HEADER TRANSCRIPTION 18-MAR-25 9QJ9 TITLE CRYSTAL STRUCTURE OF THE HUMAN RETINOID X RECEPTOR DNA-BINDING DOMAIN TITLE 2 BOUND TO TRIM16 IR1 RESPONSE ELEMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: RETINOIC ACID RECEPTOR RXR-ALPHA; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: NUCLEAR RECEPTOR SUBFAMILY 2 GROUP B MEMBER 1,RETINOID X COMPND 5 RECEPTOR ALPHA; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(P*GP*GP*GP*GP*TP*CP*AP*TP*GP*AP*CP*CP*CP*T)-3'); COMPND 9 CHAIN: C; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(P*GP*GP*GP*GP*TP*CP*AP*TP*GP*AP*CP*CP*CP*T)-3'); COMPND 13 CHAIN: D; COMPND 14 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: RXRA, NR2B1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_TAXID: 9606 KEYWDS DNA COMPLEX, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR N.ROCHEL REVDAT 1 28-JAN-26 9QJ9 0 JRNL AUTH I.TAMBONES,A.SAGAR,P.VANKOVA,D.LOGINOV,C.CARIVENC,N.ROCHEL, JRNL AUTH 2 W.BOURGUET,P.MAN,P.BERNADO,A.LE MAIRE JRNL TITL NEW STRUCTURAL INSIGHTS INTO THE CONTROL OF THE RETINOIC JRNL TITL 2 ACID RECEPTORS RAR/RXR BY DNA, LIGANDS, AND TRANSCRIPTIONAL JRNL TITL 3 COREGULATORS. JRNL REF NUCLEIC ACIDS RES. V. 53 2025 JRNL REFN ESSN 1362-4962 JRNL PMID 41036627 JRNL DOI 10.1093/NAR/GKAF967 REMARK 2 REMARK 2 RESOLUTION. 3.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_1426 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) : 3.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 3712 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.270 REMARK 3 R VALUE (WORKING SET) : 0.267 REMARK 3 FREE R VALUE : 0.335 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.420 REMARK 3 FREE R VALUE TEST SET COUNT : 164 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 3.6250 - 3.5000 0.98 3548 164 0.2668 0.3352 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.400 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 40.530 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.014 1766 REMARK 3 ANGLE : 2.315 2478 REMARK 3 CHIRALITY : 0.095 262 REMARK 3 PLANARITY : 0.009 222 REMARK 3 DIHEDRAL : 24.977 710 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' REMARK 3 ORIGIN FOR THE GROUP (A): 20.8544 -6.4470 -14.4967 REMARK 3 T TENSOR REMARK 3 T11: 0.6785 T22: 0.5787 REMARK 3 T33: 0.5144 T12: -0.0891 REMARK 3 T13: -0.0967 T23: -0.1925 REMARK 3 L TENSOR REMARK 3 L11: 8.4167 L22: 4.7111 REMARK 3 L33: 4.2266 L12: -1.5513 REMARK 3 L13: -2.0206 L23: -1.6382 REMARK 3 S TENSOR REMARK 3 S11: 0.4275 S12: -0.3564 S13: 0.6510 REMARK 3 S21: -0.5060 S22: -0.0777 S23: -1.1334 REMARK 3 S31: -0.8631 S32: -0.4122 S33: -0.1340 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' REMARK 3 ORIGIN FOR THE GROUP (A): 19.8306 -16.6703 14.0042 REMARK 3 T TENSOR REMARK 3 T11: 0.1565 T22: 0.5771 REMARK 3 T33: 0.5190 T12: 0.3112 REMARK 3 T13: 0.1384 T23: -0.1018 REMARK 3 L TENSOR REMARK 3 L11: 4.7348 L22: 4.8567 REMARK 3 L33: 5.9645 L12: 1.0985 REMARK 3 L13: 3.2794 L23: 3.0650 REMARK 3 S TENSOR REMARK 3 S11: 1.5075 S12: -0.4787 S13: -0.5252 REMARK 3 S21: 1.7756 S22: -0.3730 S23: 0.1027 REMARK 3 S31: 2.1455 S32: -0.4828 S33: 0.9377 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN 'C') OR (CHAIN 'D') REMARK 3 ORIGIN FOR THE GROUP (A): 11.9531 -13.5389 -1.1169 REMARK 3 T TENSOR REMARK 3 T11: 0.8057 T22: 0.9758 REMARK 3 T33: 0.9186 T12: -0.1091 REMARK 3 T13: 0.1290 T23: 0.0974 REMARK 3 L TENSOR REMARK 3 L11: 4.4507 L22: 0.9914 REMARK 3 L33: 3.4547 L12: -1.8594 REMARK 3 L13: 0.1695 L23: -1.1544 REMARK 3 S TENSOR REMARK 3 S11: -0.3343 S12: 0.2087 S13: 0.0275 REMARK 3 S21: 0.7820 S22: 0.0937 S23: 0.2470 REMARK 3 S31: 0.8496 S32: -1.1556 S33: -0.0174 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 9QJ9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-MAR-25. REMARK 100 THE DEPOSITION ID IS D_1292146452. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-SEP-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 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 : 3712 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.500 REMARK 200 RESOLUTION RANGE LOW (A) : 33.842 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.63 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 1000, 0.2M MGCL2 0.1M NACL, REMARK 280 0.05M NA CACODYLATE PH6.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 84.93550 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.00950 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.00950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 42.46775 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.00950 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.00950 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 127.40325 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.00950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.00950 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 42.46775 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.00950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.00950 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 127.40325 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 84.93550 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: 3950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 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 A 127 REMARK 465 SER A 128 REMARK 465 HIS A 129 REMARK 465 MET A 130 REMARK 465 PHE A 131 REMARK 465 THR A 132 REMARK 465 LYS A 133 REMARK 465 HIS A 134 REMARK 465 ALA A 205 REMARK 465 VAL A 206 REMARK 465 GLN A 207 REMARK 465 GLU A 208 REMARK 465 GLU A 209 REMARK 465 ARG A 210 REMARK 465 GLN A 211 REMARK 465 ARG A 212 REMARK 465 GLY A 213 REMARK 465 GLY B 127 REMARK 465 SER B 128 REMARK 465 HIS B 129 REMARK 465 MET B 130 REMARK 465 PHE B 131 REMARK 465 THR B 132 REMARK 465 LYS B 133 REMARK 465 HIS B 134 REMARK 465 ALA B 205 REMARK 465 VAL B 206 REMARK 465 GLN B 207 REMARK 465 GLU B 208 REMARK 465 GLU B 209 REMARK 465 ARG B 210 REMARK 465 GLN B 211 REMARK 465 ARG B 212 REMARK 465 GLY B 213 REMARK 465 DT C 0 REMARK 465 DC C 1 REMARK 465 DA D 22 REMARK 465 DG D 37 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 LYS A 182 NZ REMARK 470 LYS A 202 CG CD CE NZ REMARK 470 ARG A 203 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 204 CG CD OE1 OE2 REMARK 470 LYS B 146 CG CD CE NZ REMARK 470 LYS B 176 CG CD CE NZ REMARK 470 LYS B 182 NZ REMARK 470 LYS B 202 CG CD CE NZ 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 O6 DG C 4 N4 DC D 34 2.07 REMARK 500 NE2 GLN B 189 OP1 DT C 9 2.11 REMARK 500 N4 DC C 14 O6 DG D 24 2.17 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 ND2 ASN A 175 OG1 THR B 169 7655 1.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DG C 10 O3' DG C 10 C3' -0.053 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 LEU A 168 CA - CB - CG ANGL. DEV. = -18.1 DEGREES REMARK 500 DA C 2 C3' - C2' - C1' ANGL. DEV. = -5.5 DEGREES REMARK 500 DA C 2 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG C 4 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG C 5 O4' - C1' - C2' ANGL. DEV. = -5.5 DEGREES REMARK 500 DG C 5 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DT C 6 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC C 7 C3' - C2' - C1' ANGL. DEV. = -8.7 DEGREES REMARK 500 DC C 7 C6 - N1 - C2 ANGL. DEV. = 3.0 DEGREES REMARK 500 DA C 8 O4' - C1' - N9 ANGL. DEV. = -5.5 DEGREES REMARK 500 DT C 9 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DT C 9 N3 - C4 - O4 ANGL. DEV. = 4.5 DEGREES REMARK 500 DT C 9 C5 - C4 - O4 ANGL. DEV. = -5.7 DEGREES REMARK 500 DA C 11 O4' - C1' - N9 ANGL. DEV. = -4.6 DEGREES REMARK 500 DC C 12 C3' - C2' - C1' ANGL. DEV. = -6.6 DEGREES REMARK 500 DC C 13 C3' - C2' - C1' ANGL. DEV. = -4.8 DEGREES REMARK 500 DC C 13 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC C 14 C3' - C2' - C1' ANGL. DEV. = -9.1 DEGREES REMARK 500 DC C 14 C6 - N1 - C2 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG D 24 C3' - C2' - C1' ANGL. DEV. = -8.6 DEGREES REMARK 500 DG D 24 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG D 25 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 DG D 25 N3 - C4 - C5 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG D 26 C1' - O4' - C4' ANGL. DEV. = -6.1 DEGREES REMARK 500 DG D 26 O4' - C1' - N9 ANGL. DEV. = 7.2 DEGREES REMARK 500 DT D 27 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DA D 29 O4' - C1' - N9 ANGL. DEV. = -6.7 DEGREES REMARK 500 DT D 30 C1' - O4' - C4' ANGL. DEV. = -6.1 DEGREES REMARK 500 DG D 31 C3' - C2' - C1' ANGL. DEV. = -5.5 DEGREES REMARK 500 DA D 32 O4' - C1' - N9 ANGL. DEV. = -4.4 DEGREES REMARK 500 DC D 33 C1' - O4' - C4' ANGL. DEV. = -6.2 DEGREES REMARK 500 DC D 33 O4' - C1' - C2' ANGL. DEV. = -6.1 DEGREES REMARK 500 DC D 33 O4' - C1' - N1 ANGL. DEV. = 8.5 DEGREES REMARK 500 DC D 34 C3' - C2' - C1' ANGL. DEV. = -8.6 DEGREES REMARK 500 DC D 34 O4' - C1' - N1 ANGL. DEV. = 5.5 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 174 -125.21 -103.00 REMARK 500 ASP A 177 43.24 -145.43 REMARK 500 ASP B 174 -126.93 -102.99 REMARK 500 ASP B 177 43.63 -144.80 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 A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 136 SG REMARK 620 2 CYS A 139 SG 159.2 REMARK 620 3 CYS A 153 SG 95.8 104.2 REMARK 620 4 CYS A 156 SG 88.9 99.2 82.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 172 SG REMARK 620 2 CYS A 178 SG 97.1 REMARK 620 3 CYS A 188 SG 118.8 92.9 REMARK 620 4 CYS A 191 SG 148.0 80.2 93.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 136 SG REMARK 620 2 CYS B 139 SG 104.5 REMARK 620 3 CYS B 153 SG 137.4 106.0 REMARK 620 4 CYS B 156 SG 127.0 93.9 79.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 188 SG REMARK 620 2 CYS B 191 SG 101.3 REMARK 620 N 1 DBREF 9QJ9 A 131 213 UNP P19793 RXRA_HUMAN 33 115 DBREF 9QJ9 B 131 213 UNP P19793 RXRA_HUMAN 33 115 DBREF 9QJ9 C 0 15 PDB 9QJ9 9QJ9 0 15 DBREF 9QJ9 D 22 37 PDB 9QJ9 9QJ9 22 37 SEQADV 9QJ9 GLY A 127 UNP P19793 EXPRESSION TAG SEQADV 9QJ9 SER A 128 UNP P19793 EXPRESSION TAG SEQADV 9QJ9 HIS A 129 UNP P19793 EXPRESSION TAG SEQADV 9QJ9 MET A 130 UNP P19793 EXPRESSION TAG SEQADV 9QJ9 GLY B 127 UNP P19793 EXPRESSION TAG SEQADV 9QJ9 SER B 128 UNP P19793 EXPRESSION TAG SEQADV 9QJ9 HIS B 129 UNP P19793 EXPRESSION TAG SEQADV 9QJ9 MET B 130 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 16 DT DC DA DG DG DG DT DC DA DT DG DA DC SEQRES 2 C 16 DC DC DC SEQRES 1 D 16 DA DG DG DG DG DT DC DA DT DG DA DC DC SEQRES 2 D 16 DC DT DG HET ZN A 301 1 HET ZN A 302 1 HET ZN B 301 1 HET ZN B 302 1 HETNAM ZN ZINC ION FORMUL 5 ZN 4(ZN 2+) HELIX 1 AA1 CYS A 153 LYS A 166 1 14 HELIX 2 AA2 CYS A 188 GLY A 200 1 13 HELIX 3 AA3 CYS B 153 LYS B 166 1 14 HELIX 4 AA4 CYS B 188 GLY B 200 1 13 SHEET 1 AA1 2 GLY A 145 HIS A 147 0 SHEET 2 AA1 2 VAL A 150 SER A 152 -1 O VAL A 150 N HIS A 147 SHEET 1 AA2 2 GLY B 145 HIS B 147 0 SHEET 2 AA2 2 VAL B 150 SER B 152 -1 O VAL B 150 N HIS B 147 LINK SG CYS A 136 ZN ZN A 301 1555 1555 2.41 LINK SG CYS A 139 ZN ZN A 301 1555 1555 2.10 LINK SG CYS A 153 ZN ZN A 301 1555 1555 2.47 LINK SG CYS A 156 ZN ZN A 301 1555 1555 2.33 LINK SG CYS A 172 ZN ZN A 302 1555 1555 2.26 LINK SG CYS A 178 ZN ZN A 302 1555 1555 2.95 LINK SG CYS A 188 ZN ZN A 302 1555 1555 2.46 LINK SG CYS A 191 ZN ZN A 302 1555 1555 2.48 LINK SG CYS B 136 ZN ZN B 301 1555 1555 2.87 LINK SG CYS B 139 ZN ZN B 301 1555 1555 2.17 LINK SG CYS B 153 ZN ZN B 301 1555 1555 2.57 LINK SG CYS B 156 ZN ZN B 301 1555 1555 2.53 LINK SG CYS B 188 ZN ZN B 302 1555 1555 2.06 LINK SG CYS B 191 ZN ZN B 302 1555 1555 2.87 CRYST1 56.019 56.019 169.871 90.00 90.00 90.00 P 41 21 2 16 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 0.017851 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017851 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005887 0.00000 CONECT 14 1689 CONECT 33 1689 CONECT 138 1689 CONECT 157 1689 CONECT 294 1690 CONECT 344 1690 CONECT 432 1690 CONECT 459 1690 CONECT 569 1691 CONECT 588 1691 CONECT 689 1691 CONECT 708 1691 CONECT 979 1692 CONECT 1006 1692 CONECT 1689 14 33 138 157 CONECT 1690 294 344 432 459 CONECT 1691 569 588 689 708 CONECT 1692 979 1006 MASTER 475 0 4 4 4 0 0 6 1688 4 18 18 END