HEADER ONCOPROTEIN 21-SEP-20 7AFW TITLE BETA-CATENIN IN COMPLEX WITH COMPOUND 6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATENIN BETA-1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BETA-CATENIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CTNNB1, CTNNB, OK/SW-CL.35, PRO2286; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FRAGMENT, ONCOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.BOETTCHER,D.KESSLER REVDAT 3 31-JAN-24 7AFW 1 REMARK REVDAT 2 19-MAY-21 7AFW 1 JRNL REVDAT 1 16-DEC-20 7AFW 0 JRNL AUTH D.KESSLER,M.MAYER,S.K.ZAHN,M.ZEEB,S.WOHRLE,A.BERGNER, JRNL AUTH 2 J.BRUCHHAUS,T.CIFTCI,G.DAHMANN,M.DETTLING,S.DOBEL,J.E.FUCHS, JRNL AUTH 3 L.GEIST,W.HELA,C.KOFINK,R.KOUSEK,F.MOSER,T.PUCHNER,K.RUMPEL, JRNL AUTH 4 M.SCHARNWEBER,P.WERNI,B.WOLKERSTORFER,D.BREITSPRECHER, JRNL AUTH 5 P.BAASKE,M.PEARSON,D.B.MCCONNELL,J.BOTTCHER JRNL TITL GETTING A GRIP ON THE UNDRUGGED: TARGETING BETA-CATENIN WITH JRNL TITL 2 FRAGMENT-BASED METHODS. JRNL REF CHEMMEDCHEM V. 16 1420 2021 JRNL REFN ESSN 1860-7187 JRNL PMID 33275320 JRNL DOI 10.1002/CMDC.202000839 REMARK 2 REMARK 2 RESOLUTION. 1.81 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.7 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 87.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 80.8 REMARK 3 NUMBER OF REFLECTIONS : 11045 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.281 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 551 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.81 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 21.05 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : NULL REMARK 3 BIN R VALUE (WORKING + TEST SET) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2498 REMARK 3 BIN FREE R VALUE : 0.3613 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 24 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1224 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 21 REMARK 3 SOLVENT ATOMS : 69 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.06 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.32370 REMARK 3 B22 (A**2) : 2.32370 REMARK 3 B33 (A**2) : -4.64750 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.350 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.222 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.192 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.210 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.188 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.872 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.811 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1261 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 1706 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 456 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 211 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1261 ; 10.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 174 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 1133 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 0.97 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.68 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 17.42 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): 70.298 -30.7596 22.2517 REMARK 3 T TENSOR REMARK 3 T11: -0.0392 T22: 0.03 REMARK 3 T33: -0.0939 T12: 0.0073 REMARK 3 T13: 0.0392 T23: 0.0358 REMARK 3 L TENSOR REMARK 3 L11: 0.7963 L22: 0.7771 REMARK 3 L33: 2.6755 L12: 0.3018 REMARK 3 L13: 0.4623 L23: 0.3635 REMARK 3 S TENSOR REMARK 3 S11: -0.0628 S12: -0.0536 S13: -0.0236 REMARK 3 S21: -0.0536 S22: -0.0037 S23: 0.3457 REMARK 3 S31: -0.0236 S32: 0.3457 S33: 0.0665 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7AFW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1292111332. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-NOV-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-003 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.541800 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC, XDS JAN 26, 201 REMARK 200 DATA SCALING SOFTWARE : AUTOPROC 1.1.7, AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11045 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.814 REMARK 200 RESOLUTION RANGE LOW (A) : 87.545 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 80.9 REMARK 200 DATA REDUNDANCY : 8.300 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : 0.07500 REMARK 200 FOR THE DATA SET : 24.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.81 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 24.5 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.82500 REMARK 200 R SYM FOR SHELL (I) : 0.82500 REMARK 200 FOR SHELL : 1.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 3SLA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3350, 100 MM BIS-TRIS BUFFER REMARK 280 PH 5.5 AND 0.2 M MAGNESIUM CHLORIDE, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 278K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-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 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 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: 8370 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 565 LIES ON A SPECIAL POSITION. 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 GLY A 139 REMARK 465 SER A 140 REMARK 465 ASN A 141 REMARK 465 TYR A 142 REMARK 465 GLN A 143 REMARK 465 ALA A 305 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 LEU A 286 -6.58 -59.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue R9Q A 401 DBREF 7AFW A 141 305 UNP P35222 CTNB1_HUMAN 141 305 SEQADV 7AFW GLY A 139 UNP P35222 EXPRESSION TAG SEQADV 7AFW SER A 140 UNP P35222 EXPRESSION TAG SEQRES 1 A 167 GLY SER ASN TYR GLN ASP ASP ALA GLU LEU ALA THR ARG SEQRES 2 A 167 ALA ILE PRO GLU LEU THR LYS LEU LEU ASN ASP GLU ASP SEQRES 3 A 167 GLN VAL VAL VAL ASN LYS ALA ALA VAL MET VAL HIS GLN SEQRES 4 A 167 LEU SER LYS LYS GLU ALA SER ARG HIS ALA ILE MET ARG SEQRES 5 A 167 SER PRO GLN MET VAL SER ALA ILE VAL ARG THR MET GLN SEQRES 6 A 167 ASN THR ASN ASP VAL GLU THR ALA ARG CYS THR ALA GLY SEQRES 7 A 167 THR LEU HIS ASN LEU SER HIS HIS ARG GLU GLY LEU LEU SEQRES 8 A 167 ALA ILE PHE LYS SER GLY GLY ILE PRO ALA LEU VAL LYS SEQRES 9 A 167 MET LEU GLY SER PRO VAL ASP SER VAL LEU PHE TYR ALA SEQRES 10 A 167 ILE THR THR LEU HIS ASN LEU LEU LEU HIS GLN GLU GLY SEQRES 11 A 167 ALA LYS MET ALA VAL ARG LEU ALA GLY GLY LEU GLN LYS SEQRES 12 A 167 MET VAL ALA LEU LEU ASN LYS THR ASN VAL LYS PHE LEU SEQRES 13 A 167 ALA ILE THR THR ASP CYS LEU GLN ILE LEU ALA HET R9Q A 401 21 HETNAM R9Q 3-[(2~{R})-4-METHYL-5-OXIDANYLIDENE-2,3-DIHYDRO-1,4- HETNAM 2 R9Q BENZOXAZEPIN-2-YL]BENZENECARBONITRILE FORMUL 2 R9Q C17 H14 N2 O2 FORMUL 3 HOH *69(H2 O) HELIX 1 AA1 ASP A 144 ASN A 161 1 18 HELIX 2 AA2 ASP A 164 LYS A 180 1 17 HELIX 3 AA3 LYS A 181 ARG A 190 1 10 HELIX 4 AA4 SER A 191 THR A 205 1 15 HELIX 5 AA5 ASP A 207 SER A 222 1 16 HELIX 6 AA6 HIS A 224 SER A 234 1 11 HELIX 7 AA7 GLY A 235 LEU A 244 1 10 HELIX 8 AA8 VAL A 248 GLN A 266 1 19 HELIX 9 AA9 GLY A 268 ALA A 276 1 9 HELIX 10 AB1 GLY A 277 LEU A 285 1 9 HELIX 11 AB2 LEU A 286 LYS A 288 5 3 HELIX 12 AB3 ASN A 290 LEU A 304 1 15 SITE 1 AC1 12 THR A 205 ASN A 206 VAL A 208 ALA A 211 SITE 2 AC1 12 LYS A 242 MET A 243 GLY A 245 SER A 246 SITE 3 AC1 12 PRO A 247 VAL A 248 PHE A 253 LYS A 292 CRYST1 53.453 53.453 87.545 90.00 90.00 120.00 P 3 2 1 6 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 0.018708 0.010801 0.000000 0.00000 SCALE2 0.000000 0.021602 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011423 0.00000