HEADER DE NOVO PROTEIN 09-OCT-24 9DWB TITLE CRYSTAL STRUCTURE OF FABLE, PEG 400 CONDITION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DE NOVO DESIGNED FABLE PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS PROTEIN DESIGN, FOUR-HELIX BUNDLE, APIXABAN, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.J.CORREY,J.S.FRASER REVDAT 1 20-AUG-25 9DWB 0 JRNL AUTH G.J.CORREY,J.S.FRASER JRNL TITL FRAGMENT SCREEN AGAINST ABLE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.68 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.1_5286 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.68 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 29243 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.770 REMARK 3 FREE R VALUE TEST SET COUNT : 1395 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 47.9800 - 3.6200 0.98 2825 162 0.1785 0.1994 REMARK 3 2 3.6200 - 2.8700 0.99 2760 153 0.2048 0.2343 REMARK 3 3 2.8700 - 2.5100 0.99 2801 155 0.1838 0.2095 REMARK 3 4 2.5100 - 2.2800 0.99 2783 136 0.1656 0.2109 REMARK 3 5 2.2800 - 2.1200 1.00 2794 135 0.1910 0.2566 REMARK 3 6 2.1200 - 1.9900 1.00 2804 136 0.1996 0.2265 REMARK 3 7 1.9900 - 1.8900 1.00 2746 148 0.2299 0.2846 REMARK 3 8 1.8900 - 1.8100 1.00 2804 117 0.2791 0.3038 REMARK 3 9 1.8100 - 1.7400 1.00 2794 111 0.3355 0.3755 REMARK 3 10 1.7400 - 1.6800 0.97 2737 142 0.3506 0.3855 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.820 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 2004 REMARK 3 ANGLE : 0.949 2701 REMARK 3 CHIRALITY : 0.045 309 REMARK 3 PLANARITY : 0.009 349 REMARK 3 DIHEDRAL : 12.905 729 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 9DWB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-OCT-24. REMARK 100 THE DEPOSITION ID IS D_1000288966. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.11585 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 JUN 30, 2023 REMARK 200 DATA SCALING SOFTWARE : XDS JUN 30, 2023 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29306 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.680 REMARK 200 RESOLUTION RANGE LOW (A) : 47.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 1.45200 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 2.8.3 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM SODIUM CHLORIDE, 100 MM CHES PH REMARK 280 9.5, 50% (V/V) PEG 400, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 292K 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 21.58850 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP B 31 78.67 -103.43 REMARK 500 REMARK 500 REMARK: NULL DBREF 9DWB A 1 126 PDB 9DWB 9DWB 1 126 DBREF 9DWB B 1 126 PDB 9DWB 9DWB 1 126 SEQRES 1 A 126 SER ILE LYS SER GLU PHE ALA GLU GLY ALA ALA VAL PHE SEQRES 2 A 126 VAL GLU GLY VAL ALA VAL PHE LEU THR MET MET ALA ALA SEQRES 3 A 126 PHE GLN ASN GLY ASP LYS GLU ALA VAL ALA GLN TYR LEU SEQRES 4 A 126 ALA ARG GLY ALA SER LEU TYR THR ARG HIS GLU GLU LEU SEQRES 5 A 126 LEU ASN ARG LEU LEU GLN LYS LEU ARG ARG GLU GLY ASN SEQRES 6 A 126 LYS GLU ALA VAL THR LEU MET ASN GLU PHE THR ALA THR SEQRES 7 A 126 PHE GLN THR GLY LYS SER LEU ALA ASN ALA LEU ILE ALA SEQRES 8 A 126 ALA PHE LYS ASN GLY ASP ASP ASP SER PHE GLU SER TYR SEQRES 9 A 126 LEU GLN ALA ILE TRP LYS VAL ILE ALA LYS MET ALA THR SEQRES 10 A 126 ILE LEU ASP GLN ILE ALA LYS ALA ILE SEQRES 1 B 126 SER ILE LYS SER GLU PHE ALA GLU GLY ALA ALA VAL PHE SEQRES 2 B 126 VAL GLU GLY VAL ALA VAL PHE LEU THR MET MET ALA ALA SEQRES 3 B 126 PHE GLN ASN GLY ASP LYS GLU ALA VAL ALA GLN TYR LEU SEQRES 4 B 126 ALA ARG GLY ALA SER LEU TYR THR ARG HIS GLU GLU LEU SEQRES 5 B 126 LEU ASN ARG LEU LEU GLN LYS LEU ARG ARG GLU GLY ASN SEQRES 6 B 126 LYS GLU ALA VAL THR LEU MET ASN GLU PHE THR ALA THR SEQRES 7 B 126 PHE GLN THR GLY LYS SER LEU ALA ASN ALA LEU ILE ALA SEQRES 8 B 126 ALA PHE LYS ASN GLY ASP ASP ASP SER PHE GLU SER TYR SEQRES 9 B 126 LEU GLN ALA ILE TRP LYS VAL ILE ALA LYS MET ALA THR SEQRES 10 B 126 ILE LEU ASP GLN ILE ALA LYS ALA ILE FORMUL 3 HOH *74(H2 O) HELIX 1 AA1 SER A 1 ASN A 29 1 29 HELIX 2 AA2 ASP A 31 GLY A 64 1 34 HELIX 3 AA3 ASN A 65 GLY A 82 1 18 HELIX 4 AA4 GLY A 82 ASN A 95 1 14 HELIX 5 AA5 ASP A 97 ILE A 126 1 30 HELIX 6 AA6 ILE B 2 ASN B 29 1 28 HELIX 7 AA7 ASP B 31 GLY B 64 1 34 HELIX 8 AA8 ASN B 65 GLY B 96 1 32 HELIX 9 AA9 ASP B 97 ILE B 126 1 30 CRYST1 54.218 43.177 60.864 90.00 114.27 90.00 P 1 21 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 0.018444 0.000000 0.008316 0.00000 SCALE2 0.000000 0.023160 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018023 0.00000 MASTER 218 0 0 9 0 0 0 6 2026 2 0 20 END