HEADER TRANSCRIPTION 05-JAN-22 7QPP
TITLE HIGH RESOLUTION STRUCTURE OF HUMAN VDR LIGAND BINDING DOMAIN IN
TITLE 2 COMPLEX WITH CALCITRIOL
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 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;
COMPND 6 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: VDR, NR1I1;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008
KEYWDS VDR, CALCITRIOL, TRANSCRIPTION
EXPDTA X-RAY DIFFRACTION
AUTHOR N.ROCHEL
REVDAT 2 31-JAN-24 7QPP 1 REMARK
REVDAT 1 28-DEC-22 7QPP 0
JRNL AUTH R.SIGUEIRO,L.BIANCHETTI,C.PELUSO-ILTIS,S.CHALHOUB,
JRNL AUTH 2 A.DEJAEGERE,J.OSZ,N.ROCHEL
JRNL TITL ADVANCES IN VITAMIN D RECEPTOR FUNCTION AND EVOLUTION BASED
JRNL TITL 2 ON THE 3D STRUCTURE OF THE LAMPREY LIGAND-BINDING DOMAIN.
JRNL REF J.MED.CHEM. V. 65 5821 2022
JRNL REFN ISSN 0022-2623
JRNL PMID 35302785
JRNL DOI 10.1021/ACS.JMEDCHEM.2C00171
REMARK 2
REMARK 2 RESOLUTION. 1.52 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.17_3644
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 : GEOSTD + MONOMER LIBRARY + CDL V1.2
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.52
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.80
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8
REMARK 3 NUMBER OF REFLECTIONS : 46307
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.142
REMARK 3 R VALUE (WORKING SET) : 0.139
REMARK 3 FREE R VALUE : 0.166
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.050
REMARK 3 FREE R VALUE TEST SET COUNT : 4655
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 19.8000 - 4.7100 0.97 1546 156 0.2079 0.2219
REMARK 3 2 4.7100 - 3.7400 0.99 1477 158 0.1370 0.1668
REMARK 3 3 3.7400 - 3.2700 0.99 1477 149 0.1428 0.1660
REMARK 3 4 3.2700 - 2.9800 1.00 1457 163 0.1448 0.1626
REMARK 3 5 2.9800 - 2.7600 1.00 1455 167 0.1459 0.1639
REMARK 3 6 2.7600 - 2.6000 1.00 1439 161 0.1357 0.1611
REMARK 3 7 2.6000 - 2.4700 0.99 1432 158 0.1265 0.1525
REMARK 3 8 2.4700 - 2.3600 0.99 1386 180 0.1254 0.1691
REMARK 3 9 2.3600 - 2.2700 1.00 1430 189 0.1215 0.1540
REMARK 3 10 2.2700 - 2.1900 0.99 1420 157 0.1213 0.1593
REMARK 3 11 2.1900 - 2.1300 0.99 1419 154 0.1232 0.1577
REMARK 3 12 2.1300 - 2.0600 0.99 1416 159 0.1259 0.1626
REMARK 3 13 2.0600 - 2.0100 0.99 1428 165 0.1295 0.1537
REMARK 3 14 2.0100 - 1.9600 0.99 1382 179 0.1298 0.1591
REMARK 3 15 1.9600 - 1.9200 0.99 1419 165 0.1312 0.1718
REMARK 3 16 1.9200 - 1.8800 0.99 1394 155 0.1362 0.1686
REMARK 3 17 1.8800 - 1.8400 0.98 1400 155 0.1357 0.1516
REMARK 3 18 1.8400 - 1.8000 0.99 1402 152 0.1326 0.1594
REMARK 3 19 1.8000 - 1.7700 0.98 1415 141 0.1298 0.1626
REMARK 3 20 1.7700 - 1.7400 0.97 1388 148 0.1284 0.1733
REMARK 3 21 1.7400 - 1.7100 0.97 1336 185 0.1335 0.1674
REMARK 3 22 1.7100 - 1.6900 0.96 1395 146 0.1305 0.1652
REMARK 3 23 1.6900 - 1.6600 0.96 1329 138 0.1282 0.1570
REMARK 3 24 1.6600 - 1.6400 0.94 1345 165 0.1305 0.1578
REMARK 3 25 1.6400 - 1.6200 0.95 1334 131 0.1314 0.1786
REMARK 3 26 1.6200 - 1.6000 0.93 1332 130 0.1260 0.1713
REMARK 3 27 1.6000 - 1.5800 0.93 1349 139 0.1348 0.1528
REMARK 3 28 1.5800 - 1.5600 0.92 1260 141 0.1248 0.1387
REMARK 3 29 1.5600 - 1.5400 0.90 1298 145 0.1347 0.1606
REMARK 3 30 1.5400 - 1.5200 0.78 1092 124 0.1364 0.1708
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) : 0.087
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.888
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 11.22
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.37
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 : 0.011 2135
REMARK 3 ANGLE : 1.268 2901
REMARK 3 CHIRALITY : 0.238 333
REMARK 3 PLANARITY : 0.009 368
REMARK 3 DIHEDRAL : 21.949 818
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 10
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 119 THROUGH 142 )
REMARK 3 ORIGIN FOR THE GROUP (A): 23.3220 7.6404 53.9264
REMARK 3 T TENSOR
REMARK 3 T11: 0.1770 T22: 0.1325
REMARK 3 T33: 0.1026 T12: 0.0443
REMARK 3 T13: -0.0625 T23: -0.0101
REMARK 3 L TENSOR
REMARK 3 L11: 1.8382 L22: 0.6442
REMARK 3 L33: 1.8278 L12: 0.7903
REMARK 3 L13: 1.2842 L23: 0.4275
REMARK 3 S TENSOR
REMARK 3 S11: 0.1177 S12: -0.1955 S13: -0.1922
REMARK 3 S21: 0.3437 S22: 0.0410 S23: -0.1251
REMARK 3 S31: 0.3334 S32: 0.2371 S33: -0.1436
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 143 THROUGH 226 )
REMARK 3 ORIGIN FOR THE GROUP (A): 8.8867 23.2171 24.5323
REMARK 3 T TENSOR
REMARK 3 T11: 0.0696 T22: 0.0940
REMARK 3 T33: 0.0941 T12: 0.0057
REMARK 3 T13: -0.0089 T23: 0.0029
REMARK 3 L TENSOR
REMARK 3 L11: 0.9832 L22: 1.7064
REMARK 3 L33: 0.9791 L12: -0.7836
REMARK 3 L13: 0.1980 L23: -0.3149
REMARK 3 S TENSOR
REMARK 3 S11: 0.1191 S12: 0.1600 S13: 0.1070
REMARK 3 S21: -0.2434 S22: -0.1285 S23: 0.0081
REMARK 3 S31: -0.0381 S32: 0.0329 S33: 0.0224
REMARK 3 TLS GROUP : 3
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 227 THROUGH 255 )
REMARK 3 ORIGIN FOR THE GROUP (A): 7.5141 12.2420 42.2053
REMARK 3 T TENSOR
REMARK 3 T11: 0.0518 T22: 0.0531
REMARK 3 T33: 0.0731 T12: -0.0173
REMARK 3 T13: 0.0004 T23: -0.0053
REMARK 3 L TENSOR
REMARK 3 L11: 0.7256 L22: 1.0396
REMARK 3 L33: 1.2886 L12: -0.2394
REMARK 3 L13: 0.4204 L23: 0.0039
REMARK 3 S TENSOR
REMARK 3 S11: 0.0180 S12: -0.0826 S13: -0.0062
REMARK 3 S21: 0.0920 S22: -0.0507 S23: 0.0804
REMARK 3 S31: 0.1610 S32: -0.1085 S33: -0.0484
REMARK 3 TLS GROUP : 4
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 256 THROUGH 290 )
REMARK 3 ORIGIN FOR THE GROUP (A): 13.5135 20.0842 39.7482
REMARK 3 T TENSOR
REMARK 3 T11: 0.0476 T22: 0.0422
REMARK 3 T33: 0.0611 T12: -0.0061
REMARK 3 T13: -0.0255 T23: -0.0125
REMARK 3 L TENSOR
REMARK 3 L11: 3.0077 L22: 1.5589
REMARK 3 L33: 3.8757 L12: 0.8694
REMARK 3 L13: -2.0840 L23: -1.0000
REMARK 3 S TENSOR
REMARK 3 S11: -0.0090 S12: -0.0001 S13: 0.1142
REMARK 3 S21: 0.0457 S22: -0.0298 S23: 0.0079
REMARK 3 S31: -0.0414 S32: -0.1177 S33: 0.0292
REMARK 3 TLS GROUP : 5
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 291 THROUGH 306 )
REMARK 3 ORIGIN FOR THE GROUP (A): 13.1654 26.6227 26.2303
REMARK 3 T TENSOR
REMARK 3 T11: 0.0842 T22: 0.1102
REMARK 3 T33: 0.0860 T12: -0.0273
REMARK 3 T13: -0.0338 T23: 0.0341
REMARK 3 L TENSOR
REMARK 3 L11: 3.4917 L22: 6.6620
REMARK 3 L33: 2.5286 L12: -1.3964
REMARK 3 L13: 0.7347 L23: 0.4516
REMARK 3 S TENSOR
REMARK 3 S11: 0.0113 S12: 0.2719 S13: 0.1483
REMARK 3 S21: -0.3244 S22: -0.0686 S23: -0.1339
REMARK 3 S31: -0.1222 S32: 0.1625 S33: 0.0301
REMARK 3 TLS GROUP : 6
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 307 THROUGH 323 )
REMARK 3 ORIGIN FOR THE GROUP (A): 19.1873 30.4588 39.1131
REMARK 3 T TENSOR
REMARK 3 T11: 0.0834 T22: 0.0547
REMARK 3 T33: 0.1559 T12: -0.0235
REMARK 3 T13: -0.0388 T23: 0.0206
REMARK 3 L TENSOR
REMARK 3 L11: 5.5678 L22: 3.4244
REMARK 3 L33: 3.5221 L12: -2.4018
REMARK 3 L13: 1.4131 L23: -1.1707
REMARK 3 S TENSOR
REMARK 3 S11: -0.1491 S12: 0.1802 S13: 0.6896
REMARK 3 S21: 0.0324 S22: -0.1277 S23: -0.1745
REMARK 3 S31: -0.2232 S32: 0.1022 S33: 0.2077
REMARK 3 TLS GROUP : 7
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 324 THROUGH 348 )
REMARK 3 ORIGIN FOR THE GROUP (A): 14.3543 17.8815 51.7092
REMARK 3 T TENSOR
REMARK 3 T11: 0.0764 T22: 0.0491
REMARK 3 T33: 0.0399 T12: -0.0021
REMARK 3 T13: -0.0219 T23: -0.0142
REMARK 3 L TENSOR
REMARK 3 L11: 4.0027 L22: 1.7426
REMARK 3 L33: 2.7757 L12: -0.2809
REMARK 3 L13: -1.0382 L23: 0.0907
REMARK 3 S TENSOR
REMARK 3 S11: 0.0718 S12: -0.0049 S13: 0.1256
REMARK 3 S21: 0.1409 S22: -0.0508 S23: 0.0065
REMARK 3 S31: -0.0214 S32: -0.1579 S33: 0.0086
REMARK 3 TLS GROUP : 8
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 349 THROUGH 378 )
REMARK 3 ORIGIN FOR THE GROUP (A): 23.0434 16.8026 57.5641
REMARK 3 T TENSOR
REMARK 3 T11: 0.1373 T22: 0.1179
REMARK 3 T33: 0.0993 T12: 0.0144
REMARK 3 T13: -0.0452 T23: -0.0141
REMARK 3 L TENSOR
REMARK 3 L11: 4.1400 L22: 1.6394
REMARK 3 L33: 2.6264 L12: 0.3311
REMARK 3 L13: -0.9033 L23: -0.1838
REMARK 3 S TENSOR
REMARK 3 S11: -0.0203 S12: -0.2736 S13: 0.1678
REMARK 3 S21: 0.2247 S22: 0.0146 S23: -0.2478
REMARK 3 S31: 0.0262 S32: 0.3173 S33: 0.0216
REMARK 3 TLS GROUP : 9
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 379 THROUGH 406 )
REMARK 3 ORIGIN FOR THE GROUP (A): 10.1391 29.2456 44.8288
REMARK 3 T TENSOR
REMARK 3 T11: 0.0920 T22: 0.0865
REMARK 3 T33: 0.1225 T12: 0.0084
REMARK 3 T13: -0.0200 T23: -0.0236
REMARK 3 L TENSOR
REMARK 3 L11: 6.4444 L22: 0.8398
REMARK 3 L33: 4.8561 L12: -1.4765
REMARK 3 L13: 5.3986 L23: -1.0996
REMARK 3 S TENSOR
REMARK 3 S11: -0.2829 S12: -0.3727 S13: 0.4493
REMARK 3 S21: 0.0899 S22: 0.0542 S23: -0.0978
REMARK 3 S31: -0.2886 S32: -0.3080 S33: 0.2038
REMARK 3 TLS GROUP : 10
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 407 THROUGH 424 )
REMARK 3 ORIGIN FOR THE GROUP (A): -3.4703 22.8169 33.4180
REMARK 3 T TENSOR
REMARK 3 T11: 0.0557 T22: 0.1098
REMARK 3 T33: 0.1474 T12: 0.0080
REMARK 3 T13: -0.0041 T23: -0.0130
REMARK 3 L TENSOR
REMARK 3 L11: 2.4710 L22: 5.7219
REMARK 3 L33: 2.6413 L12: -2.0839
REMARK 3 L13: 0.9140 L23: -2.8494
REMARK 3 S TENSOR
REMARK 3 S11: -0.0646 S12: -0.2411 S13: -0.0749
REMARK 3 S21: 0.1825 S22: 0.1386 S23: 0.2988
REMARK 3 S31: -0.0917 S32: -0.2421 S33: -0.0769
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 7QPP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-JAN-22.
REMARK 100 THE DEPOSITION ID IS D_1292120049.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 02-MAY-00
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ESRF
REMARK 200 BEAMLINE : BM30A
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.98
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46307
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.520
REMARK 200 RESOLUTION RANGE LOW (A) : 20.100
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2
REMARK 200 DATA REDUNDANCY : 3.400
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.00500
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.7000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.52
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.56
REMARK 200 COMPLETENESS FOR SHELL (%) : 66.6
REMARK 200 DATA REDUNDANCY IN SHELL : 3.40
REMARK 200 R MERGE FOR SHELL (I) : 0.12200
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 9.800
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHENIX
REMARK 200 STARTING MODEL: 1DB1
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 51.93
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, PH 6.0, VAPOR
REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K
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 22.46300
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 66.15850
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.65850
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 66.15850
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.46300
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.65850
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 1180 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 12220 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL
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 GLY A 114
REMARK 465 SER A 115
REMARK 465 HIS A 116
REMARK 465 MET A 117
REMARK 465 ASP A 118
REMARK 465 GLU A 425
REMARK 465 ILE A 426
REMARK 465 SER A 427
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 HIS A 377 CG ND1 CD2 CE1 NE2
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 HD22 ASN A 290 O HOH A 603 1.41
REMARK 500 HH12 ARG A 402 O HOH A 609 1.47
REMARK 500 HH TYR A 147 O HOH A 601 1.58
REMARK 500 OH TYR A 147 O HOH A 601 1.71
REMARK 500 O HOH A 618 O HOH A 665 1.80
REMARK 500 O HOH A 900 O HOH A 941 1.95
REMARK 500 O HOH A 915 O HOH A 961 1.96
REMARK 500 O HOH A 933 O HOH A 1000 1.98
REMARK 500 O HOH A 736 O HOH A 847 2.00
REMARK 500 O HOH A 944 O HOH A 967 2.01
REMARK 500 O HOH A 604 O HOH A 859 2.02
REMARK 500 O HOH A 640 O HOH A 833 2.02
REMARK 500 O HOH A 643 O HOH A 889 2.02
REMARK 500 O HOH A 988 O HOH A 999 2.04
REMARK 500 O HOH A 672 O HOH A 889 2.04
REMARK 500 O HOH A 969 O HOH A 1004 2.07
REMARK 500 O HOH A 869 O HOH A 941 2.09
REMARK 500 OE1 GLN A 129 O HOH A 602 2.12
REMARK 500 O HOH A 747 O HOH A 918 2.13
REMARK 500 O HOH A 842 O HOH A 915 2.13
REMARK 500 O HOH A 901 O HOH A 902 2.14
REMARK 500 O HOH A 657 O HOH A 896 2.15
REMARK 500 O HOH A 915 O HOH A 974 2.16
REMARK 500 O HOH A 820 O HOH A 879 2.17
REMARK 500 ND2 ASN A 290 O HOH A 603 2.17
REMARK 500 NH2 ARG A 130 O HOH A 604 2.18
REMARK 500 O HOH A 809 O HOH A 830 2.18
REMARK 500 NZ LYS A 123 O HOH A 605 2.19
REMARK 500 O HOH A 951 O HOH A 968 2.19
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 O HOH A 764 O HOH A 896 1455 2.18
REMARK 500 O HOH A 618 O HOH A 903 3655 2.18
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 161 47.84 -149.05
REMARK 500 LEU A 224 50.98 39.17
REMARK 500 ASP A 283 15.76 -142.69
REMARK 500 ASP A 342 64.17 -102.69
REMARK 500 LEU A 414 -154.05 -96.85
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH A1009 DISTANCE = 6.25 ANGSTROMS
REMARK 525 HOH A1010 DISTANCE = 6.31 ANGSTROMS
DBREF 7QPP A 118 216 UNP P11473 VDR_HUMAN 118 165
DBREF 7QPP A 217 427 UNP P11473 VDR_HUMAN 217 427
SEQADV 7QPP GLY A 114 UNP P11473 EXPRESSION TAG
SEQADV 7QPP SER A 115 UNP P11473 EXPRESSION TAG
SEQADV 7QPP HIS A 116 UNP P11473 EXPRESSION TAG
SEQADV 7QPP MET A 117 UNP P11473 EXPRESSION TAG
SEQRES 1 A 263 GLY SER HIS MET ASP SER LEU ARG PRO LYS LEU SER GLU
SEQRES 2 A 263 GLU GLN GLN ARG ILE ILE ALA ILE LEU LEU ASP ALA HIS
SEQRES 3 A 263 HIS LYS THR TYR ASP PRO THR TYR SER ASP PHE CYS GLN
SEQRES 4 A 263 PHE ARG PRO PRO VAL ARG VAL ASN ASP GLY GLY GLY SER
SEQRES 5 A 263 VAL THR LEU GLU LEU SER GLN LEU SER MET LEU PRO HIS
SEQRES 6 A 263 LEU ALA ASP LEU VAL SER TYR SER ILE GLN LYS VAL ILE
SEQRES 7 A 263 GLY PHE ALA LYS MET ILE PRO GLY PHE ARG ASP LEU THR
SEQRES 8 A 263 SER GLU ASP GLN ILE VAL LEU LEU LYS SER SER ALA ILE
SEQRES 9 A 263 GLU VAL ILE MET LEU ARG SER ASN GLU SER PHE THR MET
SEQRES 10 A 263 ASP ASP MET SER TRP THR CYS GLY ASN GLN ASP TYR LYS
SEQRES 11 A 263 TYR ARG VAL SER ASP VAL THR LYS ALA GLY HIS SER LEU
SEQRES 12 A 263 GLU LEU ILE GLU PRO LEU ILE LYS PHE GLN VAL GLY LEU
SEQRES 13 A 263 LYS LYS LEU ASN LEU HIS GLU GLU GLU HIS VAL LEU LEU
SEQRES 14 A 263 MET ALA ILE CYS ILE VAL SER PRO ASP ARG PRO GLY VAL
SEQRES 15 A 263 GLN ASP ALA ALA LEU ILE GLU ALA ILE GLN ASP ARG LEU
SEQRES 16 A 263 SER ASN THR LEU GLN THR TYR ILE ARG CYS ARG HIS PRO
SEQRES 17 A 263 PRO PRO GLY SER HIS LEU LEU TYR ALA LYS MET ILE GLN
SEQRES 18 A 263 LYS LEU ALA ASP LEU ARG SER LEU ASN GLU GLU HIS SER
SEQRES 19 A 263 LYS GLN TYR ARG CYS LEU SER PHE GLN PRO GLU CYS SER
SEQRES 20 A 263 MET LYS LEU THR PRO LEU VAL LEU GLU VAL PHE GLY ASN
SEQRES 21 A 263 GLU ILE SER
HET VDX A 501 74
HET SO4 A 502 5
HETNAM VDX 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-
HETNAM 2 VDX OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-
HETNAM 3 VDX CYCLOHEXANE-1,3-DIOL
HETNAM SO4 SULFATE ION
HETSYN VDX 1,25 DIHYDROXY VITAMIN D3
FORMUL 2 VDX C27 H44 O3
FORMUL 3 SO4 O4 S 2-
FORMUL 4 HOH *410(H2 O)
HELIX 1 AA1 SER A 125 TYR A 143 1 19
HELIX 2 AA2 ASP A 149 PHE A 153 5 5
HELIX 3 AA3 SER A 216 LEU A 224 1 9
HELIX 4 AA4 MET A 226 MET A 247 1 22
HELIX 5 AA5 GLY A 250 LEU A 254 5 5
HELIX 6 AA6 THR A 255 SER A 275 1 21
HELIX 7 AA7 ASN A 290 ASP A 292 5 3
HELIX 8 AA8 ARG A 296 LYS A 302 1 7
HELIX 9 AA9 SER A 306 LEU A 323 1 18
HELIX 10 AB1 HIS A 326 VAL A 339 1 14
HELIX 11 AB2 ASP A 348 HIS A 371 1 24
HELIX 12 AB3 LEU A 378 PHE A 406 1 29
HELIX 13 AB4 GLU A 409 LEU A 414 1 6
HELIX 14 AB5 THR A 415 GLY A 423 1 9
SHEET 1 AA1 3 PHE A 279 THR A 280 0
SHEET 2 AA1 3 SER A 285 THR A 287 -1 O SER A 285 N THR A 280
SHEET 3 AA1 3 LYS A 294 TYR A 295 -1 O TYR A 295 N TRP A 286
CISPEP 1 PRO A 373 PRO A 374 0 0.50
CRYST1 44.926 51.317 132.317 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 0.022259 0.000000 0.000000 0.00000
SCALE2 0.000000 0.019487 0.000000 0.00000
SCALE3 0.000000 0.000000 0.007558 0.00000