HEADER TRANSCRIPTION/DNA 21-JAN-14 4CN5 TITLE CRYSTAL STRUCTURE OF THE HUMAN RETINOID X RECEPTOR DNA-BINDING DOMAIN TITLE 2 BOUND TO THE HUMAN NR1D1 RESPONSE ELEMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: RETINOIC ACID RECEPTOR RXR-ALPHA; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: DNA-BINDING DOMAIN, RESIDUES 126-212; COMPND 5 SYNONYM: NUCLEAR RECEPTOR SUBFAMILY 2 GROUP B MEMBER 1, RETINOID X COMPND 6 RECEPTOR ALPHA; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: 5'-D(*TP*GP*GP*GP*GP*TP*CP*AP*GP*AP*GP*TP*TP*CP *AP*AP*TP)- COMPND 10 3'; COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: 5'-D(*AP*TP*TP*GP*AP*AP*CP*TP*CP*TP*GP*AP*CP*CP *CP*CP*AP)- COMPND 15 3'; COMPND 16 CHAIN: D; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PHXGW; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 17 ORGANISM_COMMON: HUMAN; SOURCE 18 ORGANISM_TAXID: 9606 KEYWDS TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.G.MCEWEN,P.POUSSIN-COURMONTAGNE,J.OSZ,N.ROCHEL REVDAT 2 20-DEC-23 4CN5 1 REMARK LINK REVDAT 1 18-FEB-15 4CN5 0 JRNL AUTH J.OSZ,A.G.MCEWEN,P.POUSSIN-COURMONTAGNE,E.MOUTIER,C.BIRCK, JRNL AUTH 2 I.DAVIDSON,D.MORAS,N.ROCHEL JRNL TITL STRUCTURAL BASIS OF NATURAL PROMOTER RECOGNITION BY THE JRNL TITL 2 RETINOID X NUCLEAR RECEPTOR. JRNL REF SCI.REP. V. 5 8216 2015 JRNL REFN ESSN 2045-2322 JRNL PMID 25645674 JRNL DOI 10.1038/SREP08216 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.09 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.910 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 19153 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1881 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 43.1025 - 4.7008 0.92 2491 174 0.1389 0.1650 REMARK 3 2 4.7008 - 3.7318 0.93 2542 158 0.1307 0.2086 REMARK 3 3 3.7318 - 3.2603 0.92 2548 155 0.1375 0.1802 REMARK 3 4 3.2603 - 2.9623 0.98 2726 118 0.1712 0.2525 REMARK 3 5 2.9623 - 2.7500 0.99 2737 149 0.1842 0.2786 REMARK 3 6 2.7500 - 2.5879 0.99 2751 120 0.1774 0.2668 REMARK 3 7 2.5879 - 2.4583 0.99 2733 127 0.1683 0.2091 REMARK 3 8 2.4583 - 2.3513 0.99 2739 150 0.1690 0.2208 REMARK 3 9 2.3513 - 2.2608 0.93 2592 157 0.2097 0.2400 REMARK 3 10 2.2608 - 2.1828 0.81 2182 161 0.3113 0.4136 REMARK 3 11 2.1828 - 2.1145 0.99 2726 137 0.1977 0.2364 REMARK 3 12 2.1145 - 2.0541 0.99 2700 162 0.1942 0.2656 REMARK 3 13 2.0541 - 2.0000 0.97 2682 113 0.2056 0.2970 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.550 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.12 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.23 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 : 0.006 2068 REMARK 3 ANGLE : 1.184 2899 REMARK 3 CHIRALITY : 0.063 303 REMARK 3 PLANARITY : 0.004 254 REMARK 3 DIHEDRAL : 21.202 848 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): -25.6533 -4.7635 26.4335 REMARK 3 T TENSOR REMARK 3 T11: 0.2008 T22: 0.0898 REMARK 3 T33: 0.1703 T12: -0.0305 REMARK 3 T13: -0.0657 T23: 0.0040 REMARK 3 L TENSOR REMARK 3 L11: 3.8760 L22: 4.7768 REMARK 3 L33: 4.3401 L12: 0.4304 REMARK 3 L13: 1.1954 L23: 0.6922 REMARK 3 S TENSOR REMARK 3 S11: -0.2072 S12: 0.0859 S13: 0.1852 REMARK 3 S21: 0.0594 S22: 0.0928 S23: 0.0048 REMARK 3 S31: -0.2353 S32: 0.2443 S33: 0.0547 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): -38.7137 -29.5021 10.0335 REMARK 3 T TENSOR REMARK 3 T11: 0.3708 T22: 0.1975 REMARK 3 T33: 0.4098 T12: -0.0574 REMARK 3 T13: -0.1566 T23: 0.0465 REMARK 3 L TENSOR REMARK 3 L11: 3.7310 L22: 3.6143 REMARK 3 L33: 4.0449 L12: -0.3281 REMARK 3 L13: 1.4582 L23: 0.3482 REMARK 3 S TENSOR REMARK 3 S11: 0.4105 S12: 0.1044 S13: -0.9020 REMARK 3 S21: 0.0995 S22: 0.2336 S23: 0.3426 REMARK 3 S31: 0.9579 S32: -0.1702 S33: -0.1518 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN C REMARK 3 ORIGIN FOR THE GROUP (A): -26.1252 -13.2603 12.5427 REMARK 3 T TENSOR REMARK 3 T11: 0.1736 T22: 0.2491 REMARK 3 T33: 0.2263 T12: -0.0133 REMARK 3 T13: -0.0240 T23: -0.0066 REMARK 3 L TENSOR REMARK 3 L11: 2.0393 L22: 1.4344 REMARK 3 L33: 2.7333 L12: 1.5406 REMARK 3 L13: 1.2175 L23: 1.3800 REMARK 3 S TENSOR REMARK 3 S11: -0.3192 S12: 0.3414 S13: -0.0960 REMARK 3 S21: -0.1085 S22: 0.2876 S23: -0.2239 REMARK 3 S31: -0.2684 S32: 0.5439 S33: 0.0302 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN D REMARK 3 ORIGIN FOR THE GROUP (A): -25.9815 -15.6222 12.7459 REMARK 3 T TENSOR REMARK 3 T11: 0.0638 T22: 0.1805 REMARK 3 T33: 0.1714 T12: 0.0155 REMARK 3 T13: -0.0120 T23: -0.0387 REMARK 3 L TENSOR REMARK 3 L11: 2.0459 L22: 2.4823 REMARK 3 L33: 4.5425 L12: 0.0983 REMARK 3 L13: 0.1873 L23: 0.4341 REMARK 3 S TENSOR REMARK 3 S11: -0.2396 S12: 0.3051 S13: -0.2149 REMARK 3 S21: -0.0563 S22: 0.4091 S23: -0.2177 REMARK 3 S31: -0.2902 S32: 0.6818 S33: 0.1417 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 4CN5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1290059526. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-FEB-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.6 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) : 1.2833 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19176 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 43.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.03000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.2000 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) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.12000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 9.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1DSZ REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.2M KNO3, PH 6.6 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 51.64300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.16350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 51.64300 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.16350 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -87.1 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 126 REMARK 465 SER A 127 REMARK 465 HIS A 128 REMARK 465 GLN A 210 REMARK 465 ARG A 211 REMARK 465 GLY A 212 REMARK 465 GLY B 126 REMARK 465 SER B 127 REMARK 465 HIS B 128 REMARK 465 MET B 129 REMARK 465 PHE B 130 REMARK 465 THR B 131 REMARK 465 ARG B 172 REMARK 465 ASP B 173 REMARK 465 ASN B 174 REMARK 465 GLN B 210 REMARK 465 ARG B 211 REMARK 465 GLY B 212 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 O HOH B 2037 O HOH B 2038 2.16 REMARK 500 OP1 DG C 2 O HOH C 2001 2.18 REMARK 500 O HOH A 2091 O HOH A 2092 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 DG C 5 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DA C 8 O4' - C1' - N9 ANGL. DEV. = -5.5 DEGREES REMARK 500 DG C 9 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 DT C 12 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT C 13 O4' - C1' - N1 ANGL. DEV. = -8.8 DEGREES REMARK 500 DG D 4 C3' - C2' - C1' ANGL. DEV. = -5.8 DEGREES REMARK 500 DA D 5 O4' - C1' - N9 ANGL. DEV. = -4.4 DEGREES REMARK 500 DA D 6 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT D 10 O4' - C1' - N1 ANGL. DEV. = -5.0 DEGREES REMARK 500 DC D 13 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DA D 17 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES REMARK 500 DA D 17 O4' - C1' - N9 ANGL. DEV. = 2.0 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 ASP A 173 -128.12 -116.20 REMARK 500 TYR B 150 109.86 -58.52 REMARK 500 ASP B 176 65.41 -155.56 REMARK 500 ASP B 180 -169.21 -124.78 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 C2074 DISTANCE = 6.39 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1210 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 135 SG REMARK 620 2 CYS A 138 SG 116.7 REMARK 620 3 CYS A 152 SG 111.5 103.7 REMARK 620 4 CYS A 155 SG 104.4 117.0 102.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1211 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 171 SG REMARK 620 2 CYS A 177 SG 104.5 REMARK 620 3 CYS A 187 SG 110.2 117.0 REMARK 620 4 CYS A 190 SG 115.7 105.8 104.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1210 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 135 SG REMARK 620 2 CYS B 138 SG 109.0 REMARK 620 3 CYS B 152 SG 114.6 106.5 REMARK 620 4 CYS B 155 SG 109.3 110.2 107.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1211 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 171 SG REMARK 620 2 CYS B 177 SG 103.1 REMARK 620 3 CYS B 187 SG 108.5 105.8 REMARK 620 4 CYS B 190 SG 117.5 113.3 107.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K D1018 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B2064 O REMARK 620 2 HOH C2027 O 83.7 REMARK 620 3 DT D 10 O2 161.6 90.8 REMARK 620 4 DG D 11 O4' 94.4 177.8 91.3 REMARK 620 5 NO3 D1019 O3 82.0 106.7 82.8 74.2 REMARK 620 6 NO3 D1019 O1 91.4 61.1 70.7 120.2 47.9 REMARK 620 7 HOH D2027 O 87.0 102.0 111.4 76.6 147.8 163.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K C1019 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT C 6 O2 REMARK 620 2 DC C 7 O4' 100.1 REMARK 620 3 DC C 7 O2 80.4 62.4 REMARK 620 4 HOH C2016 O 78.7 76.6 129.3 REMARK 620 5 HOH C2018 O 148.3 89.0 77.1 133.0 REMARK 620 6 HOH C2064 O 92.0 165.3 128.6 97.8 84.9 REMARK 620 7 HOH C2065 O 112.9 101.8 161.8 47.4 94.4 65.4 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K C1020 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DA C 8 N7 REMARK 620 2 DG C 9 O6 77.8 REMARK 620 3 HOH C2023 O 85.6 163.3 REMARK 620 4 HOH C2025 O 84.0 90.9 87.5 REMARK 620 5 HOH C2033 O 92.3 83.7 96.9 174.0 REMARK 620 6 HOH C2034 O 140.0 71.7 122.9 121.1 59.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K C1018 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT C 13 O2 REMARK 620 2 DC C 14 O2 81.2 REMARK 620 3 DC C 14 O4' 95.3 63.8 REMARK 620 4 HOH C2046 O 151.1 73.9 86.7 REMARK 620 5 HOH C2048 O 124.1 144.7 87.6 84.7 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1210 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1211 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1210 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1211 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K D 1018 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K C 1018 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K C 1019 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K C 1020 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 D 1019 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1212 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1213 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL D 1020 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL C 1021 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1214 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4CN2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HUMAN RETINOID X RECEPTOR DNA -BINDING REMARK 900 DOMAIN BOUND TO THE HUMAN RAMP2 RESPONSE ELEMENT REMARK 900 RELATED ID: 4CN3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HUMAN RETINOID X RECEPTOR DNA -BINDING REMARK 900 DOMAIN BOUND TO THE HUMAN GDE1SPA RESPONSE ELEMENT REMARK 900 RELATED ID: 4CN7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HUMAN RETINOID X RECEPTOR DNA -BINDING REMARK 900 DOMAIN BOUND TO AN IDEALIZED DR1 RESPONSE ELEMENT DBREF 4CN5 A 130 212 UNP P19793 RXRA_HUMAN 130 212 DBREF 4CN5 B 130 212 UNP P19793 RXRA_HUMAN 130 212 DBREF 4CN5 C 1 17 PDB 4CN5 4CN5 1 17 DBREF 4CN5 D 1 17 PDB 4CN5 4CN5 1 17 SEQADV 4CN5 GLY A 126 UNP P19793 EXPRESSION TAG SEQADV 4CN5 SER A 127 UNP P19793 EXPRESSION TAG SEQADV 4CN5 HIS A 128 UNP P19793 EXPRESSION TAG SEQADV 4CN5 MET A 129 UNP P19793 EXPRESSION TAG SEQADV 4CN5 GLY B 126 UNP P19793 EXPRESSION TAG SEQADV 4CN5 SER B 127 UNP P19793 EXPRESSION TAG SEQADV 4CN5 HIS B 128 UNP P19793 EXPRESSION TAG SEQADV 4CN5 MET B 129 UNP P19793 EXPRESSION TAG SEQRES 1 A 87 GLY SER HIS MET PHE THR LYS HIS ILE CYS ALA ILE CYS SEQRES 2 A 87 GLY ASP ARG SER SER GLY LYS HIS TYR GLY VAL TYR SER SEQRES 3 A 87 CYS GLU GLY CYS LYS GLY PHE PHE LYS ARG THR VAL ARG SEQRES 4 A 87 LYS ASP LEU THR TYR THR CYS ARG ASP ASN LYS ASP CYS SEQRES 5 A 87 LEU ILE ASP LYS ARG GLN ARG ASN ARG CYS GLN TYR CYS SEQRES 6 A 87 ARG TYR GLN LYS CYS LEU ALA MET GLY MET LYS ARG GLU SEQRES 7 A 87 ALA VAL GLN GLU GLU ARG GLN ARG GLY SEQRES 1 B 87 GLY SER HIS MET PHE THR LYS HIS ILE CYS ALA ILE CYS SEQRES 2 B 87 GLY ASP ARG SER SER GLY LYS HIS TYR GLY VAL TYR SER SEQRES 3 B 87 CYS GLU GLY CYS LYS GLY PHE PHE LYS ARG THR VAL ARG SEQRES 4 B 87 LYS ASP LEU THR TYR THR CYS ARG ASP ASN LYS ASP CYS SEQRES 5 B 87 LEU ILE ASP LYS ARG GLN ARG ASN ARG CYS GLN TYR CYS SEQRES 6 B 87 ARG TYR GLN LYS CYS LEU ALA MET GLY MET LYS ARG GLU SEQRES 7 B 87 ALA VAL GLN GLU GLU ARG GLN ARG GLY SEQRES 1 C 17 DT DG DG DG DG DT DC DA DG DA DG DT DT SEQRES 2 C 17 DC DA DA DT SEQRES 1 D 17 DA DT DT DG DA DA DC DT DC DT DG DA DC SEQRES 2 D 17 DC DC DC DA HET ZN A1210 1 HET ZN A1211 1 HET CL A1212 1 HET CL A1213 1 HET CL A1214 1 HET ZN B1210 1 HET ZN B1211 1 HET K C1018 1 HET K C1019 1 HET K C1020 1 HET CL C1021 1 HET K D1018 1 HET NO3 D1019 4 HET CL D1020 1 HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETNAM K POTASSIUM ION HETNAM NO3 NITRATE ION FORMUL 5 ZN 4(ZN 2+) FORMUL 7 CL 5(CL 1-) FORMUL 12 K 4(K 1+) FORMUL 17 NO3 N O3 1- FORMUL 19 HOH *315(H2 O) HELIX 1 1 CYS A 152 LYS A 165 1 14 HELIX 2 2 CYS A 187 MET A 198 1 12 HELIX 3 3 LYS A 201 VAL A 205 5 5 HELIX 4 4 CYS B 152 LYS B 165 1 14 HELIX 5 5 GLN B 183 ARG B 186 5 4 HELIX 6 6 CYS B 187 MET B 198 1 12 HELIX 7 7 LYS B 201 VAL B 205 5 5 SHEET 1 AA 2 HIS A 133 ILE A 134 0 SHEET 2 AA 2 ARG A 141 SER A 142 -1 O SER A 142 N HIS A 133 SHEET 1 AB 2 GLY A 144 HIS A 146 0 SHEET 2 AB 2 VAL A 149 SER A 151 -1 O VAL A 149 N HIS A 146 SHEET 1 BA 2 LYS B 145 HIS B 146 0 SHEET 2 BA 2 VAL B 149 TYR B 150 -1 O VAL B 149 N HIS B 146 LINK SG CYS A 135 ZN ZN A1210 1555 1555 2.41 LINK SG CYS A 138 ZN ZN A1210 1555 1555 2.23 LINK SG CYS A 152 ZN ZN A1210 1555 1555 2.40 LINK SG CYS A 155 ZN ZN A1210 1555 1555 2.39 LINK SG CYS A 171 ZN ZN A1211 1555 1555 2.49 LINK SG CYS A 177 ZN ZN A1211 1555 1555 2.32 LINK SG CYS A 187 ZN ZN A1211 1555 1555 2.38 LINK SG CYS A 190 ZN ZN A1211 1555 1555 2.39 LINK SG CYS B 135 ZN ZN B1210 1555 1555 2.42 LINK SG CYS B 138 ZN ZN B1210 1555 1555 2.34 LINK SG CYS B 152 ZN ZN B1210 1555 1555 2.30 LINK SG CYS B 155 ZN ZN B1210 1555 1555 2.29 LINK SG CYS B 171 ZN ZN B1211 1555 1555 2.47 LINK SG CYS B 177 ZN ZN B1211 1555 1555 2.38 LINK SG CYS B 187 ZN ZN B1211 1555 1555 2.30 LINK SG CYS B 190 ZN ZN B1211 1555 1555 2.36 LINK O HOH B2064 K K D1018 1555 1555 2.65 LINK O2 DT C 6 K K C1019 1555 1555 2.70 LINK O4' DC C 7 K K C1019 1555 1555 3.01 LINK O2 DC C 7 K K C1019 1555 1555 2.85 LINK N7 DA C 8 K K C1020 1555 1555 2.97 LINK O6 DG C 9 K K C1020 1555 1555 2.81 LINK O2 DT C 13 K K C1018 1555 1555 2.79 LINK O2 DC C 14 K K C1018 1555 1555 3.01 LINK O4' DC C 14 K K C1018 1555 1555 2.84 LINK K K C1018 O HOH C2046 1555 1555 2.78 LINK K K C1018 O HOH C2048 1555 1555 2.83 LINK K K C1019 O HOH C2016 1555 1555 3.10 LINK K K C1019 O HOH C2018 1555 1555 2.80 LINK K K C1019 O HOH C2064 1555 1555 2.74 LINK K K C1019 O HOH C2065 1555 1555 3.33 LINK K K C1020 O HOH C2023 1555 1555 3.25 LINK K K C1020 O HOH C2025 1555 1555 3.05 LINK K K C1020 O HOH C2033 1555 1555 2.87 LINK K K C1020 O HOH C2034 1555 1555 3.07 LINK O HOH C2027 K K D1018 1555 1555 2.94 LINK O2 DT D 10 K K D1018 1555 1555 2.70 LINK O4' DG D 11 K K D1018 1555 1555 2.94 LINK K K D1018 O3 NO3 D1019 1555 1555 3.02 LINK K K D1018 O1 NO3 D1019 1555 1555 2.89 LINK K K D1018 O HOH D2027 1555 1555 2.80 SITE 1 AC1 4 CYS A 135 CYS A 138 CYS A 152 CYS A 155 SITE 1 AC2 4 CYS A 171 CYS A 177 CYS A 187 CYS A 190 SITE 1 AC3 4 CYS B 135 CYS B 138 CYS B 152 CYS B 155 SITE 1 AC4 4 CYS B 171 CYS B 177 CYS B 187 CYS B 190 SITE 1 AC5 6 HOH B2064 HOH C2027 DT D 10 DG D 11 SITE 2 AC5 6 NO3 D1019 HOH D2027 SITE 1 AC6 4 DT C 13 DC C 14 HOH C2046 HOH C2048 SITE 1 AC7 5 DT C 6 DC C 7 HOH C2016 HOH C2018 SITE 2 AC7 5 HOH C2064 SITE 1 AC8 5 DA C 8 DG C 9 HOH C2025 HOH C2033 SITE 2 AC8 5 HOH C2034 SITE 1 AC9 9 HOH A2083 GLN B 206 ARG B 209 DG C 9 SITE 2 AC9 9 DA C 10 HOH C2027 DT D 10 DG D 11 SITE 3 AC9 9 K D1018 SITE 1 BC1 2 TYR A 169 TYR A 189 SITE 1 BC2 5 LYS A 181 ARG A 182 LEU A 196 HOH A2069 SITE 2 BC2 5 HOH A2103 SITE 1 BC3 4 GLN A 188 HOH A2046 HOH A2093 DC D 9 SITE 1 BC4 3 LYS B 160 DT C 12 DT C 13 SITE 1 BC5 2 ARG A 172 CYS A 187 CRYST1 103.286 44.327 63.915 90.00 98.95 90.00 C 1 2 1 8 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 0.009682 0.000000 0.001525 0.00000 SCALE2 0.000000 0.022560 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015839 0.00000