HEADER DE NOVO PROTEIN 21-JUL-25 9PPU TITLE BETA-SANDWICH FORMING METALLOPEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DE NOVO DESIGNED METALLOPEPTIDE; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DE NOVO DESIGNED METALLOPEPTIDE; COMPND 7 CHAIN: A; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630 KEYWDS BETA-SANDWICH, COPPER, METALLOPEPTIDE, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR V.T.DANG,A.I.NGUYEN REVDAT 1 22-APR-26 9PPU 0 JRNL AUTH V.T.DANG,A.DRENA,J.TELSER,L.WOFFORD,A.I.NGUYEN JRNL TITL A BIS-MACROCYLIC PEPTIDE LIGAND MIMICKING THE BETA-SANDWICH JRNL TITL 2 ACTIVE SITE OF MULTICOPPER OXIDASES. JRNL REF DALTON TRANS 2026 JRNL REFN ESSN 1477-9234 JRNL PMID 41969027 JRNL DOI 10.1039/D6DT00494F REMARK 2 REMARK 2 RESOLUTION. 1.49 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) : 1.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 14061 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.159 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.130 REMARK 3 FREE R VALUE TEST SET COUNT : 1425 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 32.7000 - 3.2100 0.99 1288 146 0.1536 0.2093 REMARK 3 2 3.2100 - 2.5500 1.00 1295 151 0.1649 0.1856 REMARK 3 3 2.5500 - 2.2300 1.00 1307 145 0.1777 0.2136 REMARK 3 4 2.2300 - 2.0200 1.00 1299 146 0.1464 0.1634 REMARK 3 5 2.0200 - 1.8800 1.00 1279 148 0.1262 0.1824 REMARK 3 6 1.8800 - 1.7700 1.00 1306 149 0.1452 0.1675 REMARK 3 7 1.7700 - 1.6800 1.00 1323 143 0.1476 0.1749 REMARK 3 8 1.6800 - 1.6100 1.00 1283 144 0.1434 0.1456 REMARK 3 9 1.6100 - 1.5400 0.97 1262 143 0.1509 0.1989 REMARK 3 10 1.5400 - 1.4900 0.77 994 110 0.2091 0.2130 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.143 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.932 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.63 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 : 0.009 249 REMARK 3 ANGLE : 1.346 317 REMARK 3 CHIRALITY : 0.097 28 REMARK 3 PLANARITY : 0.005 34 REMARK 3 DIHEDRAL : 13.416 80 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 9PPU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JUL-25. REMARK 100 THE DEPOSITION ID IS D_1000298139. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-SEP-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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) : 1.362460 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 : 148327 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.490 REMARK 200 RESOLUTION RANGE LOW (A) : 32.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 18.90 REMARK 200 R MERGE (I) : 0.12560 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.3100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 0.37020 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.060 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX 1.20.1_4487 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 6.0 M AMMONIUM NITRATE, 0.1 M BIS TRIS REMARK 280 PROPANE PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 26.74650 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 20.66000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 20.66000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 13.37325 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 20.66000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 20.66000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 40.11975 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 20.66000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 20.66000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 13.37325 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 20.66000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 20.66000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 40.11975 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 26.74650 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 2310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 NE ORN B 5 O HIS B 4 2.13 REMARK 500 O HOH B 207 O HOH B 224 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 101 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 2 NE2 REMARK 620 2 HIS A 4 NE2 93.3 REMARK 620 3 HIS A 8 ND1 171.0 85.4 REMARK 620 4 HIS A 10 NE2 95.2 158.4 89.2 REMARK 620 5 FMT A 103 O2 88.8 97.5 82.6 102.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU B 101 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 4 NE2 REMARK 620 2 HIS B 8 ND1 89.1 REMARK 620 3 HIS B 10 NE2 164.8 90.0 REMARK 620 4 HIS A 2 NE2 92.7 170.3 90.7 REMARK 620 5 HOH A 206 O 101.4 87.1 93.7 83.1 REMARK 620 N 1 2 3 4 DBREF 9PPU B 5 4 PDB 9PPU 9PPU 5 4 DBREF 9PPU A 11 10 PDB 9PPU 9PPU 11 10 SEQRES 1 B 12 ORN LYS ILE HIS TRP HIS ORN GLN PHE HIS SER HIS SEQRES 1 A 12 ORN GLN LEU HIS SER HIS ORN LYS PHE HIS LEU HIS HET ORN B 5 8 HET ORN B 11 8 HET ORN A 11 8 HET ORN A 5 8 HET CU B 101 1 HET FMT B 102 3 HET ACA B 103 8 HET CU A 101 1 HET FMT A 102 3 HET FMT A 103 3 HET FMT A 104 3 HETNAM ORN L-ORNITHINE HETNAM CU COPPER (II) ION HETNAM FMT FORMIC ACID HETNAM ACA 6-AMINOHEXANOIC ACID HETSYN ACA AMINOCAPROIC ACID FORMUL 1 ORN 4(C5 H12 N2 O2) FORMUL 3 CU 2(CU 2+) FORMUL 4 FMT 4(C H2 O2) FORMUL 5 ACA C6 H13 N O2 FORMUL 10 HOH *41(H2 O) SHEET 1 AA1 2 LYS B 6 TRP B 9 0 SHEET 2 AA1 2 PHE B 1 HIS B 4 -1 O HIS B 4 N LYS B 6 SHEET 1 AA2 2 GLN A 12 SER A 3 0 SHEET 2 AA2 2 PHE A 7 HIS A 10 -1 O HIS A 8 N HIS A 2 LINK C HIS B 4 NE ORN B 5 1555 1555 1.43 LINK C ORN B 5 N LYS B 6 1555 1555 1.33 LINK C HIS B 10 NE ORN B 11 1555 1555 1.43 LINK C ORN B 11 N GLN B 12 1555 1555 1.33 LINK CD GLN B 12 N ACA B 103 1555 1555 1.43 LINK C ACA B 103 NZ LYS A 6 1555 1555 1.43 LINK C HIS A 4 NE ORN A 5 1555 1555 1.43 LINK C ORN A 5 N LYS A 6 1555 1555 1.33 LINK C HIS A 10 NE ORN A 11 1555 1555 1.43 LINK C ORN A 11 N GLN A 12 1555 1555 1.34 LINK NE2 HIS B 2 CU CU A 101 1555 1555 2.13 LINK NE2 HIS B 4 CU CU B 101 1555 1555 1.99 LINK ND1 HIS B 8 CU CU B 101 1555 1555 2.26 LINK NE2 HIS B 10 CU CU B 101 1555 1555 2.08 LINK CU CU B 101 NE2 HIS A 2 1555 1555 2.21 LINK CU CU B 101 O HOH A 206 1555 1555 2.38 LINK NE2 HIS A 4 CU CU A 101 1555 1555 2.03 LINK ND1 HIS A 8 CU CU A 101 1555 1555 2.37 LINK NE2 HIS A 10 CU CU A 101 1555 1555 2.03 LINK CU CU A 101 O2 FMT A 103 1555 1555 2.48 CRYST1 41.320 41.320 53.493 90.00 90.00 90.00 P 41 21 2 8 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 0.024201 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024201 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018694 0.00000 CONECT 1 2 CONECT 2 1 3 7 CONECT 3 2 4 CONECT 4 3 5 CONECT 5 4 6 CONECT 6 5 105 CONECT 7 2 8 9 CONECT 8 7 CONECT 9 7 CONECT 32 228 CONECT 52 65 CONECT 59 228 CONECT 60 61 CONECT 61 60 62 66 CONECT 62 61 63 CONECT 63 62 64 CONECT 64 63 65 CONECT 65 52 64 CONECT 66 61 67 68 CONECT 67 66 CONECT 68 66 CONECT 74 239 CONECT 96 240 CONECT 105 6 CONECT 112 228 CONECT 114 115 CONECT 115 114 116 120 CONECT 116 115 117 CONECT 117 116 118 CONECT 118 117 119 CONECT 119 118 219 CONECT 120 115 121 122 CONECT 121 120 CONECT 122 120 CONECT 148 228 CONECT 163 176 CONECT 170 240 CONECT 171 172 CONECT 172 171 173 177 CONECT 173 172 174 CONECT 174 173 175 CONECT 175 174 176 CONECT 176 163 175 CONECT 177 172 178 179 CONECT 178 177 CONECT 179 177 CONECT 187 232 CONECT 205 240 CONECT 219 119 CONECT 226 240 CONECT 228 32 59 112 148 CONECT 228 281 CONECT 229 230 231 CONECT 230 229 CONECT 231 229 CONECT 232 187 233 234 CONECT 233 232 CONECT 234 232 235 CONECT 235 234 236 CONECT 236 235 237 CONECT 237 236 238 CONECT 238 237 239 CONECT 239 74 238 CONECT 240 96 170 205 226 CONECT 240 246 CONECT 241 242 243 CONECT 242 241 CONECT 243 241 CONECT 244 245 246 CONECT 245 244 CONECT 246 240 244 CONECT 247 248 249 CONECT 248 247 CONECT 249 247 CONECT 281 228 MASTER 252 0 11 0 4 0 0 6 282 2 75 2 END