HEADER DE NOVO PROTEIN 08-OCT-24 7HJG TITLE PANDDA ANALYSIS GROUP DEPOSITION -- CRYSTAL STRUCTURE OF ABLE IN TITLE 2 COMPLEX WITH ZINC000001394131 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DE NOVO DESIGNED ABLE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: HIS6 PURIFICATION TAG (MHHHHHHENLYFQ) CLEAVED WITH TEV COMPND 6 PROTEASE 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; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET11A 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 7HJG 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. 1.57 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 15058 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 766 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 45.0700 - 2.6800 0.99 2946 151 0.1700 0.2391 REMARK 3 2 2.6800 - 2.1300 0.98 2855 181 0.1942 0.2380 REMARK 3 3 2.1300 - 1.8600 0.98 2854 166 0.2233 0.2918 REMARK 3 4 1.8600 - 1.6900 0.97 2869 132 0.2888 0.3666 REMARK 3 5 1.6900 - 1.5700 0.95 2768 136 0.3967 0.4155 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 37.460 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.05 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.92 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7HJG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-OCT-24. REMARK 100 THE DEPOSITION ID IS D_1001407550. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 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) : 1.11583 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS JUN 30, 2023 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.8.2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15089 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.570 REMARK 200 RESOLUTION RANGE LOW (A) : 47.230 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.57 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 1.60000 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 (%): 40.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 220 MM SODIUM MALONATE, 22% PEG 3350, REMARK 280 PH 5.0, VAPOR DIFFUSION, HANGING DROP, 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 23.61450 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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: 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 HE21 GLN A 80 O HOH A 310 1.58 REMARK 500 O HOH A 318 O HOH A 343 2.10 REMARK 500 O HOH A 376 O HOH A 380 2.12 REMARK 500 O ALA A 125 O HOH A 301 2.12 REMARK 500 REMARK 500 REMARK: NULL 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 415 DISTANCE = 5.88 ANGSTROMS DBREF 7HJG A 1 126 PDB 7HJG 7HJG 1 126 SEQRES 1 A 126 SER VAL LYS SER GLU TYR ALA GLU ALA ALA ALA VAL GLY SEQRES 2 A 126 GLN GLU ALA VAL ALA VAL PHE ASN THR MET LYS 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 LEU ALA SER LEU TYR THR ARG HIS GLU GLU LEU SEQRES 5 A 126 LEU ASN ARG ILE LEU GLU LYS ALA 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 ILE PHE ASN ALA MET VAL 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 LEU GLU LYS VAL THR ALA LYS GLY GLU THR SEQRES 10 A 126 LEU ALA ASP GLN ILE ALA LYS ALA LEU HET 0NX A 201 22 HETNAM 0NX (5-PHENYL-1,2-OXAZOL-3-YL)METHANOL FORMUL 2 0NX C10 H9 N O2 FORMUL 3 HOH *115(H2 O) HELIX 1 AA1 SER A 1 ASN A 29 1 29 HELIX 2 AA2 ASP A 31 GLU A 63 1 33 HELIX 3 AA3 ASN A 65 ASN A 95 1 31 HELIX 4 AA4 ASP A 97 GLY A 115 1 19 HELIX 5 AA5 GLY A 115 LEU A 126 1 12 CRYST1 26.167 47.229 46.314 90.00 103.32 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 0.038216 0.000000 0.009048 0.00000 SCALE2 0.000000 0.021173 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022189 0.00000 CONECT 3248 3249 3261 CONECT 3249 3248 3250 3262 3263 CONECT 3250 3249 3251 3252 CONECT 3251 3250 3254 3264 CONECT 3252 3250 3253 CONECT 3253 3252 3254 CONECT 3254 3251 3253 3255 CONECT 3255 3254 3256 3257 CONECT 3256 3255 3260 3265 CONECT 3257 3255 3258 3266 CONECT 3258 3257 3259 3267 CONECT 3259 3258 3260 3268 CONECT 3260 3256 3259 3269 CONECT 3261 3248 CONECT 3262 3249 CONECT 3263 3249 CONECT 3264 3251 CONECT 3265 3256 CONECT 3266 3257 CONECT 3267 3258 CONECT 3268 3259 CONECT 3269 3260 MASTER 214 0 1 5 0 0 0 6 1099 1 22 10 END