HEADER DE NOVO PROTEIN 01-JUN-20 6X8N TITLE CRYSTAL STRUCTURE OF H49A ABLE MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: DE NOVO DESIGNED ABLE 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; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET11 KEYWDS 4-HELIX BUNDLE, DE NOVO, LIGAND-BINDING, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.F.POLIZZI REVDAT 4 03-APR-24 6X8N 1 REMARK REVDAT 3 06-MAR-24 6X8N 1 REMARK REVDAT 2 23-SEP-20 6X8N 1 JRNL REVDAT 1 26-AUG-20 6X8N 0 JRNL AUTH N.F.POLIZZI,W.F.DEGRADO JRNL TITL A DEFINED STRUCTURAL UNIT ENABLES DE NOVO DESIGN OF JRNL TITL 2 SMALL-MOLECULE-BINDING PROTEINS. JRNL REF SCIENCE V. 369 1227 2020 JRNL REFN ESSN 1095-9203 JRNL PMID 32883865 JRNL DOI 10.1126/SCIENCE.ABB8330 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 32479 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.250 REMARK 3 FREE R VALUE TEST SET COUNT : 1381 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 43.8510 - 3.4467 0.95 3133 143 0.1782 0.2245 REMARK 3 2 3.4467 - 2.7358 0.96 3133 142 0.1781 0.2001 REMARK 3 3 2.7358 - 2.3900 0.96 3182 137 0.1749 0.1918 REMARK 3 4 2.3900 - 2.1715 0.93 3053 138 0.1872 0.2168 REMARK 3 5 2.1715 - 2.0159 0.96 3130 137 0.2128 0.2392 REMARK 3 6 2.0159 - 1.8970 0.94 3109 134 0.2577 0.3306 REMARK 3 7 1.8970 - 1.8020 0.95 3107 146 0.2759 0.3566 REMARK 3 8 1.8020 - 1.7236 0.95 3111 142 0.3019 0.3243 REMARK 3 9 1.7236 - 1.6572 0.94 3072 131 0.3417 0.4188 REMARK 3 10 1.6572 - 1.6000 0.93 3068 131 0.3819 0.4289 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.030 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.83 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 6X8N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1000247739. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-FEB-20 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 7.6 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) : 1.04457 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32545 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 43.851 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.9100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 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: PHENIX REMARK 200 STARTING MODEL: APO ABLE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.03 M CITRIC ACID, 0.07 M BIS-TRIS REMARK 280 PROPANE / PH 7.6 WITH 20% W/V POLYETHYLENE GLYCOL 3,350 (HAMPTON REMARK 280 PEG/ION 2 SCREEN CONDITION 40), VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 51 CD OE1 OE2 REMARK 470 GLN A 106 CD OE1 NE2 REMARK 470 LYS A 110 CG CD CE NZ REMARK 470 LYS A 114 CG CD CE NZ REMARK 470 GLU A 116 CG CD OE1 OE2 REMARK 470 ASP A 120 CG OD1 OD2 REMARK 470 LYS A 124 CG CD CE NZ REMARK 470 GLU B 33 CD OE1 OE2 REMARK 470 GLU B 58 CD OE1 OE2 REMARK 470 GLN B 106 CD OE1 NE2 REMARK 470 LYS B 114 CG CD CE NZ REMARK 470 GLU B 116 CG CD OE1 OE2 REMARK 470 THR B 117 OG1 CG2 REMARK 470 ASP B 120 CG OD1 OD2 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 331 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH B 330 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH B 331 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH B 332 DISTANCE = 6.23 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6W70 RELATED DB: PDB REMARK 900 APIXABAN-BOUND ABLE REMARK 900 RELATED ID: 6W6X RELATED DB: PDB REMARK 900 DRUG-FREE ABLE DBREF 6X8N A 1 126 PDB 6X8N 6X8N 1 126 DBREF 6X8N B 1 126 PDB 6X8N 6X8N 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 ALA 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 SEQRES 1 B 126 SER VAL LYS SER GLU TYR ALA GLU ALA ALA ALA VAL GLY SEQRES 2 B 126 GLN GLU ALA VAL ALA VAL PHE ASN THR MET LYS 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 LEU ALA SER LEU TYR THR ARG ALA GLU GLU LEU SEQRES 5 B 126 LEU ASN ARG ILE LEU GLU LYS ALA 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 ILE PHE ASN ALA MET VAL 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 LEU GLU LYS VAL THR ALA LYS GLY GLU THR SEQRES 10 B 126 LEU ALA ASP GLN ILE ALA LYS ALA LEU FORMUL 3 HOH *263(H2 O) HELIX 1 AA1 SER A 1 GLY A 30 1 30 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 HELIX 6 AA6 VAL B 2 GLY B 30 1 29 HELIX 7 AA7 ASP B 31 GLU B 63 1 33 HELIX 8 AA8 ASN B 65 ASN B 95 1 31 HELIX 9 AA9 ASP B 97 GLY B 115 1 19 HELIX 10 AB1 GLU B 116 LEU B 126 1 11 CRYST1 36.750 46.440 47.000 90.13 117.66 106.89 P 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 0.027211 0.008262 0.015808 0.00000 SCALE2 0.000000 0.022504 0.003691 0.00000 SCALE3 0.000000 0.000000 0.024343 0.00000