HEADER TRANSCRIPTION 23-JAN-20 6XWG TITLE CRYSTAL STRUCTURE OF THE HUMAN RXR/RAR DNA-BINDING DOMAIN HETERODIMER TITLE 2 BOUND TO THE HUMAN RARB2 DR5 RESPONSE ELEMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: RARB2 DR5 RESPONSE ELEMENT, 5'-3' STRAND; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RARB2 DR5 RESPONSE ELEMENT, 3'-5' STRAND; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: RETINOIC ACID RECEPTOR RXR-ALPHA; COMPND 11 CHAIN: C; COMPND 12 SYNONYM: NUCLEAR RECEPTOR SUBFAMILY 2 GROUP B MEMBER 1,RETINOID X COMPND 13 RECEPTOR ALPHA; COMPND 14 ENGINEERED: YES; COMPND 15 OTHER_DETAILS: DNA-BINDING DOMAIN; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: RETINOIC ACID RECEPTOR ALPHA; COMPND 18 CHAIN: D; COMPND 19 SYNONYM: RAR-ALPHA,NUCLEAR RECEPTOR SUBFAMILY 1 GROUP B MEMBER 1; COMPND 20 ENGINEERED: YES; COMPND 21 OTHER_DETAILS: DNA-BINDING DOMAIN SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: RXRA, NR2B1; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 MOL_ID: 4; SOURCE 19 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 20 ORGANISM_COMMON: HUMAN; SOURCE 21 ORGANISM_TAXID: 9606; SOURCE 22 GENE: RARA, NR1B1; SOURCE 23 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 24 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS PROTEIN-DNA COMPLEX, NUCLEAR RECEPTOR, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR A.G.MCEWEN,P.POUSSIN-COURMONTAGNE,C.PELUSO-ILTIS,N.ROCHEL REVDAT 3 24-JAN-24 6XWG 1 REMARK REVDAT 2 07-OCT-20 6XWG 1 JRNL REVDAT 1 09-SEP-20 6XWG 0 JRNL AUTH J.OSZ,A.G.MCEWEN,M.BOURGUET,F.PRZYBILLA,C.PELUSO-ILTIS, JRNL AUTH 2 P.POUSSIN-COURMONTAGNE,Y.MELY,S.CIANFERANI,C.M.JEFFRIES, JRNL AUTH 3 D.I.SVERGUN,N.ROCHEL JRNL TITL STRUCTURAL BASIS FOR DNA RECOGNITION AND ALLOSTERIC CONTROL JRNL TITL 2 OF THE RETINOIC ACID RECEPTORS RAR-RXR. JRNL REF NUCLEIC ACIDS RES. V. 48 9969 2020 JRNL REFN ESSN 1362-4962 JRNL PMID 32974652 JRNL DOI 10.1093/NAR/GKAA697 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.51 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 75.6 REMARK 3 NUMBER OF REFLECTIONS : 12203 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.450 REMARK 3 FREE R VALUE TEST SET COUNT : 543 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.000 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.63 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 21.86 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 818 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2170 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 781 REMARK 3 BIN R VALUE (WORKING SET) : 0.2150 REMARK 3 BIN FREE R VALUE : 0.2620 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.52 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 37 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1295 REMARK 3 NUCLEIC ACID ATOMS : 855 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 36 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 81.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 83.26 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.72560 REMARK 3 B22 (A**2) : -1.72560 REMARK 3 B33 (A**2) : 3.45120 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.000 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.486 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.238 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.397 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.228 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 2278 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 3224 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 715 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 30 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 237 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 2278 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 4 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 286 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 2255 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 0.98 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.88 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 22.96 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { C|132 - C|302 } REMARK 3 ORIGIN FOR THE GROUP (A): 14.1964 -22.1246 -17.5576 REMARK 3 T TENSOR REMARK 3 T11: -0.0413 T22: -0.0224 REMARK 3 T33: -0.1591 T12: 0.1520 REMARK 3 T13: -0.0872 T23: 0.0372 REMARK 3 L TENSOR REMARK 3 L11: 6.2718 L22: 6.2332 REMARK 3 L33: 6.7539 L12: -0.7474 REMARK 3 L13: -0.5326 L23: -1.5262 REMARK 3 S TENSOR REMARK 3 S11: -0.0762 S12: -0.2280 S13: -0.1764 REMARK 3 S21: 0.1690 S22: 0.1103 S23: -0.0161 REMARK 3 S31: -0.2085 S32: 0.0196 S33: -0.0341 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { D|82 - D|302 } REMARK 3 ORIGIN FOR THE GROUP (A): -8.3268 -0.3352 -31.2499 REMARK 3 T TENSOR REMARK 3 T11: -0.1515 T22: -0.1746 REMARK 3 T33: 0.0924 T12: 0.0085 REMARK 3 T13: -0.0513 T23: 0.0336 REMARK 3 L TENSOR REMARK 3 L11: 8.3155 L22: 6.2621 REMARK 3 L33: 5.6766 L12: 0.6765 REMARK 3 L13: -0.7362 L23: 1.4829 REMARK 3 S TENSOR REMARK 3 S11: -0.1148 S12: 0.1161 S13: -0.0425 REMARK 3 S21: -0.1096 S22: -0.1089 S23: 0.5442 REMARK 3 S31: 0.1654 S32: -0.2618 S33: 0.2237 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: { A|1 - A|51 B|1 - B|21 } REMARK 3 ORIGIN FOR THE GROUP (A): 3.0336 -6.8335 -11.1681 REMARK 3 T TENSOR REMARK 3 T11: -0.1865 T22: -0.1043 REMARK 3 T33: -0.1654 T12: 0.1520 REMARK 3 T13: -0.1470 T23: 0.0847 REMARK 3 L TENSOR REMARK 3 L11: 3.9483 L22: 6.0475 REMARK 3 L33: 4.7873 L12: -2.1428 REMARK 3 L13: 1.1783 L23: -2.9104 REMARK 3 S TENSOR REMARK 3 S11: -0.1607 S12: -0.5442 S13: 0.1428 REMARK 3 S21: 0.5442 S22: -0.1022 S23: 0.3519 REMARK 3 S31: -0.0483 S32: 0.4893 S33: 0.2629 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6XWG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1292106347. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-NOV-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.006 REMARK 200 MONOCHROMATOR : SI(111) 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16005 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 26.510 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 9.756 REMARK 200 R MERGE (I) : 0.11100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.7700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : 8.81 REMARK 200 R MERGE FOR SHELL (I) : 5.95500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.290 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: 4CN5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3350, 0.2 M LI2SO4, 0.1 M BIS REMARK 280 -TRIS PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 119.18200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.35700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.35700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 178.77300 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.35700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.35700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 59.59100 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.35700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.35700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 178.77300 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.35700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.35700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 59.59100 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 119.18200 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: 5860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 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 C 126 REMARK 465 SER C 127 REMARK 465 HIS C 128 REMARK 465 MET C 129 REMARK 465 PHE C 130 REMARK 465 THR C 131 REMARK 465 ARG C 211 REMARK 465 GLY C 212 REMARK 465 GLY D 78 REMARK 465 SER D 79 REMARK 465 HIS D 80 REMARK 465 MET D 81 REMARK 465 ARG D 162 REMARK 465 ASN D 163 REMARK 465 LYS D 164 REMARK 465 LYS D 165 REMARK 465 LYS D 166 REMARK 465 LYS D 167 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 GLN C 210 CG CD OE1 NE2 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 A 2 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC B 7 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC B 18 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC B 20 O4' - C1' - N1 ANGL. DEV. = 1.8 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 C 173 -139.45 -97.84 REMARK 500 ASN C 174 41.66 -106.03 REMARK 500 HIS D 125 35.76 -97.81 REMARK 500 ARG D 126 -129.45 -145.41 REMARK 500 LYS D 128 -8.20 78.43 REMARK 500 REMARK 500 REMARK: NULL 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 C 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 135 SG REMARK 620 2 CYS C 138 SG 106.9 REMARK 620 3 CYS C 152 SG 115.5 98.9 REMARK 620 4 CYS C 155 SG 116.4 121.0 96.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 171 SG REMARK 620 2 CYS C 177 SG 103.1 REMARK 620 3 CYS C 187 SG 110.6 114.8 REMARK 620 4 CYS C 190 SG 121.5 101.3 105.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS D 88 SG REMARK 620 2 CYS D 91 SG 116.8 REMARK 620 3 CYS D 105 SG 111.1 105.1 REMARK 620 4 CYS D 108 SG 107.6 116.9 97.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS D 124 SG REMARK 620 2 CYS D 130 SG 103.0 REMARK 620 3 CYS D 140 SG 106.7 144.0 REMARK 620 4 CYS D 143 SG 96.6 102.2 94.2 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN C 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL C 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN D 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN D 302 DBREF 6XWG A 1 21 PDB 6XWG 6XWG 1 21 DBREF 6XWG B 1 21 PDB 6XWG 6XWG 1 21 DBREF 6XWG C 130 212 UNP P19793 RXRA_HUMAN 33 115 DBREF 6XWG D 82 167 UNP P10276 RARA_HUMAN 82 167 SEQADV 6XWG GLY C 126 UNP P19793 EXPRESSION TAG SEQADV 6XWG SER C 127 UNP P19793 EXPRESSION TAG SEQADV 6XWG HIS C 128 UNP P19793 EXPRESSION TAG SEQADV 6XWG MET C 129 UNP P19793 EXPRESSION TAG SEQADV 6XWG GLY D 78 UNP P10276 EXPRESSION TAG SEQADV 6XWG SER D 79 UNP P10276 EXPRESSION TAG SEQADV 6XWG HIS D 80 UNP P10276 EXPRESSION TAG SEQADV 6XWG MET D 81 UNP P10276 EXPRESSION TAG SEQRES 1 A 21 DA DG DG DG DT DT DC DA DC DC DG DA DA SEQRES 2 A 21 DA DG DT DT DC DA DC DT SEQRES 1 B 21 DA DG DT DG DA DA DC DT DT DT DC DG DG SEQRES 2 B 21 DT DG DA DA DC DC DC DT SEQRES 1 C 87 GLY SER HIS MET PHE THR LYS HIS ILE CYS ALA ILE CYS SEQRES 2 C 87 GLY ASP ARG SER SER GLY LYS HIS TYR GLY VAL TYR SER SEQRES 3 C 87 CYS GLU GLY CYS LYS GLY PHE PHE LYS ARG THR VAL ARG SEQRES 4 C 87 LYS ASP LEU THR TYR THR CYS ARG ASP ASN LYS ASP CYS SEQRES 5 C 87 LEU ILE ASP LYS ARG GLN ARG ASN ARG CYS GLN TYR CYS SEQRES 6 C 87 ARG TYR GLN LYS CYS LEU ALA MET GLY MET LYS ARG GLU SEQRES 7 C 87 ALA VAL GLN GLU GLU ARG GLN ARG GLY SEQRES 1 D 90 GLY SER HIS MET PRO ARG ILE TYR LYS PRO CYS PHE VAL SEQRES 2 D 90 CYS GLN ASP LYS SER SER GLY TYR HIS TYR GLY VAL SER SEQRES 3 D 90 ALA CYS GLU GLY CYS LYS GLY PHE PHE ARG ARG SER ILE SEQRES 4 D 90 GLN LYS ASN MET VAL TYR THR CYS HIS ARG ASP LYS ASN SEQRES 5 D 90 CYS ILE ILE ASN LYS VAL THR ARG ASN ARG CYS GLN TYR SEQRES 6 D 90 CYS ARG LEU GLN LYS CYS PHE GLU VAL GLY MET SER LYS SEQRES 7 D 90 GLU SER VAL ARG ASN ASP ARG ASN LYS LYS LYS LYS HET ZN C 301 1 HET ZN C 302 1 HET GOL C 303 6 HET CL C 304 1 HET ZN D 301 1 HET ZN D 302 1 HETNAM ZN ZINC ION HETNAM GOL GLYCEROL HETNAM CL CHLORIDE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 ZN 4(ZN 2+) FORMUL 7 GOL C3 H8 O3 FORMUL 8 CL CL 1- FORMUL 11 HOH *36(H2 O) HELIX 1 AA1 CYS C 152 LYS C 165 1 14 HELIX 2 AA2 CYS C 187 MET C 198 1 12 HELIX 3 AA3 LYS C 201 VAL C 205 5 5 HELIX 4 AA4 CYS D 105 LYS D 118 1 14 HELIX 5 AA5 CYS D 140 GLY D 152 1 13 HELIX 6 AA6 SER D 154 VAL D 158 5 5 SHEET 1 AA1 2 HIS C 133 ILE C 134 0 SHEET 2 AA1 2 ARG C 141 SER C 142 -1 O SER C 142 N HIS C 133 SHEET 1 AA2 2 GLY C 144 HIS C 146 0 SHEET 2 AA2 2 VAL C 149 SER C 151 -1 O VAL C 149 N HIS C 146 SHEET 1 AA3 2 GLY D 97 HIS D 99 0 SHEET 2 AA3 2 VAL D 102 ALA D 104 -1 O VAL D 102 N HIS D 99 LINK SG CYS C 135 ZN ZN C 301 1555 1555 2.18 LINK SG CYS C 138 ZN ZN C 301 1555 1555 2.22 LINK SG CYS C 152 ZN ZN C 301 1555 1555 2.36 LINK SG CYS C 155 ZN ZN C 301 1555 1555 2.36 LINK SG CYS C 171 ZN ZN C 302 1555 1555 2.23 LINK SG CYS C 177 ZN ZN C 302 1555 1555 2.32 LINK SG CYS C 187 ZN ZN C 302 1555 1555 2.25 LINK SG CYS C 190 ZN ZN C 302 1555 1555 2.52 LINK SG CYS D 88 ZN ZN D 301 1555 1555 2.18 LINK SG CYS D 91 ZN ZN D 301 1555 1555 2.32 LINK SG CYS D 105 ZN ZN D 301 1555 1555 2.40 LINK SG CYS D 108 ZN ZN D 301 1555 1555 2.27 LINK SG CYS D 124 ZN ZN D 302 1555 1555 2.53 LINK SG CYS D 130 ZN ZN D 302 1555 1555 2.17 LINK SG CYS D 140 ZN ZN D 302 1555 1555 2.25 LINK SG CYS D 143 ZN ZN D 302 1555 1555 2.60 SITE 1 AC1 4 CYS C 135 CYS C 138 CYS C 152 CYS C 155 SITE 1 AC2 4 CYS C 171 CYS C 177 CYS C 187 CYS C 190 SITE 1 AC3 3 LYS C 145 TYR C 150 LYS D 147 SITE 1 AC4 2 ARG C 202 GLU C 203 SITE 1 AC5 4 CYS D 88 CYS D 91 CYS D 105 CYS D 108 SITE 1 AC6 4 CYS D 124 CYS D 130 CYS D 140 CYS D 143 CRYST1 56.714 56.714 238.364 90.00 90.00 90.00 P 43 21 2 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 0.017632 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017632 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004195 0.00000