HEADER GENE REGULATION 04-FEB-20 6XZK TITLE STRUCTURE OF ZVDR LBD-CALCITRIOL IN COMPLEX WITH CHIMERA 13 COMPND MOL_ID: 1; COMPND 2 MOLECULE: VITAMIN D3 RECEPTOR A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: VDR-A,1,25-DIHYDROXYVITAMIN D3 RECEPTOR A,NUCLEAR RECEPTOR COMPND 5 SUBFAMILY 1 GROUP I MEMBER 1-A; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: GLU-ASN-ALA-UIA-URL-URY-URV-UZN-LYS; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: ZEBRAFISH; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 GENE: VDRA, NR1I1A, VDR; 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: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS NUCLEAR RECEPTOR, FOLDAMER, HELIX MIMICRY, PROTEIN-PROTEIN KEYWDS 2 INTERACTION, GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR J.BURATTO,A.Y.BELORUSOVA,N.ROCHEL,G.GUICHARD REVDAT 4 24-JAN-24 6XZK 1 REMARK REVDAT 3 15-NOV-23 6XZK 1 LINK ATOM REVDAT 2 01-SEP-21 6XZK 1 JRNL REVDAT 1 17-FEB-21 6XZK 0 JRNL AUTH L.CUSSOL,L.MAURAN-AMBROSINO,J.BURATTO,A.Y.BELORUSOVA, JRNL AUTH 2 M.NEUVILLE,J.OSZ,S.FRIBOURG,J.FREMAUX,C.DOLAIN,S.R.GOUDREAU, JRNL AUTH 3 N.ROCHEL,G.GUICHARD JRNL TITL STRUCTURAL BASIS FOR ALPHA-HELIX MIMICRY AND INHIBITION OF JRNL TITL 2 PROTEIN-PROTEIN INTERACTIONS WITH OLIGOUREA FOLDAMERS. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 60 2296 2021 JRNL REFN ESSN 1521-3773 JRNL PMID 32935897 JRNL DOI 10.1002/ANIE.202008992 REMARK 2 REMARK 2 RESOLUTION. 2.00 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 23167 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 1128 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 14.9310 - 3.9781 0.98 3045 163 0.1740 0.1979 REMARK 3 2 3.9781 - 3.1674 0.99 2864 158 0.1946 0.2087 REMARK 3 3 3.1674 - 2.7699 1.00 2840 142 0.2239 0.2703 REMARK 3 4 2.7699 - 2.5180 1.00 2832 146 0.2236 0.2556 REMARK 3 5 2.5180 - 2.3382 1.00 2782 147 0.2230 0.2298 REMARK 3 6 2.3382 - 2.2008 0.99 2757 135 0.2287 0.2476 REMARK 3 7 2.2008 - 2.0909 0.96 2681 148 0.2449 0.2761 REMARK 3 8 2.0909 - 2.0001 0.80 2238 89 0.2573 0.2543 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.01 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 : 0.003 2027 REMARK 3 ANGLE : 0.708 2733 REMARK 3 CHIRALITY : 0.038 314 REMARK 3 PLANARITY : 0.005 348 REMARK 3 DIHEDRAL : 16.042 1231 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 154 THROUGH 305 ) REMARK 3 ORIGIN FOR THE GROUP (A): -33.3924 30.0256 -5.0982 REMARK 3 T TENSOR REMARK 3 T11: 0.2382 T22: 0.4080 REMARK 3 T33: 0.3037 T12: -0.0389 REMARK 3 T13: 0.0129 T23: -0.0129 REMARK 3 L TENSOR REMARK 3 L11: 1.8298 L22: 3.4009 REMARK 3 L33: 3.8304 L12: -0.8770 REMARK 3 L13: -1.1639 L23: 2.8947 REMARK 3 S TENSOR REMARK 3 S11: -0.0091 S12: -0.2541 S13: 0.1088 REMARK 3 S21: -0.2035 S22: 0.0401 S23: 0.0390 REMARK 3 S31: -0.3074 S32: 0.1258 S33: -0.0045 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 306 THROUGH 351 ) REMARK 3 ORIGIN FOR THE GROUP (A): -32.7709 12.8711 -0.8425 REMARK 3 T TENSOR REMARK 3 T11: 0.3871 T22: 0.3848 REMARK 3 T33: 0.4123 T12: -0.0192 REMARK 3 T13: 0.0853 T23: 0.0881 REMARK 3 L TENSOR REMARK 3 L11: 4.3053 L22: 4.7311 REMARK 3 L33: 7.8515 L12: -0.3658 REMARK 3 L13: -2.2386 L23: 1.5370 REMARK 3 S TENSOR REMARK 3 S11: -0.2725 S12: -0.4789 S13: -0.7812 REMARK 3 S21: 0.1722 S22: 0.0401 S23: 0.3148 REMARK 3 S31: 0.9201 S32: -0.0514 S33: 0.2656 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 352 THROUGH 404 ) REMARK 3 ORIGIN FOR THE GROUP (A): -29.6760 35.7362 8.6662 REMARK 3 T TENSOR REMARK 3 T11: 0.3098 T22: 0.6887 REMARK 3 T33: 0.3493 T12: 0.0164 REMARK 3 T13: -0.0110 T23: -0.1379 REMARK 3 L TENSOR REMARK 3 L11: 5.6662 L22: 5.0991 REMARK 3 L33: 4.5074 L12: 1.3811 REMARK 3 L13: -1.5932 L23: 0.3322 REMARK 3 S TENSOR REMARK 3 S11: -0.0844 S12: -0.9042 S13: 0.2574 REMARK 3 S21: 0.1626 S22: 0.2630 S23: -0.2013 REMARK 3 S31: -0.3959 S32: 0.4657 S33: -0.1676 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 405 THROUGH 452 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.7662 21.9032 -5.6104 REMARK 3 T TENSOR REMARK 3 T11: 0.1880 T22: 0.4085 REMARK 3 T33: 0.3430 T12: -0.0011 REMARK 3 T13: 0.0069 T23: -0.0261 REMARK 3 L TENSOR REMARK 3 L11: 3.2704 L22: 1.8605 REMARK 3 L33: 7.2659 L12: -1.3700 REMARK 3 L13: -1.7228 L23: 1.7754 REMARK 3 S TENSOR REMARK 3 S11: -0.1230 S12: -0.6501 S13: -0.0897 REMARK 3 S21: 0.0915 S22: 0.2321 S23: -0.0957 REMARK 3 S31: 0.1755 S32: 0.6984 S33: -0.1444 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 9 ) REMARK 3 ORIGIN FOR THE GROUP (A): -24.3865 36.9803 -17.8869 REMARK 3 T TENSOR REMARK 3 T11: 0.5600 T22: 0.3992 REMARK 3 T33: 0.4070 T12: -0.1203 REMARK 3 T13: 0.0409 T23: -0.0620 REMARK 3 L TENSOR REMARK 3 L11: 7.4481 L22: 7.0718 REMARK 3 L33: 2.5701 L12: 3.4280 REMARK 3 L13: -2.0640 L23: 2.3611 REMARK 3 S TENSOR REMARK 3 S11: 0.0953 S12: -0.4571 S13: 0.6761 REMARK 3 S21: -0.7341 S22: 0.0024 S23: 0.2808 REMARK 3 S31: -1.8663 S32: 1.0134 S33: -0.1005 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 6XZK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-FEB-20. REMARK 100 THE DEPOSITION ID IS D_1292106567. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-SEP-15 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 : ID30B 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23222 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 14.931 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 1.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.0400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.6 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 : 3.320 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: 2HC4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: LITHIUM SULFATE 1.8 M, MES 100 MM, PH REMARK 280 6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 174.99200 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 87.49600 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 131.24400 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 43.74800 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 218.74000 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 174.99200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 87.49600 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 43.74800 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 131.24400 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 218.74000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 683 LIES ON A SPECIAL POSITION. 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 152 REMARK 465 SER A 153 REMARK 465 GLU A 191 REMARK 465 GLY A 192 REMARK 465 PRO A 193 REMARK 465 VAL A 194 REMARK 465 THR A 195 REMARK 465 ARG A 196 REMARK 465 SER A 197 REMARK 465 ALA A 198 REMARK 465 SER A 199 REMARK 465 ARG A 200 REMARK 465 ALA A 201 REMARK 465 ALA A 202 REMARK 465 SER A 203 REMARK 465 LEU A 204 REMARK 465 HIS A 205 REMARK 465 SER A 206 REMARK 465 LEU A 207 REMARK 465 SER A 208 REMARK 465 ASP A 209 REMARK 465 ALA A 210 REMARK 465 SER A 211 REMARK 465 SER A 212 REMARK 465 ASP A 213 REMARK 465 SER A 214 REMARK 465 PHE A 215 REMARK 465 ASN A 216 REMARK 465 HIS A 217 REMARK 465 SER A 218 REMARK 465 PRO A 219 REMARK 465 GLU A 220 REMARK 465 SER A 221 REMARK 465 VAL A 222 REMARK 465 ASP A 223 REMARK 465 THR A 224 REMARK 465 LYS A 225 REMARK 465 LEU A 226 REMARK 465 ASN A 227 REMARK 465 PHE A 228 REMARK 465 SER A 229 REMARK 465 ASN A 230 REMARK 465 LEU A 231 REMARK 465 LEU A 232 REMARK 465 MET A 233 REMARK 465 MET A 234 REMARK 465 TYR A 235 REMARK 465 GLN A 236 REMARK 465 ASP A 237 REMARK 465 SER A 238 REMARK 465 GLY A 239 REMARK 465 SER A 240 REMARK 465 PRO A 241 REMARK 465 ASP A 242 REMARK 465 SER A 243 REMARK 465 SER A 244 REMARK 465 GLU A 245 REMARK 465 GLU A 246 REMARK 465 ASP A 247 REMARK 465 GLN A 248 REMARK 465 GLN A 249 REMARK 465 SER A 250 REMARK 465 GLY A 402 REMARK 465 ARG A 403 REMARK 465 SER A 453 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 MET A 155 CE REMARK 470 GLU A 159 CD OE1 OE2 REMARK 470 LYS A 173 CD CE NZ REMARK 470 ARG A 251 CD NE CZ NH1 NH2 REMARK 470 ARG A 280 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 310 OE2 REMARK 470 GLN A 375 CG CD OE1 NE2 REMARK 470 HIS A 377 CG ND1 CD2 CE1 NE2 REMARK 470 GLY A 401 CA C O REMARK 470 LEU A 404 CD1 CD2 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 URL B 5 CA - C - N ANGL. DEV. = 26.8 DEGREES REMARK 500 MFH B 6 CA - C - N ANGL. DEV. = 26.7 DEGREES REMARK 500 URV B 7 CA - C - N ANGL. DEV. = 24.3 DEGREES REMARK 500 UZN B 8 CA - C - N ANGL. DEV. = 14.7 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 LEU A 367 34.19 -88.00 REMARK 500 URV B 7 7.53 -61.30 REMARK 500 UZN B 8 23.78 -69.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 URL B 5 MFH B 6 131.24 REMARK 500 MFH B 6 URV B 7 128.64 REMARK 500 URV B 7 UZN B 8 134.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 URL B 5 -27.31 REMARK 500 MFH B 6 -29.64 REMARK 500 URV B 7 -25.41 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 VDX A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues UIA B 4 and URL B 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues URL B 5 and MFH B 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues MFH B 6 and URV B 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues URV B 7 and UZN B 8 DBREF 6XZK A 156 453 UNP Q9PTN2 VDRA_DANRE 156 453 DBREF 6XZK B 1 9 PDB 6XZK 6XZK 1 9 SEQADV 6XZK GLY A 152 UNP Q9PTN2 EXPRESSION TAG SEQADV 6XZK SER A 153 UNP Q9PTN2 EXPRESSION TAG SEQADV 6XZK HIS A 154 UNP Q9PTN2 EXPRESSION TAG SEQADV 6XZK MET A 155 UNP Q9PTN2 EXPRESSION TAG SEQRES 1 A 302 GLY SER HIS MET LEU SER ASP GLU GLN MET GLN ILE ILE SEQRES 2 A 302 ASN SER LEU VAL GLU ALA HIS HIS LYS THR TYR ASP ASP SEQRES 3 A 302 SER TYR SER ASP PHE VAL ARG PHE ARG PRO PRO VAL ARG SEQRES 4 A 302 GLU GLY PRO VAL THR ARG SER ALA SER ARG ALA ALA SER SEQRES 5 A 302 LEU HIS SER LEU SER ASP ALA SER SER ASP SER PHE ASN SEQRES 6 A 302 HIS SER PRO GLU SER VAL ASP THR LYS LEU ASN PHE SER SEQRES 7 A 302 ASN LEU LEU MET MET TYR GLN ASP SER GLY SER PRO ASP SEQRES 8 A 302 SER SER GLU GLU ASP GLN GLN SER ARG LEU SER MET LEU SEQRES 9 A 302 PRO HIS LEU ALA ASP LEU VAL SER TYR SER ILE GLN LYS SEQRES 10 A 302 VAL ILE GLY PHE ALA LYS MET ILE PRO GLY PHE ARG ASP SEQRES 11 A 302 LEU THR ALA GLU ASP GLN ILE ALA LEU LEU LYS SER SER SEQRES 12 A 302 ALA ILE GLU ILE ILE MET LEU ARG SER ASN GLN SER PHE SEQRES 13 A 302 SER LEU GLU ASP MET SER TRP SER CYS GLY GLY PRO ASP SEQRES 14 A 302 PHE LYS TYR CYS ILE ASN ASP VAL THR LYS ALA GLY HIS SEQRES 15 A 302 THR LEU GLU LEU LEU GLU PRO LEU VAL LYS PHE GLN VAL SEQRES 16 A 302 GLY LEU LYS LYS LEU LYS LEU HIS GLU GLU GLU HIS VAL SEQRES 17 A 302 LEU LEU MET ALA ILE CYS LEU LEU SER PRO ASP ARG PRO SEQRES 18 A 302 GLY VAL GLN ASP HIS VAL ARG ILE GLU ALA LEU GLN ASP SEQRES 19 A 302 ARG LEU CYS ASP VAL LEU GLN ALA TYR ILE ARG ILE GLN SEQRES 20 A 302 HIS PRO GLY GLY ARG LEU LEU TYR ALA LYS MET ILE GLN SEQRES 21 A 302 LYS LEU ALA ASP LEU ARG SER LEU ASN GLU GLU HIS SER SEQRES 22 A 302 LYS GLN TYR ARG SER LEU SER PHE GLN PRO GLU HIS SER SEQRES 23 A 302 MET GLN LEU THR PRO LEU VAL LEU GLU VAL PHE GLY SER SEQRES 24 A 302 GLU VAL SER SEQRES 1 B 9 GLU ASN ALA UIA URL MFH URV UZN LYS HET UIA B 4 7 HET URL B 5 10 HET MFH B 6 14 HET URV B 7 9 HET UZN B 8 10 HET VDX A 501 30 HET ACT A 502 4 HET ACT A 503 4 HETNAM UIA [(2~{R})-1-AZANYLPROPAN-2-YL]CARBAMIC ACID HETNAM URL [(2~{S})-2-AZANYL-4-METHYL-PENTYL]CARBAMIC ACID HETNAM MFH [(2~{S})-2-AZANYL-3-(4-HYDROXYPHENYL)PROPYL]CARBAMIC HETNAM 2 MFH ACID HETNAM URV [(2~{S})-2-AZANYL-3-METHYL-BUTYL]CARBAMIC ACID HETNAM UZN [(2~{S})-2-AZANYLHEXYL]CARBAMIC ACID 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 ACT ACETATE ION HETSYN VDX 1,25 DIHYDROXY VITAMIN D3 FORMUL 2 UIA C4 H10 N2 O2 FORMUL 2 URL C7 H16 N2 O2 FORMUL 2 MFH C10 H14 N2 O3 FORMUL 2 URV C6 H14 N2 O2 FORMUL 2 UZN C7 H16 N2 O2 FORMUL 3 VDX C27 H44 O3 FORMUL 4 ACT 2(C2 H3 O2 1-) FORMUL 6 HOH *100(H2 O) HELIX 1 AA1 SER A 157 TYR A 175 1 19 HELIX 2 AA2 TYR A 179 PHE A 185 5 7 HELIX 3 AA3 MET A 254 MET A 275 1 22 HELIX 4 AA4 GLY A 278 LEU A 282 5 5 HELIX 5 AA5 THR A 283 SER A 303 1 21 HELIX 6 AA6 CYS A 324 LYS A 330 1 7 HELIX 7 AA7 THR A 334 LEU A 351 1 18 HELIX 8 AA8 HIS A 354 LEU A 367 1 14 HELIX 9 AA9 ASP A 376 HIS A 399 1 24 HELIX 10 AB1 LEU A 405 PHE A 432 1 28 HELIX 11 AB2 GLN A 433 MET A 438 1 6 HELIX 12 AB3 THR A 441 GLY A 449 1 9 SHEET 1 AA1 3 PHE A 307 SER A 308 0 SHEET 2 AA1 3 SER A 313 SER A 315 -1 O SER A 313 N SER A 308 SHEET 3 AA1 3 LYS A 322 TYR A 323 -1 O TYR A 323 N TRP A 314 LINK C ALA B 3 N UIA B 4 1555 1555 1.34 LINK C UIA B 4 N URL B 5 1555 1555 1.35 LINK C URL B 5 N MFH B 6 1555 1555 1.34 LINK C MFH B 6 N URV B 7 1555 1555 1.34 LINK C URV B 7 N UZN B 8 1555 1555 1.34 LINK C UZN B 8 N LYS B 9 1555 1555 1.34 SITE 1 AC1 10 TYR A 175 SER A 265 ARG A 302 SER A 303 SITE 2 AC1 10 SER A 306 TRP A 314 CYS A 316 VAL A 328 SITE 3 AC1 10 HIS A 333 HIS A 423 SITE 1 AC2 8 THR A 174 TYR A 175 ASP A 176 TYR A 179 SITE 2 AC2 8 TYR A 264 LYS A 268 ARG A 302 HOH A 663 SITE 1 AC3 7 GLN A 398 SER A 431 GLY A 449 SER A 450 SITE 2 AC3 7 HOH A 605 HOH A 623 GLU B 1 SITE 1 AC4 10 ILE A 288 LYS A 292 GLU A 446 VAL A 447 SITE 2 AC4 10 HOH A 646 ASN B 2 ALA B 3 MFH B 6 SITE 3 AC4 10 URV B 7 UZN B 8 SITE 1 AC5 13 HIS A 154 ALA A 284 ILE A 288 LYS A 292 SITE 2 AC5 13 PRO A 434 GLU A 446 VAL A 447 ALA B 3 SITE 3 AC5 13 UIA B 4 URV B 7 UZN B 8 LYS B 9 SITE 4 AC5 13 HOH B 101 SITE 1 AC6 11 HIS A 154 LYS A 274 ALA A 284 PRO A 434 SITE 2 AC6 11 MET A 438 ALA B 3 UIA B 4 URL B 5 SITE 3 AC6 11 UZN B 8 LYS B 9 HOH B 101 SITE 1 AC7 7 LYS A 274 GLN A 287 MET A 438 UIA B 4 SITE 2 AC7 7 URL B 5 MFH B 6 LYS B 9 CRYST1 66.112 66.112 262.488 90.00 90.00 120.00 P 65 2 2 12 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 0.015126 0.008733 0.000000 0.00000 SCALE2 0.000000 0.017466 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003810 0.00000