HEADER TRANSCRIPTION 19-JUN-07 2Z4J TITLE CRYSTAL STRUCTURE OF AR LBD WITH SHP PEPTIDE NR BOX 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANDROGEN RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN; COMPND 5 SYNONYM: DIHYDROTESTOSTERONE RECEPTOR; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: NUCLEAR RECEPTOR 0B2; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: RESIDUES 115-124; COMPND 11 SYNONYM: SHP NR BOX 2, ORPHAN NUCLEAR RECEPTOR SHP, SMALL HETERODIMER COMPND 12 PARTNER; COMPND 13 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, NR3C4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PETDUET-1; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: SYNTHETIC PEPTIDE. THIS SEQUENCE OCCURS NATURALLY IN SOURCE 14 HUMANS. KEYWDS ANDROGEN RECEPTOR, LIGAND BINDING DOMAIN, SHP, CO-REPRESSOR, KEYWDS 2 TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR N.JOURAVEL,R.J.FLETTERICK REVDAT 3 01-NOV-23 2Z4J 1 REMARK REVDAT 2 24-FEB-09 2Z4J 1 VERSN REVDAT 1 04-DEC-07 2Z4J 0 JRNL AUTH N.JOURAVEL,E.SABLIN,L.A.ARNOLD,R.K.GUY,R.J.FLETTERICK JRNL TITL INTERACTION BETWEEN THE ANDROGEN RECEPTOR AND A SEGMENT OF JRNL TITL 2 ITS COREPRESSOR SHP JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 63 1198 2007 JRNL REFN ISSN 0907-4449 JRNL PMID 18007036 JRNL DOI 10.1107/S0907444907045702 REMARK 2 REMARK 2 RESOLUTION. 2.60 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.41 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 170678.640 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.5 REMARK 3 NUMBER OF REFLECTIONS : 7836 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) : 0.207 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 415 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.011 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.76 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1050 REMARK 3 BIN R VALUE (WORKING SET) : 0.3260 REMARK 3 BIN FREE R VALUE : 0.3300 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 6.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 69 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2110 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 21 REMARK 3 SOLVENT ATOMS : 6 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 13.58000 REMARK 3 B22 (A**2) : -11.67000 REMARK 3 B33 (A**2) : -1.92000 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) : 0.31 REMARK 3 ESD FROM SIGMAA (A) : 0.46 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) : 0.38 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.49 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.070 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) : 1.160 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.980 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.790 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.710 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 19.73 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : DHT.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : DHT.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2Z4J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-JUN-07. REMARK 100 THE DEPOSITION ID IS D_1000027511. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-SEP-04 REMARK 200 TEMPERATURE (KELVIN) : 77 REMARK 200 PH : 7.0 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) : 1.11589 REMARK 200 MONOCHROMATOR : DOUBLE FLAT CRYSTAL, SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7836 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 24.410 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.3 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 90.5 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: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1T63 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS PROPANE, 1.2M POTASSIUM REMARK 280 SODIUM TARTRATE TETRAHYDRATE, PH 7.0, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 298.0K 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 27.98950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.92100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.27100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.92100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.98950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.27100 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 849 C - N - CA ANGL. DEV. = -14.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 PHE A 697 -61.87 -22.15 REMARK 500 ARG A 726 0.43 -66.16 REMARK 500 ASN A 756 -82.41 -94.41 REMARK 500 ASN A 758 57.10 38.28 REMARK 500 SER A 759 13.45 46.27 REMARK 500 MET A 761 -158.85 -119.52 REMARK 500 LEU A 768 71.67 -157.52 REMARK 500 LYS A 845 32.94 79.90 REMARK 500 ASN A 848 -158.21 55.95 REMARK 500 PRO A 892 176.99 -58.84 REMARK 500 SER B 116 92.34 -173.21 REMARK 500 ILE B 117 -34.04 132.49 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 DHT A 931 DBREF 2Z4J A 671 918 UNP P10275 ANDR_HUMAN 671 918 DBREF 2Z4J B 115 124 UNP Q15466 SHP_HUMAN 115 124 SEQRES 1 A 248 PRO ILE PHE LEU ASN VAL LEU GLU ALA ILE GLU PRO GLY SEQRES 2 A 248 VAL VAL CYS ALA GLY HIS ASP ASN ASN GLN PRO ASP SER SEQRES 3 A 248 PHE ALA ALA LEU LEU SER SER LEU ASN GLU LEU GLY GLU SEQRES 4 A 248 ARG GLN LEU VAL HIS VAL VAL LYS TRP ALA LYS ALA LEU SEQRES 5 A 248 PRO GLY PHE ARG ASN LEU HIS VAL ASP ASP GLN MET ALA SEQRES 6 A 248 VAL ILE GLN TYR SER TRP MET GLY LEU MET VAL PHE ALA SEQRES 7 A 248 MET GLY TRP ARG SER PHE THR ASN VAL ASN SER ARG MET SEQRES 8 A 248 LEU TYR PHE ALA PRO ASP LEU VAL PHE ASN GLU TYR ARG SEQRES 9 A 248 MET HIS LYS SER ARG MET TYR SER GLN CYS VAL ARG MET SEQRES 10 A 248 ARG HIS LEU SER GLN GLU PHE GLY TRP LEU GLN ILE THR SEQRES 11 A 248 PRO GLN GLU PHE LEU CYS MET LYS ALA LEU LEU LEU PHE SEQRES 12 A 248 SER ILE ILE PRO VAL ASP GLY LEU LYS ASN GLN LYS PHE SEQRES 13 A 248 PHE ASP GLU LEU ARG MET ASN TYR ILE LYS GLU LEU ASP SEQRES 14 A 248 ARG ILE ILE ALA CYS LYS ARG LYS ASN PRO THR SER CYS SEQRES 15 A 248 SER ARG ARG PHE TYR GLN LEU THR LYS LEU LEU ASP SER SEQRES 16 A 248 VAL GLN PRO ILE ALA ARG GLU LEU HIS GLN PHE THR PHE SEQRES 17 A 248 ASP LEU LEU ILE LYS SER HIS MET VAL SER VAL ASP PHE SEQRES 18 A 248 PRO GLU MET MET ALA GLU ILE ILE SER VAL GLN VAL PRO SEQRES 19 A 248 LYS ILE LEU SER GLY LYS VAL LYS PRO ILE TYR PHE HIS SEQRES 20 A 248 THR SEQRES 1 B 10 PRO SER ILE LEU LYS LYS ILE LEU LEU GLU HET DHT A 931 21 HETNAM DHT 5-ALPHA-DIHYDROTESTOSTERONE FORMUL 3 DHT C19 H30 O2 FORMUL 4 HOH *6(H2 O) HELIX 1 1 PRO A 671 ILE A 680 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 756 1 28 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 CYS A 844 1 22 HELIX 9 9 PRO A 849 LYS A 883 1 35 HELIX 10 10 LYS A 883 SER A 888 1 6 HELIX 11 11 PRO A 892 GLN A 902 1 11 HELIX 12 12 GLN A 902 SER A 908 1 7 HELIX 13 13 ILE B 117 LEU B 123 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 9 LEU A 704 ASN A 705 GLN A 711 MET A 742 SITE 2 AC1 9 MET A 749 ARG A 752 PHE A 764 THR A 877 SITE 3 AC1 9 LEU A 880 CRYST1 55.979 66.542 71.842 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 0.017864 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015028 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013919 0.00000