HEADER HORMONE 07-FEB-19 6JEZ TITLE COVALENT LABELING OF RVDR-LBD BY TURN-ON FLUORESCENT PROBE MEDIATED BY TITLE 2 CONJUGATE ADDITION AND CYCLIZATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: VITAMIN D3 RECEPTOR,VITAMIN D3 RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: VDR,1,25-DIHYDROXYVITAMIN D3 RECEPTOR,NUCLEAR RECEPTOR COMPND 5 SUBFAMILY 1 GROUP I MEMBER 1,VDR,1,25-DIHYDROXYVITAMIN D3 RECEPTOR, COMPND 6 NUCLEAR RECEPTOR SUBFAMILY 1 GROUP I MEMBER 1; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 1; COMPND 10 CHAIN: C; COMPND 11 SYNONYM: ACTIVATOR-RECRUITED COFACTOR 205 KDA COMPONENT,ARC205, COMPND 12 MEDIATOR COMPLEX SUBUNIT 1,PEROXISOME PROLIFERATOR-ACTIVATED COMPND 13 RECEPTOR-BINDING PROTEIN,PPAR-BINDING PROTEIN,THYROID HORMONE COMPND 14 RECEPTOR-ASSOCIATED PROTEIN COMPLEX 220 KDA COMPONENT,TRAP220,THYROID COMPND 15 RECEPTOR-INTERACTING PROTEIN 2,TRIP-2,VITAMIN D RECEPTOR-INTERACTING COMPND 16 PROTEIN COMPLEX COMPONENT DRIP205,P53 REGULATORY PROTEIN RB18A; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: VDR, NR1I1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS HORMONE, TURN-ON FLUORESCENT PROBE, TCC PROBE, COVALENT LABELING, KEYWDS 2 HISTIDINE EXPDTA X-RAY DIFFRACTION AUTHOR H.KOJIMA,K.YAMAMOTO,T.ITOH REVDAT 3 22-NOV-23 6JEZ 1 COMPND HETNAM REVDAT 2 08-APR-20 6JEZ 1 JRNL REVDAT 1 12-FEB-20 6JEZ 0 JRNL AUTH H.KOJIMA,Y.FUJITA,R.TAKEUCHI,Y.IKEBE,N.OHASHI,K.YAMAMOTO, JRNL AUTH 2 T.ITOH JRNL TITL CYCLIZATION REACTION-BASED TURN-ON PROBE FOR COVALENT JRNL TITL 2 LABELING OF TARGET PROTEINS. JRNL REF CELL CHEM BIOL V. 27 334 2020 JRNL REFN ESSN 2451-9456 JRNL PMID 31991094 JRNL DOI 10.1016/J.CHEMBIOL.2020.01.006 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.18 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 11749 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) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 592 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 866 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2180 REMARK 3 BIN FREE R VALUE SET COUNT : 34 REMARK 3 BIN FREE R VALUE : 0.2680 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1998 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 46 REMARK 3 SOLVENT ATOMS : 61 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.77 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.34000 REMARK 3 B22 (A**2) : -0.09000 REMARK 3 B33 (A**2) : 0.41000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.08000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.380 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.255 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.178 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 16.123 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.928 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.874 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2096 ; 0.015 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2043 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2841 ; 1.705 ; 2.004 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4716 ; 0.877 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 250 ; 5.768 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 92 ;36.273 ;24.783 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 375 ;17.132 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;21.161 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 323 ; 0.090 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2296 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 453 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1003 ; 1.235 ; 1.769 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1004 ; 1.235 ; 1.770 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1250 ; 1.989 ; 2.638 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1250 ; 1.989 ; 2.639 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1093 ; 1.485 ; 1.914 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1094 ; 1.484 ; 1.915 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1591 ; 2.347 ; 2.804 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2439 ; 3.625 ;14.296 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2435 ; 3.625 ;14.298 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 123 A 420 REMARK 3 ORIGIN FOR THE GROUP (A): 19.4221 0.2029 19.0490 REMARK 3 T TENSOR REMARK 3 T11: 0.0923 T22: 0.0133 REMARK 3 T33: 0.0124 T12: -0.0110 REMARK 3 T13: -0.0297 T23: 0.0077 REMARK 3 L TENSOR REMARK 3 L11: 3.6807 L22: 1.3491 REMARK 3 L33: 1.8442 L12: 0.1875 REMARK 3 L13: -0.4329 L23: 0.0337 REMARK 3 S TENSOR REMARK 3 S11: -0.0186 S12: -0.0747 S13: -0.0825 REMARK 3 S21: 0.0466 S22: 0.0111 S23: -0.0272 REMARK 3 S31: -0.0168 S32: 0.0361 S33: 0.0075 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 625 C 635 REMARK 3 ORIGIN FOR THE GROUP (A): 6.1190 -10.3648 10.7041 REMARK 3 T TENSOR REMARK 3 T11: 0.2326 T22: 0.2761 REMARK 3 T33: 0.2167 T12: 0.0125 REMARK 3 T13: -0.0149 T23: -0.0969 REMARK 3 L TENSOR REMARK 3 L11: 7.3896 L22: 5.9472 REMARK 3 L33: 10.6705 L12: 1.3814 REMARK 3 L13: -5.3532 L23: -3.3047 REMARK 3 S TENSOR REMARK 3 S11: -0.0640 S12: 0.1878 S13: -0.2708 REMARK 3 S21: -0.3845 S22: -0.2003 S23: 0.0059 REMARK 3 S31: 0.9618 S32: -0.1996 S33: 0.2643 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 501 A 501 REMARK 3 ORIGIN FOR THE GROUP (A): 13.0491 3.9428 24.8295 REMARK 3 T TENSOR REMARK 3 T11: 0.0887 T22: 0.0835 REMARK 3 T33: 0.0714 T12: 0.0455 REMARK 3 T13: 0.0048 T23: 0.0346 REMARK 3 L TENSOR REMARK 3 L11: 5.6975 L22: 5.7702 REMARK 3 L33: 4.1580 L12: -2.0209 REMARK 3 L13: 2.5465 L23: 3.0032 REMARK 3 S TENSOR REMARK 3 S11: -0.0459 S12: -0.3941 S13: 0.1245 REMARK 3 S21: 0.1837 S22: -0.0219 S23: -0.0399 REMARK 3 S31: 0.1033 S32: -0.3057 S33: 0.0678 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 502 A 502 REMARK 3 ORIGIN FOR THE GROUP (A): 18.6194 9.8587 1.6552 REMARK 3 T TENSOR REMARK 3 T11: 0.2495 T22: 0.3888 REMARK 3 T33: 0.3939 T12: -0.0001 REMARK 3 T13: 0.0754 T23: 0.0007 REMARK 3 L TENSOR REMARK 3 L11: 71.2065 L22: 8.7745 REMARK 3 L33: 2.9318 L12: 24.9290 REMARK 3 L13: 14.4476 L23: 5.0623 REMARK 3 S TENSOR REMARK 3 S11: -0.4782 S12: 0.3489 S13: 1.7323 REMARK 3 S21: -0.2406 S22: 0.1472 S23: 0.4987 REMARK 3 S31: -0.1002 S32: 0.0773 S33: 0.3310 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 601 A 658 REMARK 3 RESIDUE RANGE : C 701 C 703 REMARK 3 ORIGIN FOR THE GROUP (A): 18.5226 2.7242 18.3041 REMARK 3 T TENSOR REMARK 3 T11: 0.1901 T22: 0.0605 REMARK 3 T33: 0.0742 T12: -0.0357 REMARK 3 T13: -0.0148 T23: 0.0059 REMARK 3 L TENSOR REMARK 3 L11: 3.1398 L22: 0.4789 REMARK 3 L33: 1.2985 L12: -0.2198 REMARK 3 L13: -0.2889 L23: 0.3144 REMARK 3 S TENSOR REMARK 3 S11: -0.0255 S12: 0.0076 S13: 0.0548 REMARK 3 S21: 0.0032 S22: 0.0280 S23: -0.0493 REMARK 3 S31: -0.0468 S32: 0.0363 S33: -0.0025 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6JEZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-DEC-19. REMARK 100 THE DEPOSITION ID IS D_1300010993. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-FEB-18 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 : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12346 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 41.750 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.39 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.10900 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: REFMAC REMARK 200 STARTING MODEL: 2ZLC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MOPS-NA PH 7.0, 0.1 M SODIUM REMARK 280 FORMATE, 15% PEG4000, 5% ETHYLENE GLYCOL, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 76.96500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.69500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 76.96500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.69500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 GLY A 106 REMARK 465 SER A 107 REMARK 465 HIS A 108 REMARK 465 MET A 109 REMARK 465 GLY A 110 REMARK 465 SER A 111 REMARK 465 PRO A 112 REMARK 465 ASN A 113 REMARK 465 SER A 114 REMARK 465 PRO A 115 REMARK 465 LEU A 116 REMARK 465 LYS A 117 REMARK 465 ASP A 118 REMARK 465 SER A 119 REMARK 465 LEU A 120 REMARK 465 ARG A 121 REMARK 465 PRO A 122 REMARK 465 ASP A 207 REMARK 465 GLY A 208 REMARK 465 SER A 209 REMARK 465 THR A 210 REMARK 465 GLY A 211 REMARK 465 SER A 212 REMARK 465 VAL A 213 REMARK 465 THR A 214 REMARK 465 LEU A 215 REMARK 465 ASP A 216 REMARK 465 LEU A 217 REMARK 465 GLU A 421 REMARK 465 ILE A 422 REMARK 465 SER A 423 REMARK 465 ASP C 636 REMARK 465 ASN C 637 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 123 CG CD CE NZ REMARK 470 ARG A 151 CG CD NE CZ NH1 NH2 REMARK 470 MET A 159 CG SD CE REMARK 470 LYS C 625 CG CD CE NZ 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 ND1 HIS A 140 CAQ EJO A 502 1.36 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 ASP A 279 24.33 -146.12 REMARK 500 CYS A 284 40.10 -96.45 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 YSV A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EJO A 502 DBREF 6JEZ A 116 210 UNP P13053 VDR_RAT 116 163 DBREF 6JEZ A 213 423 UNP P13053 VDR_RAT 213 423 DBREF 6JEZ C 625 637 UNP Q15648 MED1_HUMAN 640 652 SEQADV 6JEZ GLY A 106 UNP P13053 EXPRESSION TAG SEQADV 6JEZ SER A 107 UNP P13053 EXPRESSION TAG SEQADV 6JEZ HIS A 108 UNP P13053 EXPRESSION TAG SEQADV 6JEZ MET A 109 UNP P13053 EXPRESSION TAG SEQADV 6JEZ GLY A 110 UNP P13053 EXPRESSION TAG SEQADV 6JEZ SER A 111 UNP P13053 EXPRESSION TAG SEQADV 6JEZ PRO A 112 UNP P13053 EXPRESSION TAG SEQADV 6JEZ ASN A 113 UNP P13053 EXPRESSION TAG SEQADV 6JEZ SER A 114 UNP P13053 EXPRESSION TAG SEQADV 6JEZ PRO A 115 UNP P13053 EXPRESSION TAG SEQADV 6JEZ GLY A 211 UNP P13053 LINKER SEQADV 6JEZ SER A 212 UNP P13053 LINKER SEQRES 1 A 271 GLY SER HIS MET GLY SER PRO ASN SER PRO LEU LYS ASP SEQRES 2 A 271 SER LEU ARG PRO LYS LEU SER GLU GLU GLN GLN HIS ILE SEQRES 3 A 271 ILE ALA ILE LEU LEU ASP ALA HIS HIS LYS THR TYR ASP SEQRES 4 A 271 PRO THR TYR ALA ASP PHE ARG ASP PHE ARG PRO PRO VAL SEQRES 5 A 271 ARG MET ASP GLY SER THR GLY SER VAL THR LEU ASP LEU SEQRES 6 A 271 SER PRO LEU SER MET LEU PRO HIS LEU ALA ASP LEU VAL SEQRES 7 A 271 SER TYR SER ILE GLN LYS VAL ILE GLY PHE ALA LYS MET SEQRES 8 A 271 ILE PRO GLY PHE ARG ASP LEU THR SER ASP ASP GLN ILE SEQRES 9 A 271 VAL LEU LEU LYS SER SER ALA ILE GLU VAL ILE MET LEU SEQRES 10 A 271 ARG SER ASN GLN SER PHE THR MET ASP ASP MET SER TRP SEQRES 11 A 271 ASP CYS GLY SER GLN ASP TYR LYS TYR ASP VAL THR ASP SEQRES 12 A 271 VAL SER LYS ALA GLY HIS THR LEU GLU LEU ILE GLU PRO SEQRES 13 A 271 LEU ILE LYS PHE GLN VAL GLY LEU LYS LYS LEU ASN LEU SEQRES 14 A 271 HIS GLU GLU GLU HIS VAL LEU LEU MET ALA ILE CYS ILE SEQRES 15 A 271 VAL SER PRO ASP ARG PRO GLY VAL GLN ASP ALA LYS LEU SEQRES 16 A 271 VAL GLU ALA ILE GLN ASP ARG LEU SER ASN THR LEU GLN SEQRES 17 A 271 THR TYR ILE ARG CYS ARG HIS PRO PRO PRO GLY SER HIS SEQRES 18 A 271 GLN LEU TYR ALA LYS MET ILE GLN LYS LEU ALA ASP LEU SEQRES 19 A 271 ARG SER LEU ASN GLU GLU HIS SER LYS GLN TYR ARG SER SEQRES 20 A 271 LEU SER PHE GLN PRO GLU ASN SER MET LYS LEU THR PRO SEQRES 21 A 271 LEU VAL LEU GLU VAL PHE GLY ASN GLU ILE SER SEQRES 1 C 13 LYS ASN HIS PRO MET LEU MET ASN LEU LEU LYS ASP ASN HET YSV A 501 30 HET EJO A 502 16 HETNAM YSV (1R,3R)-5-(2-((1R,3AS,7AR,E)-1-((R)-6-HYDROXY-6- HETNAM 2 YSV METHYLHEPTAN-2-YL)-7A-METHYLOCTAHYDRO-4H-INDEN-4- HETNAM 3 YSV YLIDENE)ETHYLIDENE)-2- METHYLENECYCLOHEXANE-1,3-DIOL HETNAM EJO 7-(DIETHYLAMINO)CHROMEN-2-ONE HETSYN YSV 2-METHYLIDENE-19-NOR-1ALPHA,25-DIHYDROXYVITAMIN D3 FORMUL 3 YSV C27 H44 O3 FORMUL 4 EJO C13 H15 N O2 FORMUL 5 HOH *61(H2 O) HELIX 1 AA1 SER A 125 TYR A 143 1 19 HELIX 2 AA2 TYR A 147 PHE A 153 5 7 HELIX 3 AA3 MET A 222 MET A 243 1 22 HELIX 4 AA4 GLY A 246 LEU A 250 5 5 HELIX 5 AA5 THR A 251 ASN A 272 1 22 HELIX 6 AA6 SER A 286 ASP A 288 5 3 HELIX 7 AA7 ASP A 292 LYS A 298 1 7 HELIX 8 AA8 THR A 302 LEU A 319 1 18 HELIX 9 AA9 HIS A 322 VAL A 335 1 14 HELIX 10 AB1 ASP A 344 HIS A 367 1 24 HELIX 11 AB2 GLN A 374 GLN A 403 1 30 HELIX 12 AB3 GLN A 403 MET A 408 1 6 HELIX 13 AB4 THR A 411 GLY A 419 1 9 HELIX 14 AB5 HIS C 627 LYS C 635 1 9 SHEET 1 AA1 3 PHE A 275 THR A 276 0 SHEET 2 AA1 3 SER A 281 ASP A 283 -1 O SER A 281 N THR A 276 SHEET 3 AA1 3 LYS A 290 TYR A 291 -1 O TYR A 291 N TRP A 282 CISPEP 1 PRO A 369 PRO A 370 0 3.03 SITE 1 AC1 10 TYR A 143 SER A 233 ARG A 270 SER A 271 SITE 2 AC1 10 SER A 274 TRP A 282 CYS A 284 VAL A 296 SITE 3 AC1 10 HIS A 301 HIS A 393 SITE 1 AC2 4 LEU A 136 ASP A 137 HIS A 140 LYS A 141 CRYST1 153.930 43.390 42.000 90.00 95.30 90.00 C 1 2 1 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 0.006496 0.000000 0.000603 0.00000 SCALE2 0.000000 0.023047 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023912 0.00000