HEADER DE NOVO PROTEIN 22-APR-26 12YE TITLE HELLOB-GPVVIA - DE NOVO PEPTIDE WITH TERTIARY STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HELLOB-GPVVIA; 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 SYNTHETIC CONSTRUCT, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.GANATRA REVDAT 1 28-OCT-26 12YE 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. 1.07 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) : 1.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 5571 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.104 REMARK 3 R VALUE (WORKING SET) : 0.103 REMARK 3 FREE R VALUE : 0.112 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.150 REMARK 3 FREE R VALUE TEST SET COUNT : 1029 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 16.9000 - 2.0500 0.99 1336 148 0.1086 0.1142 REMARK 3 2 2.0400 - 1.6200 0.99 1296 146 0.0988 0.0928 REMARK 3 3 1.6200 - 1.4200 0.99 1332 154 0.1009 0.1349 REMARK 3 4 1.4200 - 1.2900 0.98 1250 144 0.1107 0.1228 REMARK 3 5 1.2900 - 1.2000 0.97 1328 152 0.0951 0.1215 REMARK 3 6 1.2000 - 1.1300 0.95 1257 131 0.0935 0.0965 REMARK 3 7 1.1300 - 1.0700 0.97 1308 154 0.1004 0.1107 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) : 0.005 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.897 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 7.66 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.94 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 : 0.011 171 REMARK 3 ANGLE : 1.810 243 REMARK 3 CHIRALITY : 0.096 21 REMARK 3 PLANARITY : 0.007 30 REMARK 3 DIHEDRAL : 23.619 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 12YE 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_1000307304. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-AUG-24 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) : 0.6888 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 : 5571 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.070 REMARK 200 RESOLUTION RANGE LOW (A) : 16.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.3400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.11 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 (%): 28.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.71 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 18.91900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 4.58500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 18.91900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 4.58500 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: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ALA A 18 O - C - N ANGL. DEV. = -20.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 12YE A 1 19 PDB 12YE 12YE 1 19 SEQRES 1 A 19 Z7Z ALA AIB LEU AIB ALA AIB LEU AIB GLN AIB LEU GLY SEQRES 2 A 19 PRO VAL VAL ILE ALA NH2 HET Z7Z A 1 46 HET AIB A 3 13 HET AIB A 5 13 HET AIB A 7 13 HET AIB A 9 13 HET AIB A 11 13 HET NH2 A 19 3 HET MOH A 101 6 HETNAM Z7Z BIPHENYL-4-CARBOXYLIC ACID HETNAM AIB ALPHA-AMINOISOBUTYRIC ACID HETNAM NH2 AMINO GROUP HETNAM MOH METHANOL FORMUL 1 Z7Z C13 H10 O2 FORMUL 1 AIB 5(C4 H9 N O2) FORMUL 1 NH2 H2 N FORMUL 2 MOH C H4 O FORMUL 3 HOH *5(H2 O) HELIX 1 AA1 ALA A 2 GLY A 13 1 12 LINK C1 AZ7Z A 1 N ALA A 2 1555 1555 1.43 LINK C1 BZ7Z A 1 N ALA A 2 1555 1555 1.41 LINK C ALA A 2 N AIB A 3 1555 1555 1.33 LINK C AIB A 3 N ALEU A 4 1555 1555 1.33 LINK C AIB A 3 N BLEU A 4 1555 1555 1.32 LINK C ALEU A 4 N AIB A 5 1555 1555 1.33 LINK C BLEU A 4 N AIB A 5 1555 1555 1.33 LINK C AIB A 5 N ALA A 6 1555 1555 1.33 LINK C ALA A 6 N AIB A 7 1555 1555 1.32 LINK C AIB A 7 N LEU A 8 1555 1555 1.32 LINK C LEU A 8 N AIB A 9 1555 1555 1.34 LINK C AIB A 9 N AGLN A 10 1555 1555 1.33 LINK C AIB A 9 N BGLN A 10 1555 1555 1.33 LINK C AIB A 9 N CGLN A 10 1555 1555 1.33 LINK C AGLN A 10 N AIB A 11 1555 1555 1.32 LINK C BGLN A 10 N AIB A 11 1555 1555 1.33 LINK C CGLN 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 18 N NH2 A 19 1555 1555 1.43 CRYST1 37.838 9.170 34.902 90.00 92.21 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 0.026428 0.000000 0.001020 0.00000 SCALE2 0.000000 0.109051 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028673 0.00000 CONECT 1 3 5 47 CONECT 2 4 6 47 CONECT 3 1 CONECT 4 2 CONECT 5 1 7 11 CONECT 6 2 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 1 2 CONECT 49 57 CONECT 57 49 58 63 CONECT 58 57 59 61 62 CONECT 59 58 60 70 71 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 71 59 CONECT 74 108 CONECT 75 108 CONECT 108 74 75 109 114 CONECT 109 108 110 112 113 CONECT 110 109 111 121 CONECT 111 110 CONECT 112 109 115 116 117 CONECT 113 109 118 119 120 CONECT 114 108 CONECT 115 112 CONECT 116 112 CONECT 117 112 CONECT 118 113 CONECT 119 113 CONECT 120 113 CONECT 121 110 CONECT 123 131 CONECT 131 123 132 137 CONECT 132 131 133 135 136 CONECT 133 132 134 144 CONECT 134 133 CONECT 135 132 138 139 140 CONECT 136 132 141 142 143 CONECT 137 131 CONECT 138 135 CONECT 139 135 CONECT 140 135 CONECT 141 136 CONECT 142 136 CONECT 143 136 CONECT 144 133 CONECT 146 163 CONECT 163 146 164 169 CONECT 164 163 165 167 168 CONECT 165 164 166 176 177 CONECT 165 178 CONECT 166 165 CONECT 167 164 170 171 172 CONECT 168 164 173 174 175 CONECT 169 163 CONECT 170 167 CONECT 171 167 CONECT 172 167 CONECT 173 168 CONECT 174 168 CONECT 175 168 CONECT 176 165 CONECT 177 165 CONECT 178 165 CONECT 182 227 CONECT 183 227 CONECT 184 227 CONECT 227 182 183 184 228 CONECT 227 233 CONECT 228 227 229 231 232 CONECT 229 228 230 240 CONECT 230 229 CONECT 231 228 234 235 236 CONECT 232 228 237 238 239 CONECT 233 227 CONECT 234 231 CONECT 235 231 CONECT 236 231 CONECT 237 232 CONECT 238 232 CONECT 239 232 CONECT 240 229 CONECT 333 341 CONECT 341 333 342 343 CONECT 342 341 CONECT 343 341 CONECT 345 346 347 348 349 CONECT 346 345 350 CONECT 347 345 CONECT 348 345 CONECT 349 345 CONECT 350 346 MASTER 212 0 8 1 0 0 0 6 133 1 140 2 END