HEADER GENE REGULATION 13-DEC-22 8FH1 TITLE CRYSTAL STRUCTURE OF MUTANT ANDROGEN RECEPTOR LIGAND BINDING DOMAIN TITLE 2 F877L/T878A WITH DHT COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANDROGEN RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DIHYDROTESTOSTERONE RECEPTOR,NUCLEAR RECEPTOR SUBFAMILY 3 COMPND 5 GROUP C MEMBER 4; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: AR, DHTR, NR3C4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS AR, ANDROGEN RECEPTOR, DHT, STEROID RECEPTOR, GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR S.K.DOAMEKPOR,L.TONG REVDAT 1 12-APR-23 8FH1 0 JRNL AUTH S.K.DOAMEKPOR,P.PENG,R.XU,L.MA,Y.TONG,L.TONG JRNL TITL A PARTIALLY OPEN CONFORMATION OF AN ANDROGEN RECEPTOR JRNL TITL 2 LIGAND-BINDING DOMAIN WITH DRUG-RESISTANCE MUTATIONS. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 79 95 2023 JRNL REFN ESSN 2053-230X JRNL PMID 36995121 JRNL DOI 10.1107/S2053230X23002224 REMARK 2 REMARK 2 RESOLUTION. 1.69 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX V1.2 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) : 1.69 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 30878 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.470 REMARK 3 FREE R VALUE TEST SET COUNT : 1998 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 49.0300 - 4.0800 1.00 2224 154 0.1645 0.1866 REMARK 3 2 4.0800 - 3.2400 1.00 2117 147 0.1802 0.2068 REMARK 3 3 3.2400 - 2.8300 1.00 2086 144 0.2144 0.2489 REMARK 3 4 2.8300 - 2.5700 1.00 2076 143 0.2111 0.2483 REMARK 3 5 2.5700 - 2.3900 1.00 2084 144 0.2060 0.2310 REMARK 3 6 2.3900 - 2.2500 1.00 2044 143 0.2096 0.2454 REMARK 3 7 2.2500 - 2.1300 1.00 2055 142 0.2099 0.2634 REMARK 3 8 2.1300 - 2.0400 1.00 2054 142 0.2100 0.2190 REMARK 3 9 2.0400 - 1.9600 1.00 2030 141 0.2224 0.2701 REMARK 3 10 1.9600 - 1.9000 0.99 2027 141 0.2903 0.3287 REMARK 3 11 1.9000 - 1.8400 1.00 2063 140 0.3031 0.3483 REMARK 3 12 1.8400 - 1.7800 1.00 2022 141 0.3008 0.3461 REMARK 3 13 1.7800 - 1.7400 1.00 2033 140 0.3166 0.3454 REMARK 3 14 1.7400 - 1.6900 0.96 1965 136 0.3507 0.3420 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.960 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 2048 REMARK 3 ANGLE : 1.085 2773 REMARK 3 CHIRALITY : 0.077 306 REMARK 3 PLANARITY : 0.009 346 REMARK 3 DIHEDRAL : 5.148 267 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 8FH1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-DEC-22. REMARK 100 THE DEPOSITION ID IS D_1000270737. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-OCT-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 58240 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.690 REMARK 200 RESOLUTION RANGE LOW (A) : 200.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 3.850 REMARK 200 R MERGE (I) : 0.03800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.9300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.90800 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 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.4-0.8 M SODIUM CITRATE, 0.1 M HEPES REMARK 280 PH 7.5, 20% (V/V) ETHYLENE GLYCOL, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 28.17550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.58250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.03200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.58250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.17550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.03200 REMARK 290 SMTRY3 4 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 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 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 SER A 663 REMARK 465 HIS A 664 REMARK 465 ILE A 665 REMARK 465 GLU A 666 REMARK 465 GLY A 667 REMARK 465 TYR A 668 REMARK 465 GLU A 669 REMARK 465 CYS A 670 REMARK 465 GLN A 671 REMARK 465 LYS A 846 REMARK 465 ARG A 847 REMARK 465 LYS A 848 REMARK 465 ASN A 849 REMARK 465 PRO A 850 REMARK 465 THR A 851 REMARK 465 THR A 919 REMARK 465 GLN A 920 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 ASN A 759 -0.62 67.53 REMARK 500 SER A 760 28.40 96.85 REMARK 500 REMARK 500 REMARK: NULL DBREF 8FH1 A 663 920 UNP P10275 ANDR_HUMAN 663 920 SEQADV 8FH1 LEU A 877 UNP P10275 PHE 877 ENGINEERED MUTATION SEQADV 8FH1 ALA A 878 UNP P10275 THR 878 ENGINEERED MUTATION SEQRES 1 A 258 SER HIS ILE GLU GLY TYR GLU CYS GLN PRO ILE PHE LEU SEQRES 2 A 258 ASN VAL LEU GLU ALA ILE GLU PRO GLY VAL VAL CYS ALA SEQRES 3 A 258 GLY HIS ASP ASN ASN GLN PRO ASP SER PHE ALA ALA LEU SEQRES 4 A 258 LEU SER SER LEU ASN GLU LEU GLY GLU ARG GLN LEU VAL SEQRES 5 A 258 HIS VAL VAL LYS TRP ALA LYS ALA LEU PRO GLY PHE ARG SEQRES 6 A 258 ASN LEU HIS VAL ASP ASP GLN MET ALA VAL ILE GLN TYR SEQRES 7 A 258 SER TRP MET GLY LEU MET VAL PHE ALA MET GLY TRP ARG SEQRES 8 A 258 SER PHE THR ASN VAL ASN SER ARG MET LEU TYR PHE ALA SEQRES 9 A 258 PRO ASP LEU VAL PHE ASN GLU TYR ARG MET HIS LYS SER SEQRES 10 A 258 ARG MET TYR SER GLN CYS VAL ARG MET ARG HIS LEU SER SEQRES 11 A 258 GLN GLU PHE GLY TRP LEU GLN ILE THR PRO GLN GLU PHE SEQRES 12 A 258 LEU CYS MET LYS ALA LEU LEU LEU PHE SER ILE ILE PRO SEQRES 13 A 258 VAL ASP GLY LEU LYS ASN GLN LYS PHE PHE ASP GLU LEU SEQRES 14 A 258 ARG MET ASN TYR ILE LYS GLU LEU ASP ARG ILE ILE ALA SEQRES 15 A 258 CYS LYS ARG LYS ASN PRO THR SER CYS SER ARG ARG PHE SEQRES 16 A 258 TYR GLN LEU THR LYS LEU LEU ASP SER VAL GLN PRO ILE SEQRES 17 A 258 ALA ARG GLU LEU HIS GLN LEU ALA PHE ASP LEU LEU ILE SEQRES 18 A 258 LYS SER HIS MET VAL SER VAL ASP PHE PRO GLU MET MET SEQRES 19 A 258 ALA GLU ILE ILE SER VAL GLN VAL PRO LYS ILE LEU SER SEQRES 20 A 258 GLY LYS VAL LYS PRO ILE TYR PHE HIS THR GLN HET DHT A1001 51 HET SO4 A1002 5 HETNAM DHT 5-ALPHA-DIHYDROTESTOSTERONE HETNAM SO4 SULFATE ION FORMUL 2 DHT C19 H30 O2 FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *61(H2 O) HELIX 1 AA1 PRO A 672 GLU A 682 1 11 HELIX 2 AA2 SER A 697 ALA A 722 1 26 HELIX 3 AA3 GLY A 725 LEU A 729 5 5 HELIX 4 AA4 HIS A 730 VAL A 758 1 29 HELIX 5 AA5 ASN A 772 SER A 779 1 8 HELIX 6 AA6 MET A 781 LEU A 798 1 18 HELIX 7 AA7 THR A 801 PHE A 814 1 14 HELIX 8 AA8 ASN A 824 CYS A 845 1 22 HELIX 9 AA9 CYS A 853 LYS A 884 1 32 HELIX 10 AB1 LYS A 884 SER A 889 1 6 HELIX 11 AB2 PRO A 893 GLN A 903 1 11 HELIX 12 AB3 GLN A 903 SER A 909 1 7 SHEET 1 AA1 2 LEU A 763 ALA A 766 0 SHEET 2 AA1 2 LEU A 769 PHE A 771 -1 O PHE A 771 N LEU A 763 SHEET 1 AA2 2 ILE A 816 PRO A 818 0 SHEET 2 AA2 2 VAL A 912 PRO A 914 -1 O LYS A 913 N ILE A 817 CRYST1 56.351 66.064 73.165 90.00 90.00 90.00 P 21 21 21 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 0.017746 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015137 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013668 0.00000