 367 371 CONECT 366 365 368 369 370 CONECT 367 365 CONECT 368 366 CONECT 369 366 CONECT 370 366 CONECT 371 365 MASTER 225 0 9 1 0 0 0 6 149 1 157 2 END