HEADER ISOMERASE 09-JUN-15 5BXJ TITLE COMPLEX OF THE FK1 DOMAIN MUTANT A19T OF FKBP51 WITH 4-NITROPHENOL COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE FKBP5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 16-140; COMPND 5 SYNONYM: PPIASE FKBP5,51 KDA FK506-BINDING PROTEIN,FKBP-51,54 KDA COMPND 6 PROGESTERONE RECEPTOR-ASSOCIATED IMMUNOPHILIN,ANDROGEN-REGULATED COMPND 7 PROTEIN 6,FF1 ANTIGEN,FK506-BINDING PROTEIN 5,FKBP-5,FKBP54,P54, COMPND 8 HSP90-BINDING IMMUNOPHILIN,ROTAMASE; COMPND 9 EC: 5.2.1.8; COMPND 10 ENGINEERED: YES; COMPND 11 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: FKBP5, AIG6, FKBP51; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COCHAPERONE, FK506, 4-NITROPHENOL, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.WU,X.TAO,Z.CHEN,J.HAN,W.JIA,X.LI,Z.WANG,Y.X.HE REVDAT 2 20-MAR-24 5BXJ 1 JRNL REMARK REVDAT 1 25-MAY-16 5BXJ 0 JRNL AUTH D.WU,X.TAO,Z.P.CHEN,J.T.HAN,W.J.JIA,N.ZHU,X.LI,Z.WANG,Y.X.HE JRNL TITL THE ENVIRONMENTAL ENDOCRINE DISRUPTOR P-NITROPHENOL JRNL TITL 2 INTERACTS WITH FKBP51, A POSITIVE REGULATOR OF ANDROGEN JRNL TITL 3 RECEPTOR AND INHIBITS ANDROGEN RECEPTOR SIGNALING IN HUMAN JRNL TITL 4 CELLS JRNL REF J. HAZARD. MATER. V. 307 193 2016 JRNL REFN ESSN 1873-3336 JRNL PMID 26780698 JRNL DOI 10.1016/J.JHAZMAT.2015.12.045 REMARK 2 REMARK 2 RESOLUTION. 1.24 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.24 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.02 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 36547 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1828 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 28.0311 - 2.9152 0.98 2809 155 0.1919 0.2102 REMARK 3 2 2.9152 - 2.3142 1.00 2740 140 0.1906 0.2301 REMARK 3 3 2.3142 - 2.0218 1.00 2690 152 0.1812 0.2075 REMARK 3 4 2.0218 - 1.8370 1.00 2680 148 0.1709 0.2030 REMARK 3 5 1.8370 - 1.7053 1.00 2679 140 0.1644 0.1788 REMARK 3 6 1.7053 - 1.6048 1.00 2675 143 0.1604 0.1968 REMARK 3 7 1.6048 - 1.5244 1.00 2652 140 0.1546 0.1979 REMARK 3 8 1.5244 - 1.4581 1.00 2653 140 0.1527 0.1773 REMARK 3 9 1.4581 - 1.4019 1.00 2657 135 0.1585 0.1999 REMARK 3 10 1.4019 - 1.3536 1.00 2654 135 0.1568 0.1921 REMARK 3 11 1.3536 - 1.3112 1.00 2664 127 0.1585 0.1945 REMARK 3 12 1.3112 - 1.2738 1.00 2617 144 0.1584 0.2030 REMARK 3 13 1.2738 - 1.2402 0.96 2549 129 0.1766 0.2079 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.760 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 : 0.010 1006 REMARK 3 ANGLE : 1.303 1350 REMARK 3 CHIRALITY : 0.073 144 REMARK 3 PLANARITY : 0.007 173 REMARK 3 DIHEDRAL : 13.268 376 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 5BXJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-JUN-15. REMARK 100 THE DEPOSITION ID IS D_1000210204. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAY-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36610 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.240 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 3350, 0.2 M AMMONIUM ACETATE REMARK 280 AND 0.1 M HEPES PH 7.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 289K 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 21.06350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.02400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.86000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 28.02400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.06350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.86000 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 MET A 12 REMARK 465 GLU A 140 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HZ2 LYS A 29 O HOH A 301 1.33 REMARK 500 O HOH A 306 O HOH A 371 1.62 REMARK 500 NZ LYS A 29 O HOH A 301 2.09 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 ALA A 112 -117.25 -136.19 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 NPO A 201 DBREF 5BXJ A 16 140 UNP Q13451 FKBP5_HUMAN 16 140 SEQADV 5BXJ MET A 12 UNP Q13451 INITIATING METHIONINE SEQADV 5BXJ GLY A 13 UNP Q13451 EXPRESSION TAG SEQADV 5BXJ ALA A 14 UNP Q13451 EXPRESSION TAG SEQADV 5BXJ PRO A 15 UNP Q13451 EXPRESSION TAG SEQADV 5BXJ THR A 19 UNP Q13451 ALA 19 ENGINEERED MUTATION SEQRES 1 A 129 MET GLY ALA PRO ALA THR VAL THR GLU GLN GLY GLU ASP SEQRES 2 A 129 ILE THR SER LYS LYS ASP ARG GLY VAL LEU LYS ILE VAL SEQRES 3 A 129 LYS ARG VAL GLY ASN GLY GLU GLU THR PRO MET ILE GLY SEQRES 4 A 129 ASP LYS VAL TYR VAL HIS TYR LYS GLY LYS LEU SER ASN SEQRES 5 A 129 GLY LYS LYS PHE ASP SER SER HIS ASP ARG ASN GLU PRO SEQRES 6 A 129 PHE VAL PHE SER LEU GLY LYS GLY GLN VAL ILE LYS ALA SEQRES 7 A 129 TRP ASP ILE GLY VAL ALA THR MET LYS LYS GLY GLU ILE SEQRES 8 A 129 CYS HIS LEU LEU CYS LYS PRO GLU TYR ALA TYR GLY SER SEQRES 9 A 129 ALA GLY SER LEU PRO LYS ILE PRO SER ASN ALA THR LEU SEQRES 10 A 129 PHE PHE GLU ILE GLU LEU LEU ASP PHE LYS GLY GLU HET NPO A 201 14 HETNAM NPO P-NITROPHENOL FORMUL 2 NPO C6 H5 N O3 FORMUL 3 HOH *137(H2 O) HELIX 1 AA1 GLY A 13 GLY A 22 1 10 HELIX 2 AA2 HIS A 71 ASN A 74 5 4 HELIX 3 AA3 ILE A 87 THR A 96 1 10 HELIX 4 AA4 PRO A 109 ALA A 112 5 4 SHEET 1 AA1 6 GLU A 23 ASP A 24 0 SHEET 2 AA1 6 VAL A 33 ARG A 39 -1 O LYS A 35 N GLU A 23 SHEET 3 AA1 6 ILE A 102 CYS A 107 -1 O ILE A 102 N LYS A 38 SHEET 4 AA1 6 LEU A 128 LYS A 138 -1 O LEU A 128 N CYS A 107 SHEET 5 AA1 6 LYS A 52 LEU A 61 -1 N HIS A 56 O GLU A 133 SHEET 6 AA1 6 LYS A 66 SER A 69 -1 O ASP A 68 N GLY A 59 SHEET 1 AA2 6 GLU A 23 ASP A 24 0 SHEET 2 AA2 6 VAL A 33 ARG A 39 -1 O LYS A 35 N GLU A 23 SHEET 3 AA2 6 ILE A 102 CYS A 107 -1 O ILE A 102 N LYS A 38 SHEET 4 AA2 6 LEU A 128 LYS A 138 -1 O LEU A 128 N CYS A 107 SHEET 5 AA2 6 LYS A 52 LEU A 61 -1 N HIS A 56 O GLU A 133 SHEET 6 AA2 6 PHE A 77 SER A 80 -1 O PHE A 79 N VAL A 53 CISPEP 1 LEU A 119 PRO A 120 0 3.06 SITE 1 AC1 8 TYR A 57 ASP A 68 PHE A 77 VAL A 86 SITE 2 AC1 8 ILE A 87 TRP A 90 TYR A 113 HOH A 351 CRYST1 42.127 53.720 56.048 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 0.023738 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018615 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017842 0.00000