HEADER DE NOVO PROTEIN 15-MAR-23 8GJG TITLE DE NOVO DESIGN OF HIGH-AFFINITY PROTEIN BINDERS TO BIOACTIVE HELICAL TITLE 2 PEPTIDES COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUC_A04_0005 BINDER; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: GLUC_A04_0005; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 9 ORGANISM_TAXID: 32630 KEYWDS ALPHA-HELICAL PEPTIDES, PROTEIN DESIGN, DIFFUSION, DEEP LEARNING, DE KEYWDS 2 NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.J.Y.LEUNG,A.K.BERA,S.V.TORRES,D.BAKER,A.KANG REVDAT 2 14-FEB-24 8GJG 1 JRNL REVDAT 1 10-JAN-24 8GJG 0 JRNL AUTH S.VAZQUEZ TORRES,P.J.Y.LEUNG,P.VENKATESH,I.D.LUTZ,F.HINK, JRNL AUTH 2 H.H.HUYNH,J.BECKER,A.H.YEH,D.JUERGENS,N.R.BENNETT, JRNL AUTH 3 A.N.HOOFNAGLE,E.HUANG,M.J.MACCOSS,M.EXPOSIT,G.R.LEE, JRNL AUTH 4 A.K.BERA,A.KANG,J.DE LA CRUZ,P.M.LEVINE,X.LI,M.LAMB, JRNL AUTH 5 S.R.GERBEN,A.MURRAY,P.HEINE,E.N.KORKMAZ,J.NIVALA,L.STEWART, JRNL AUTH 6 J.L.WATSON,J.M.ROGERS,D.BAKER JRNL TITL DE NOVO DESIGN OF HIGH-AFFINITY BINDERS OF BIOACTIVE HELICAL JRNL TITL 2 PEPTIDES. JRNL REF NATURE V. 626 435 2024 JRNL REFN ESSN 1476-4687 JRNL PMID 38109936 JRNL DOI 10.1038/S41586-023-06953-1 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_4761 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 63.09 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.310 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 15425 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 775 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 63.0900 - 3.5500 0.98 2511 143 0.1707 0.2117 REMARK 3 2 3.5500 - 2.8100 0.98 2491 125 0.2401 0.2705 REMARK 3 3 2.8100 - 2.4600 0.99 2477 131 0.2415 0.2972 REMARK 3 4 2.4600 - 2.2300 0.99 2493 132 0.2517 0.3139 REMARK 3 5 2.2300 - 2.0700 0.96 2402 133 0.3190 0.3587 REMARK 3 6 2.0700 - 1.9500 0.90 2276 111 0.4225 0.4472 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) : 0.332 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.571 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 53.78 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 68.56 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 : 0.002 1555 REMARK 3 ANGLE : 0.435 2078 REMARK 3 CHIRALITY : 0.030 233 REMARK 3 PLANARITY : 0.004 267 REMARK 3 DIHEDRAL : 15.492 634 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESSEQ 1:162) REMARK 3 ORIGIN FOR THE GROUP (A): 4.4854 1.0991 13.6258 REMARK 3 T TENSOR REMARK 3 T11: 0.4023 T22: 0.3179 REMARK 3 T33: 0.4201 T12: 0.0454 REMARK 3 T13: -0.1233 T23: 0.0343 REMARK 3 L TENSOR REMARK 3 L11: 6.5591 L22: 3.1294 REMARK 3 L33: 6.6738 L12: 3.2904 REMARK 3 L13: -5.6603 L23: -2.8379 REMARK 3 S TENSOR REMARK 3 S11: -0.0525 S12: 0.1634 S13: -0.0741 REMARK 3 S21: -0.1361 S22: 0.0979 S23: -0.0785 REMARK 3 S31: 0.0029 S32: -0.2074 S33: -0.0475 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN B AND RESSEQ 173:197) REMARK 3 ORIGIN FOR THE GROUP (A): 6.0992 11.9360 19.3800 REMARK 3 T TENSOR REMARK 3 T11: 0.6171 T22: 0.5324 REMARK 3 T33: 0.6376 T12: 0.0140 REMARK 3 T13: 0.0100 T23: -0.1409 REMARK 3 L TENSOR REMARK 3 L11: 3.5867 L22: 0.8531 REMARK 3 L33: 7.9438 L12: -0.2022 REMARK 3 L13: -2.2938 L23: 0.2258 REMARK 3 S TENSOR REMARK 3 S11: 0.1837 S12: -0.1561 S13: 0.4127 REMARK 3 S21: -0.1366 S22: -0.0516 S23: -0.0933 REMARK 3 S31: -1.1912 S32: 0.1195 S33: -0.0743 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 8GJG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-MAR-23. REMARK 100 THE DEPOSITION ID IS D_1000273036. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15425 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 63.090 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 2.00100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.600 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 (%): 47.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.9 M HALOGENS, 0.1 M TRIS- BICINE PH REMARK 280 8.5 BUFFER, AND 37.5% OF 25% V/V MPD; 25% PEG 1000; 25% W/V PEG REMARK 280 3350 MIXTURE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 22.95000 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -2 REMARK 465 SER A -1 REMARK 465 GLY A 0 REMARK 465 LYS A 163 REMARK 465 GLU A 164 REMARK 465 PHE A 165 REMARK 465 ARG A 166 REMARK 465 LYS A 167 REMARK 465 LEU A 168 REMARK 465 HIS A 169 REMARK 465 SER A 170 REMARK 465 GLN A 171 DBREF 8GJG A -2 171 PDB 8GJG 8GJG -2 171 DBREF 8GJG B 173 197 PDB 8GJG 8GJG 173 197 SEQRES 1 A 174 MET SER GLY MET LEU ASP GLU LEU PHE SER LEU LEU ASN SEQRES 2 A 174 LYS MET PHE GLU LEU SER ASP LYS TYR ARG GLU LEU ARG SEQRES 3 A 174 LYS GLU LEU ARG LYS ALA ILE GLU SER GLY ALA PRO GLU SEQRES 4 A 174 GLU GLU LEU ARG GLU LEU LEU GLU LYS MET LEU GLU ILE SEQRES 5 A 174 ALA LYS LYS LEU LEU GLU LEU THR LYS GLU LEU LYS LYS SEQRES 6 A 174 LEU VAL GLU ASP VAL LEU LYS ASN ASN PRO ASP PRO VAL SEQRES 7 A 174 GLU ARG ALA LYS ALA VAL LEU LEU TYR ALA VAL GLY VAL SEQRES 8 A 174 HIS ILE LEU TYR SER GLU SER SER GLU LEU GLU VAL ILE SEQRES 9 A 174 ALA GLU ARG LEU GLY PHE LYS ASP ILE ALA GLU LYS ALA SEQRES 10 A 174 LYS GLU ILE ALA ASP LYS ALA ARG GLU LEU LYS GLU GLU SEQRES 11 A 174 VAL LYS ARG LYS LEU ARG GLU ILE ARG GLU GLU VAL PRO SEQRES 12 A 174 ASP PRO GLU ILE ARG LYS ALA ALA GLU GLU ALA ILE GLU SEQRES 13 A 174 MET LEU GLU SER ASN ASP LYS ARG LEU LYS GLU PHE ARG SEQRES 14 A 174 LYS LEU HIS SER GLN SEQRES 1 B 25 GLY PHE THR SER ASP TYR SER LYS TYR LEU ASP SER ARG SEQRES 2 B 25 ARG ALA GLN ASP PHE VAL GLN TRP LEU MET ASN THR FORMUL 3 HOH *26(H2 O) HELIX 1 AA1 MET A 1 SER A 32 1 32 HELIX 2 AA2 PRO A 35 ASN A 71 1 37 HELIX 3 AA3 ASP A 73 GLY A 106 1 34 HELIX 4 AA4 PHE A 107 VAL A 139 1 33 HELIX 5 AA5 ASP A 141 LEU A 162 1 22 HELIX 6 AA6 SER B 176 MET B 195 1 20 CRYST1 37.793 45.900 63.607 90.00 97.31 90.00 P 1 21 1 2 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 0.026460 0.000000 0.003395 0.00000 SCALE2 0.000000 0.021786 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015850 0.00000