HEADER TRANSCRIPTION 23-JUN-16 5GIC TITLE CRYSTAL STRUCTURE OF VDR IN COMPLEX WITH DLAM-2P COMPND MOL_ID: 1; COMPND 2 MOLECULE: VITAMIN D3 RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 124-164,UNP RESIDUES 212-420; COMPND 5 SYNONYM: VDR,1,25-DIHYDROXYVITAMIN D3 RECEPTOR,NUCLEAR RECEPTOR COMPND 6 SUBFAMILY 1 GROUP I MEMBER 1; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: SRC1; COMPND 10 CHAIN: C; COMPND 11 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: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS NUCLEAR RECEPTOR, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR T.SHIMIZU,L.ASANO REVDAT 3 17-MAY-23 5GIC 1 COMPND HETNAM FORMUL REVDAT 2 26-FEB-20 5GIC 1 JRNL REMARK REVDAT 1 07-DEC-16 5GIC 0 JRNL AUTH L.ASANO,T.WAKU,R.ABE,N.KUWABARA,I.ITO,J.YANAGISAWA, JRNL AUTH 2 K.NAGASAWA,T.SHIMIZU JRNL TITL REGULATION OF THE VITAMIN D RECEPTOR BY VITAMIN D LACTAM JRNL TITL 2 DERIVATIVES. JRNL REF FEBS LETT. V. 590 3270 2016 JRNL REFN ISSN 0014-5793 JRNL PMID 27500498 JRNL DOI 10.1002/1873-3468.12348 REMARK 2 REMARK 2 RESOLUTION. 2.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155) 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) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 11424 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 2149 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 30.0125 - 5.7879 0.96 1287 138 0.1662 0.2070 REMARK 3 2 5.7879 - 4.5994 0.98 1288 141 0.1757 0.2198 REMARK 3 3 4.5994 - 4.0195 0.98 1313 148 0.1578 0.1906 REMARK 3 4 4.0195 - 3.6527 0.99 1294 144 0.1865 0.2430 REMARK 3 5 3.6527 - 3.3913 0.98 1321 145 0.2078 0.2162 REMARK 3 6 3.3913 - 3.1916 0.98 1279 142 0.2332 0.2517 REMARK 3 7 3.1916 - 3.0319 0.99 1277 147 0.2629 0.3068 REMARK 3 8 3.0319 - 2.9000 0.99 1357 153 0.2753 0.2915 REMARK 3 9 2.9000 - 2.7885 0.98 1259 138 0.2655 0.3211 REMARK 3 10 2.7885 - 2.6923 0.98 1327 149 0.2863 0.3478 REMARK 3 11 2.6923 - 2.6082 0.98 1261 141 0.2861 0.2942 REMARK 3 12 2.6082 - 2.5337 0.98 1336 150 0.3270 0.3222 REMARK 3 13 2.5337 - 2.4670 0.99 1302 145 0.3407 0.3852 REMARK 3 14 2.4670 - 2.4068 0.98 1306 139 0.3311 0.3726 REMARK 3 15 2.4068 - 2.3522 0.90 1161 129 0.3642 0.3243 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) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.590 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 : 0.004 1981 REMARK 3 ANGLE : 0.922 2700 REMARK 3 CHIRALITY : 0.044 319 REMARK 3 PLANARITY : 0.005 343 REMARK 3 DIHEDRAL : 16.125 1213 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 124 THROUGH 222 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.6168 6.2780 8.5007 REMARK 3 T TENSOR REMARK 3 T11: 0.4831 T22: 0.4004 REMARK 3 T33: 0.4302 T12: -0.0186 REMARK 3 T13: 0.0089 T23: -0.0609 REMARK 3 L TENSOR REMARK 3 L11: 5.3442 L22: 1.1473 REMARK 3 L33: 3.2685 L12: 0.2267 REMARK 3 L13: -0.6195 L23: -1.0193 REMARK 3 S TENSOR REMARK 3 S11: -0.0506 S12: -0.1502 S13: 0.1285 REMARK 3 S21: 0.2520 S22: -0.2200 S23: -0.2594 REMARK 3 S31: -0.3800 S32: -0.0968 S33: -0.0439 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 223 THROUGH 283 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.8900 -0.0140 3.6297 REMARK 3 T TENSOR REMARK 3 T11: 0.3561 T22: 0.4347 REMARK 3 T33: 0.3984 T12: 0.0101 REMARK 3 T13: -0.0307 T23: -0.0065 REMARK 3 L TENSOR REMARK 3 L11: 6.0429 L22: 2.1683 REMARK 3 L33: 2.6369 L12: -0.5266 REMARK 3 L13: 0.0862 L23: -0.3468 REMARK 3 S TENSOR REMARK 3 S11: 0.0407 S12: 0.0781 S13: -0.1530 REMARK 3 S21: 0.0498 S22: -0.0806 S23: 0.0836 REMARK 3 S31: -0.1949 S32: 0.1203 S33: 0.0593 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 284 THROUGH 301 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.6502 10.9699 -9.4112 REMARK 3 T TENSOR REMARK 3 T11: 0.8464 T22: 0.6853 REMARK 3 T33: 0.9520 T12: -0.0060 REMARK 3 T13: 0.1652 T23: 0.2154 REMARK 3 L TENSOR REMARK 3 L11: 4.2311 L22: 0.7548 REMARK 3 L33: 1.9913 L12: -0.6856 REMARK 3 L13: -0.5572 L23: -0.8179 REMARK 3 S TENSOR REMARK 3 S11: 0.6138 S12: 1.2702 S13: 0.0857 REMARK 3 S21: -0.5851 S22: 0.4303 S23: -0.6022 REMARK 3 S31: -1.0307 S32: 0.3968 S33: 0.0255 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 302 THROUGH 319 ) REMARK 3 ORIGIN FOR THE GROUP (A): -25.5947 3.7392 -9.3554 REMARK 3 T TENSOR REMARK 3 T11: 0.5234 T22: 0.6914 REMARK 3 T33: 0.3821 T12: 0.0786 REMARK 3 T13: -0.0188 T23: 0.0746 REMARK 3 L TENSOR REMARK 3 L11: 5.0315 L22: 2.4623 REMARK 3 L33: 2.8885 L12: 0.4199 REMARK 3 L13: 0.4771 L23: -1.1374 REMARK 3 S TENSOR REMARK 3 S11: -0.2672 S12: 0.7235 S13: 0.0456 REMARK 3 S21: 0.1090 S22: 0.0548 S23: 0.0454 REMARK 3 S31: 0.0077 S32: -0.3477 S33: -0.0001 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 320 THROUGH 345 ) REMARK 3 ORIGIN FOR THE GROUP (A): -27.6741 -4.9385 6.4292 REMARK 3 T TENSOR REMARK 3 T11: 0.3821 T22: 0.4814 REMARK 3 T33: 0.4381 T12: -0.0152 REMARK 3 T13: 0.0162 T23: -0.0262 REMARK 3 L TENSOR REMARK 3 L11: 6.0775 L22: 1.8873 REMARK 3 L33: 3.8393 L12: -0.0770 REMARK 3 L13: 0.3645 L23: -0.0464 REMARK 3 S TENSOR REMARK 3 S11: 0.0548 S12: 0.2042 S13: -0.7072 REMARK 3 S21: 0.1921 S22: -0.2571 S23: 0.3631 REMARK 3 S31: 0.0458 S32: -0.4841 S33: -0.0034 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 346 THROUGH 374 ) REMARK 3 ORIGIN FOR THE GROUP (A): -37.9399 -2.6813 9.5388 REMARK 3 T TENSOR REMARK 3 T11: 0.3323 T22: 0.7284 REMARK 3 T33: 0.5503 T12: 0.0153 REMARK 3 T13: -0.0024 T23: 0.0893 REMARK 3 L TENSOR REMARK 3 L11: 5.6808 L22: 2.7049 REMARK 3 L33: 3.5676 L12: -1.3881 REMARK 3 L13: 0.4771 L23: -1.1740 REMARK 3 S TENSOR REMARK 3 S11: -0.0073 S12: -1.0278 S13: -0.6816 REMARK 3 S21: 0.0790 S22: 0.2090 S23: 0.6555 REMARK 3 S31: -0.0195 S32: -0.9582 S33: -0.1230 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 375 THROUGH 402 ) REMARK 3 ORIGIN FOR THE GROUP (A): -23.7510 -5.4424 -5.9130 REMARK 3 T TENSOR REMARK 3 T11: 0.3980 T22: 0.6734 REMARK 3 T33: 0.4535 T12: 0.0696 REMARK 3 T13: -0.0694 T23: -0.1997 REMARK 3 L TENSOR REMARK 3 L11: 4.9043 L22: 1.7376 REMARK 3 L33: 2.9902 L12: -0.0297 REMARK 3 L13: -0.9214 L23: -0.1681 REMARK 3 S TENSOR REMARK 3 S11: 0.4026 S12: 1.1125 S13: -0.5446 REMARK 3 S21: -0.3981 S22: -0.3248 S23: 0.0341 REMARK 3 S31: -0.2078 S32: -0.1189 S33: 0.0422 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 403 THROUGH 420 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.3309 -5.5972 -4.0353 REMARK 3 T TENSOR REMARK 3 T11: 0.4154 T22: 0.9045 REMARK 3 T33: 0.5537 T12: 0.0508 REMARK 3 T13: 0.0527 T23: -0.0368 REMARK 3 L TENSOR REMARK 3 L11: 6.6988 L22: 2.4681 REMARK 3 L33: 4.5761 L12: -0.5628 REMARK 3 L13: -0.8961 L23: -0.2495 REMARK 3 S TENSOR REMARK 3 S11: -0.3283 S12: 1.5178 S13: -0.6065 REMARK 3 S21: -0.4053 S22: -0.4309 S23: -0.1905 REMARK 3 S31: 0.5924 S32: -0.0363 S33: 0.2603 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 626 THROUGH 635 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.8822 -10.0670 10.9727 REMARK 3 T TENSOR REMARK 3 T11: 0.4273 T22: 1.1667 REMARK 3 T33: 0.8908 T12: 0.0600 REMARK 3 T13: -0.0087 T23: 0.2310 REMARK 3 L TENSOR REMARK 3 L11: 6.8316 L22: 2.8225 REMARK 3 L33: 3.7889 L12: -0.0500 REMARK 3 L13: 0.0008 L23: -0.6782 REMARK 3 S TENSOR REMARK 3 S11: -0.0725 S12: -0.7253 S13: -1.2792 REMARK 3 S21: -0.3479 S22: -0.3991 S23: -0.6903 REMARK 3 S31: 0.8381 S32: 0.3903 S33: 0.2491 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE ENTRY CONTAINS FRIEDEL PAIRS IN REMARK 3 I_PLUS/MINUS COLUMNS REMARK 4 REMARK 4 5GIC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1300000825. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JAN-13 REMARK 200 TEMPERATURE (KELVIN) : 90 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-NE3A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 130 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11424 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.3000 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 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: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL, PEG 8000, NACL, VAPOR REMARK 280 DIFFUSION, 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 77.15750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.22200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 77.15750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.22200 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, 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 MET A 159 REMARK 465 ASP A 160 REMARK 465 GLY A 161 REMARK 465 SER A 162 REMARK 465 THR A 163 REMARK 465 GLY A 164 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 SER A 218 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 ARG A 151 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 158 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 242 CG CD CE NZ REMARK 470 ARG A 248 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 253 CG OD1 OD2 REMARK 470 GLN A 287 CG CD OE1 NE2 REMARK 470 ASP A 288 CG OD1 OD2 REMARK 470 LYS A 290 CG CD CE NZ REMARK 470 LYS A 298 CG CD CE NZ REMARK 470 HIS A 301 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 311 CG CD CE NZ REMARK 470 GLN A 343 CG CD OE1 NE2 REMARK 470 LYS A 346 CG CD CE NZ REMARK 470 GLU A 349 CG CD OE1 OE2 REMARK 470 LYS A 395 CG CD CE NZ REMARK 470 ARG A 398 CG CD NE CZ NH1 NH2 REMARK 470 PHE A 402 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLN A 403 CG CD OE1 NE2 REMARK 470 GLU A 405 CG CD OE1 OE2 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 NE2 HIS A 393 O4 DLC A 501 2.14 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 GLN A 287 61.16 -151.92 REMARK 500 ASP A 288 -107.13 51.34 REMARK 500 TYR A 289 40.37 -98.36 REMARK 500 GLN A 343 -83.00 -83.82 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 DLC A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5GID RELATED DB: PDB REMARK 900 RELATED ID: 5GIE RELATED DB: PDB DBREF 5GIC A 124 164 UNP P13053 VDR_RAT 124 164 DBREF 5GIC A 212 420 UNP P13053 VDR_RAT 212 420 DBREF 5GIC C 626 635 PDB 5GIC 5GIC 626 635 SEQRES 1 A 250 LEU SER GLU GLU GLN GLN HIS ILE ILE ALA ILE LEU LEU SEQRES 2 A 250 ASP ALA HIS HIS LYS THR TYR ASP PRO THR TYR ALA ASP SEQRES 3 A 250 PHE ARG ASP PHE ARG PRO PRO VAL ARG MET ASP GLY SER SEQRES 4 A 250 THR GLY SER VAL THR LEU ASP LEU SER PRO LEU SER MET SEQRES 5 A 250 LEU PRO HIS LEU ALA ASP LEU VAL SER TYR SER ILE GLN SEQRES 6 A 250 LYS VAL ILE GLY PHE ALA LYS MET ILE PRO GLY PHE ARG SEQRES 7 A 250 ASP LEU THR SER ASP ASP GLN ILE VAL LEU LEU LYS SER SEQRES 8 A 250 SER ALA ILE GLU VAL ILE MET LEU ARG SER ASN GLN SER SEQRES 9 A 250 PHE THR MET ASP ASP MET SER TRP ASP CYS GLY SER GLN SEQRES 10 A 250 ASP TYR LYS TYR ASP VAL THR ASP VAL SER LYS ALA GLY SEQRES 11 A 250 HIS THR LEU GLU LEU ILE GLU PRO LEU ILE LYS PHE GLN SEQRES 12 A 250 VAL GLY LEU LYS LYS LEU ASN LEU HIS GLU GLU GLU HIS SEQRES 13 A 250 VAL LEU LEU MET ALA ILE CYS ILE VAL SER PRO ASP ARG SEQRES 14 A 250 PRO GLY VAL GLN ASP ALA LYS LEU VAL GLU ALA ILE GLN SEQRES 15 A 250 ASP ARG LEU SER ASN THR LEU GLN THR TYR ILE ARG CYS SEQRES 16 A 250 ARG HIS PRO PRO PRO GLY SER HIS GLN LEU TYR ALA LYS SEQRES 17 A 250 MET ILE GLN LYS LEU ALA ASP LEU ARG SER LEU ASN GLU SEQRES 18 A 250 GLU HIS SER LYS GLN TYR ARG SER LEU SER PHE GLN PRO SEQRES 19 A 250 GLU ASN SER MET LYS LEU THR PRO LEU VAL LEU GLU VAL SEQRES 20 A 250 PHE GLY ASN SEQRES 1 C 10 ASN HIS PRO MET LEU MET ASN LEU LEU LYS HET DLC A 501 40 HETNAM DLC (3~{R},5~{S})-5-[(2~{R})-2-[(1~{R},3~{A}~{S},4~{Z}, HETNAM 2 DLC 7~{A}~{R})-7~{A}-METHYL-4-[(2~{E})-2-[(3~{S},5~{R})-2- HETNAM 3 DLC METHYLIDENE-3,5-BIS(OXIDANYL) HETNAM 4 DLC CYCLOHEXYLIDENE]ETHYLIDENE]-2,3,3~{A},5,6,7-HEXAHYDRO- HETNAM 5 DLC 1~{H}-INDEN-1-YL]PROPYL]-3-METHYL-3-OXIDANYL-1-(2- HETNAM 6 DLC PHENYLETHYL)PYRROLIDIN-2-ONE FORMUL 3 DLC C35 H49 N O4 FORMUL 4 HOH *30(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 THR A 251 SER A 271 1 21 HELIX 5 AA5 ASP A 292 SER A 297 1 6 HELIX 6 AA6 THR A 302 LYS A 318 1 17 HELIX 7 AA7 HIS A 322 VAL A 335 1 14 HELIX 8 AA8 ALA A 345 HIS A 367 1 23 HELIX 9 AA9 GLN A 374 PHE A 402 1 29 HELIX 10 AB1 GLN A 403 MET A 408 1 6 HELIX 11 AB2 THR A 411 PHE A 418 1 8 HELIX 12 AB3 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 GLN A 287 ASP A 288 0 7.54 CISPEP 2 PRO A 369 PRO A 370 0 -0.50 SITE 1 AC1 13 TYR A 143 LEU A 223 SER A 233 ILE A 267 SITE 2 AC1 13 ARG A 270 SER A 271 SER A 274 TRP A 282 SITE 3 AC1 13 VAL A 296 LEU A 305 HIS A 393 TYR A 397 SITE 4 AC1 13 LEU A 400 CRYST1 154.315 42.444 42.106 90.00 96.53 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 0.006480 0.000000 0.000741 0.00000 SCALE2 0.000000 0.023560 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023904 0.00000