HEADER DE NOVO PROTEIN 17-APR-26 12TJ TITLE HELLOB-GGVHCA - DE NOVO PEPTIDE WITH TERTIARY STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HELLOB-GGVHCA; 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 12TJ 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. 1.34 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) : 1.34 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.430 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 2909 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.098 REMARK 3 R VALUE (WORKING SET) : 0.094 REMARK 3 FREE R VALUE : 0.131 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.920 REMARK 3 FREE R VALUE TEST SET COUNT : 519 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 17.4300 - 2.1300 0.99 1163 134 0.0875 0.1160 REMARK 3 2 2.1300 - 1.6900 1.00 1191 133 0.1032 0.1373 REMARK 3 3 1.6900 - 1.4800 1.00 1153 126 0.0850 0.1350 REMARK 3 4 1.4700 - 1.3400 0.99 1207 126 0.1122 0.1785 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) : 0.094 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.173 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 7.81 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.66 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 : 0.008 169 REMARK 3 ANGLE : 1.463 241 REMARK 3 CHIRALITY : 0.060 21 REMARK 3 PLANARITY : 0.005 30 REMARK 3 DIHEDRAL : 20.260 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 12TJ 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_1000307247. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUN-23 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 : ESRF REMARK 200 BEAMLINE : ID23-1 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 PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2909 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.340 REMARK 200 RESOLUTION RANGE LOW (A) : 17.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.3500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.34 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.39 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 (%): 28.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: ACETONITRILE, METHANOL, WATER, SLOW REMARK 280 COOLING, 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 19.06850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 4.51900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 19.06850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 4.51900 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 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 114 DISTANCE = 6.35 ANGSTROMS REMARK 525 HOH A 115 DISTANCE = 6.84 ANGSTROMS REMARK 525 HOH A 116 DISTANCE = 7.16 ANGSTROMS REMARK 525 HOH A 117 DISTANCE = 8.69 ANGSTROMS REMARK 525 HOH A 118 DISTANCE = 9.45 ANGSTROMS DBREF 12TJ A 1 19 PDB 12TJ 12TJ 1 19 SEQRES 1 A 19 Z7Z ALA AIB LEU AIB ALA AIB LEU AIB GLN AIB LEU GLY SEQRES 2 A 19 GLY VAL HIS CYS ALA NH2 HET Z7Z A 1 23 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 HETNAM Z7Z BIPHENYL-4-CARBOXYLIC ACID HETNAM AIB ALPHA-AMINOISOBUTYRIC ACID HETNAM NH2 AMINO GROUP FORMUL 1 Z7Z C13 H10 O2 FORMUL 1 AIB 5(C4 H9 N O2) FORMUL 1 NH2 H2 N FORMUL 2 HOH *18(H2 O) HELIX 1 AA1 ALA A 2 LEU A 12 1 11 LINK C1 Z7Z A 1 N ALA A 2 1555 1555 1.42 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 1.33 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 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 1.32 LINK C BLEU A 8 N AIB A 9 1555 1555 1.33 LINK C AIB A 9 N GLN A 10 1555 1555 1.34 LINK C GLN A 10 N AIB A 11 1555 1555 1.34 LINK C AIB A 11 N LEU A 12 1555 1555 1.33 LINK C AALA A 18 N NH2 A 19 1555 1555 1.42 LINK C BALA A 18 N NH2 A 19 1555 1555 1.43 CRYST1 38.137 9.038 38.299 90.00 113.96 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 0.026221 0.000000 0.011653 0.00000 SCALE2 0.000000 0.110644 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028572 0.00000 CONECT 1 2 CONECT 2 1 3 24 CONECT 3 2 4 6 CONECT 4 3 5 15 CONECT 5 4 8 16 CONECT 6 3 7 17 CONECT 7 6 8 18 CONECT 8 5 7 9 CONECT 9 8 10 11 CONECT 10 9 12 19 CONECT 11 9 13 20 CONECT 12 10 14 21 CONECT 13 11 14 22 CONECT 14 12 13 23 CONECT 15 4 CONECT 16 5 CONECT 17 6 CONECT 18 7 CONECT 19 10 CONECT 20 11 CONECT 21 12 CONECT 22 13 CONECT 23 14 CONECT 24 2 CONECT 26 34 CONECT 34 26 35 40 CONECT 35 34 36 38 39 CONECT 36 35 37 47 48 CONECT 37 36 CONECT 38 35 41 42 43 CONECT 39 35 44 45 46 CONECT 40 34 CONECT 41 38 CONECT 42 38 CONECT 43 38 CONECT 44 39 CONECT 45 39 CONECT 46 39 CONECT 47 36 CONECT 48 36 CONECT 51 85 CONECT 52 85 CONECT 85 51 52 86 91 CONECT 86 85 87 89 90 CONECT 87 86 88 98 CONECT 88 87 CONECT 89 86 92 93 94 CONECT 90 86 95 96 97 CONECT 91 85 CONECT 92 89 CONECT 93 89 CONECT 94 89 CONECT 95 90 CONECT 96 90 CONECT 97 90 CONECT 98 87 CONECT 100 108 CONECT 108 100 109 114 CONECT 109 108 110 112 113 CONECT 110 109 111 121 122 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 122 110 CONECT 125 159 CONECT 126 159 CONECT 159 125 126 160 165 CONECT 160 159 161 163 164 CONECT 161 160 162 172 CONECT 162 161 CONECT 163 160 166 167 168 CONECT 164 160 169 170 171 CONECT 165 159 CONECT 166 163 CONECT 167 163 CONECT 168 163 CONECT 169 164 CONECT 170 164 CONECT 171 164 CONECT 172 161 CONECT 174 189 CONECT 189 174 190 195 CONECT 190 189 191 193 194 CONECT 191 190 192 202 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 318 334 CONECT 319 334 CONECT 334 318 319 335 336 CONECT 335 334 CONECT 336 334 MASTER 207 0 7 1 0 0 0 6 142 1 108 2 END