PDB Short entry for 2AX9 HEADER TRANSCRIPTION 03-SEP-05 2AX9 TITLE CRYSTAL STRUCTURE OF THE ANDROGEN RECEPTOR LIGAND BINDING DOMAIN IN TITLE 2 COMPLEX WITH R-3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANDROGEN RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LIGAND BINDING DOMAIN (RESIDUES 663-918); 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: AR; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21DE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX6P-1 KEYWDS TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR C.E.BOHL,D.D.MILLER,J.CHEN,C.E.BELL,J.T.DALTON REVDAT 5 23-AUG-23 2AX9 1 REMARK REVDAT 4 11-OCT-17 2AX9 1 REMARK REVDAT 3 24-FEB-09 2AX9 1 VERSN REVDAT 2 22-NOV-05 2AX9 1 JRNL REVDAT 1 20-SEP-05 2AX9 0 JRNL AUTH C.E.BOHL,D.D.MILLER,J.CHEN,C.E.BELL,J.T.DALTON JRNL TITL STRUCTURAL BASIS FOR ACCOMMODATION OF NONSTEROIDAL LIGANDS JRNL TITL 2 IN THE ANDROGEN RECEPTOR JRNL REF J.BIOL.CHEM. V. 280 37747 2005 JRNL REFN ISSN 0021-9258 JRNL PMID 16129672 JRNL DOI 10.1074/JBC.M507464200 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.88 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 170785.370 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 31085 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 SET) : 0.224 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3115 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.75 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4556 REMARK 3 BIN R VALUE (WORKING SET) : 0.3210 REMARK 3 BIN FREE R VALUE : 0.3390 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 525 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.015 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1951 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 21 REMARK 3 SOLVENT ATOMS : 167 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.00000 REMARK 3 B22 (A**2) : -0.93000 REMARK 3 B33 (A**2) : -1.07000 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) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.25 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.28 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 18.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.750 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.230 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.700 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.280 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.240 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 48.50 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 PARAMETER FILE 3 : HBR.PARAM REMARK 3 PARAMETER FILE 4 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : HBR.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2AX9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-SEP-05. REMARK 100 THE DEPOSITION ID IS D_1000034423. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-FEB-05 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31121 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 18.880 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.270 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 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 <I/SIGMA(I)> 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: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1Z95 (W741L AR LBD-R-BICALUTAMIDE REMARK 200 COMPLEX) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5 M SODIUM CITRATE, 0.1 M HEPES, PH REMARK 280 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 27.68950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.52750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.00600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.52750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.68950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.00600 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 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 ILE A 664 REMARK 465 GLU A 665 REMARK 465 GLY A 666 REMARK 465 TYR A 667 REMARK 465 GLU A 668 REMARK 465 CYS A 669 REMARK 465 GLN A 670 REMARK 465 PRO A 671 REMARK 465 CYS A 844 REMARK 465 LYS A 845 REMARK 465 ARG A 846 REMARK 465 LYS A 847 REMARK 465 ASN A 848 REMARK 465 PRO A 849 REMARK 465 THR A 850 REMARK 465 SER A 851 REMARK 465 THR A 918 REMARK 465 GLN A 919 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 768 71.27 -153.32 REMARK 500 PHE A 813 44.01 -106.91 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 BHM A 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2AX6 RELATED DB: PDB REMARK 900 RELATED ID: 2AX7 RELATED DB: PDB REMARK 900 RELATED ID: 2AX8 RELATED DB: PDB REMARK 900 RELATED ID: 2AXA RELATED DB: PDB DBREF 2AX9 A 664 919 UNP P10275 ANDR_HUMAN 663 918 SEQRES 1 A 256 ILE GLU GLY TYR GLU CYS GLN PRO ILE PHE LEU ASN VAL SEQRES 2 A 256 LEU GLU ALA ILE GLU PRO GLY VAL VAL CYS ALA GLY HIS SEQRES 3 A 256 ASP ASN ASN GLN PRO ASP SER PHE ALA ALA LEU LEU SER SEQRES 4 A 256 SER LEU ASN GLU LEU GLY GLU ARG GLN LEU VAL HIS VAL SEQRES 5 A 256 VAL LYS TRP ALA LYS ALA LEU PRO GLY PHE ARG ASN LEU SEQRES 6 A 256 HIS VAL ASP ASP GLN MET ALA VAL ILE GLN TYR SER TRP SEQRES 7 A 256 MET GLY LEU MET VAL PHE ALA MET GLY TRP ARG SER PHE SEQRES 8 A 256 THR ASN VAL ASN SER ARG MET LEU TYR PHE ALA PRO ASP SEQRES 9 A 256 LEU VAL PHE ASN GLU TYR ARG MET HIS LYS SER ARG MET SEQRES 10 A 256 TYR SER GLN CYS VAL ARG MET ARG HIS LEU SER GLN GLU SEQRES 11 A 256 PHE GLY TRP LEU GLN ILE THR PRO GLN GLU PHE LEU CYS SEQRES 12 A 256 MET LYS ALA LEU LEU LEU PHE SER ILE ILE PRO VAL ASP SEQRES 13 A 256 GLY LEU LYS ASN GLN LYS PHE PHE ASP GLU LEU ARG MET SEQRES 14 A 256 ASN TYR ILE LYS GLU LEU ASP ARG ILE ILE ALA CYS LYS SEQRES 15 A 256 ARG LYS ASN PRO THR SER CYS SER ARG ARG PHE TYR GLN SEQRES 16 A 256 LEU THR LYS LEU LEU ASP SER VAL GLN PRO ILE ALA ARG SEQRES 17 A 256 GLU LEU HIS GLN PHE THR PHE ASP LEU LEU ILE LYS SER SEQRES 18 A 256 HIS MET VAL SER VAL ASP PHE PRO GLU MET MET ALA GLU SEQRES 19 A 256 ILE ILE SER VAL GLN VAL PRO LYS ILE LEU SER GLY LYS SEQRES 20 A 256 VAL LYS PRO ILE TYR PHE HIS THR GLN HET BHM A 1 21 HETNAM BHM (R)-3-BROMO-2-HYDROXY-2-METHYL-N-[4-NITRO-3- HETNAM 2 BHM (TRIFLUOROMETHYL)PHENYL]PROPANAMIDE FORMUL 2 BHM C11 H10 BR F3 N2 O4 FORMUL 3 HOH *167(H2 O) HELIX 1 1 ILE A 672 GLU A 681 1 10 HELIX 2 2 SER A 696 ALA A 721 1 26 HELIX 3 3 GLY A 724 LEU A 728 5 5 HELIX 4 4 HIS A 729 ASN A 758 1 30 HELIX 5 5 ASN A 771 SER A 778 1 8 HELIX 6 6 MET A 780 LEU A 797 1 18 HELIX 7 7 THR A 800 PHE A 813 1 14 HELIX 8 8 ASN A 823 ALA A 843 1 21 HELIX 9 9 CYS A 852 SER A 884 1 33 HELIX 10 10 HIS A 885 VAL A 887 5 3 HELIX 11 11 PRO A 892 GLN A 902 1 11 HELIX 12 12 GLN A 902 SER A 908 1 7 SHEET 1 A 2 LEU A 762 ALA A 765 0 SHEET 2 A 2 LEU A 768 PHE A 770 -1 O PHE A 770 N LEU A 762 SHEET 1 B 2 ILE A 815 PRO A 817 0 SHEET 2 B 2 VAL A 911 PRO A 913 -1 O LYS A 912 N ILE A 816 SITE 1 AC1 12 LEU A 704 ASN A 705 GLN A 711 TRP A 741 SITE 2 AC1 12 MET A 745 VAL A 746 MET A 749 ARG A 752 SITE 3 AC1 12 PHE A 764 MET A 787 LEU A 873 THR A 877 CRYST1 55.379 66.012 69.055 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 0.018057 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015149 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014481 0.00000