PDB Short entry for 1XIU HEADER TRANSCRIPTION/TRANSFERASE 22-SEP-04 1XIU TITLE CRYSTAL STRUCTURE OF THE AGONIST-BOUND LIGAND-BINDING DOMAIN OF TITLE 2 BIOMPHALARIA GLABRATA RXR COMPND MOL_ID: 1; COMPND 2 MOLECULE: RXR-LIKE PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: LIGAND-BINDING DOMAIN (LBD); COMPND 5 SYNONYM: RETINOID X RECEPTOR LIGAND-BINDING DOMAIN, 9-CIS RETINOIC COMPND 6 ACID; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: NUCLEAR RECEPTOR COACTIVATOR 1; COMPND 10 CHAIN: E, F; COMPND 11 SYNONYM: NCOA-1, STEROID RECEPTOR COACTIVATOR-1, SRC-1, RIP160, HIN-2 COMPND 12 PROTEIN; COMPND 13 EC: 2.3.1.48; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BIOMPHALARIA GLABRATA; SOURCE 3 ORGANISM_TAXID: 6526; SOURCE 4 GENE: RXR; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE SOURCE 13 OF THE PEPTIDE IS DERIVED FROM HUMAN SRC-1 COACTIVATOR. KEYWDS NUCLEAR RECEPTOR, PROTEIN-LIGAND COMPLEX, RETINOID RECEPTOR, KEYWDS 2 TRANSCRIPTION-TRANSFERASE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.DE GROOT,E.DE ROSNY,C.JUILLAN-BINARD,J.-L.FERRER,V.LAUDET,E.PEBAY- AUTHOR 2 PEROULA,J.-C.FONTECILLA-CAMPS,F.BOREL REVDAT 6 23-AUG-23 1XIU 1 REMARK REVDAT 5 16-NOV-16 1XIU 1 HET HETNAM REVDAT 4 13-JUL-11 1XIU 1 VERSN REVDAT 3 24-FEB-09 1XIU 1 VERSN REVDAT 2 27-DEC-05 1XIU 1 JRNL REVDAT 1 13-SEP-05 1XIU 0 JRNL AUTH A.DE GROOT,E.DE ROSNY,C.JUILLAN-BINARD,J.-L.FERRER,V.LAUDET, JRNL AUTH 2 R.J.PIERCE,E.PEBAY-PEYROULA,J.-C.FONTECILLA-CAMPS,F.BOREL JRNL TITL CRYSTAL STRUCTURE OF A NOVEL TETRAMERIC COMPLEX OF JRNL TITL 2 AGONIST-BOUND LIGAND-BINDING DOMAIN OF BIOMPHALARIA GLABRATA JRNL TITL 3 RETINOID X RECEPTOR. JRNL REF J.MOL.BIOL. V. 354 841 2005 JRNL REFN ISSN 0022-2836 JRNL PMID 16274693 JRNL DOI 10.1016/J.JMB.2005.09.090 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 24538 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1292 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1729 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2570 REMARK 3 BIN FREE R VALUE SET COUNT : 91 REMARK 3 BIN FREE R VALUE : 0.3510 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3691 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 44 REMARK 3 SOLVENT ATOMS : 47 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.19 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.07000 REMARK 3 B22 (A**2) : 2.07000 REMARK 3 B33 (A**2) : -3.10000 REMARK 3 B12 (A**2) : 1.03000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.312 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.243 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.183 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 17.471 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3803 ; 0.029 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5140 ; 2.589 ; 1.997 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 463 ; 7.149 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 162 ;39.313 ;24.012 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 695 ;21.767 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;27.667 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 591 ; 0.162 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2795 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1885 ; 0.267 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2646 ; 0.340 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 136 ; 0.165 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 44 ; 0.297 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 7 ; 0.147 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2396 ; 1.400 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3746 ; 2.310 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1566 ; 3.824 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1394 ; 5.974 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 210 A 430 REMARK 3 RESIDUE RANGE : B 210 B 432 REMARK 3 ORIGIN FOR THE GROUP (A): 23.2564 51.2523 84.2538 REMARK 3 T TENSOR REMARK 3 T11: -0.0673 T22: -0.0092 REMARK 3 T33: -0.0714 T12: -0.0593 REMARK 3 T13: -0.0093 T23: 0.0208 REMARK 3 L TENSOR REMARK 3 L11: 1.1223 L22: 0.4323 REMARK 3 L33: 0.4167 L12: -0.4044 REMARK 3 L13: 0.3496 L23: -0.0528 REMARK 3 S TENSOR REMARK 3 S11: 0.0744 S12: -0.0373 S13: 0.0817 REMARK 3 S21: -0.0047 S22: -0.0847 S23: -0.0332 REMARK 3 S31: 0.0548 S32: -0.0407 S33: 0.0103 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 1XIU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-OCT-04. REMARK 100 THE DEPOSITION ID IS D_1000030401. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAY-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25831 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 15.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 15.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.54000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.980 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1FBY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES, SODIUM FORMATE, SODIUM REMARK 280 CHLORIDE, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 106.80000 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 213.60000 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 160.20000 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 267.00000 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 53.40000 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 106.80000 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 213.60000 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 267.00000 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 160.20000 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 53.40000 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A TETRAMER GENERATED FROM THE REMARK 300 DIMER IN THE ASYMMETRIC UNIT BY THE OPERATIONS: -X+1+Y,Y,-Z+1/2 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: OCTAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, E, F 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 87.10000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 160.20000 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 207 REMARK 465 ALA A 208 REMARK 465 ASN A 209 REMARK 465 ASN A 431 REMARK 465 PRO A 432 REMARK 465 SER A 433 REMARK 465 PRO A 434 REMARK 465 ALA A 435 REMARK 465 THR A 436 REMARK 465 GLY B 207 REMARK 465 ALA B 208 REMARK 465 SER B 433 REMARK 465 PRO B 434 REMARK 465 ALA B 435 REMARK 465 THR B 436 REMARK 465 ARG E 686 REMARK 465 PRO E 699 REMARK 465 SER E 700 REMARK 465 ARG F 686 REMARK 465 HIS F 687 REMARK 465 SER F 698 REMARK 465 PRO F 699 REMARK 465 SER F 700 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 A 365 CG CD OE1 NE2 REMARK 470 GLU A 368 CG CD OE1 OE2 REMARK 470 GLU A 384 CG CD OE1 OE2 REMARK 470 GLU B 219 CG CD OE1 OE2 REMARK 470 ASP B 237 CG OD1 OD2 REMARK 470 GLU B 269 CG CD OE1 OE2 REMARK 470 ARG B 276 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 333 CG OD1 OD2 REMARK 470 GLU B 362 CG CD OE1 OE2 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 CB ASN A 210 O HOH A 46 2.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O THR A 230 O TYR B 231 6655 2.07 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 GLU A 219 CG GLU A 219 CD 0.127 REMARK 500 ASP A 229 CB ASP A 229 CG 0.169 REMARK 500 GLU A 362 CG GLU A 362 CD 0.115 REMARK 500 GLU A 385 CD GLU A 385 OE1 0.067 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 ASP A 229 CB - CG - OD2 ANGL. DEV. = 7.3 DEGREES REMARK 500 ARG A 276 NE - CZ - NH2 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG A 290 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG A 332 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 332 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES REMARK 500 ARG A 395 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG A 400 CG - CD - NE ANGL. DEV. = -13.6 DEGREES REMARK 500 ASP B 211 N - CA - CB ANGL. DEV. = -11.1 DEGREES REMARK 500 CYS B 243 CA - CB - SG ANGL. DEV. = -12.8 DEGREES REMARK 500 LYS B 248 CD - CE - NZ ANGL. DEV. = -14.1 DEGREES REMARK 500 GLU B 281 OE1 - CD - OE2 ANGL. DEV. = -7.3 DEGREES REMARK 500 ARG B 332 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG B 332 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG B 345 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG B 345 NE - CZ - NH2 ANGL. DEV. = -5.0 DEGREES REMARK 500 GLU B 384 CB - CA - C ANGL. DEV. = -13.7 DEGREES REMARK 500 ARG B 395 NE - CZ - NH1 ANGL. DEV. = 6.7 DEGREES REMARK 500 ARG B 395 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 ARG B 400 NE - CZ - NH1 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG E 692 NE - CZ - NH1 ANGL. DEV. = 3.2 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 211 -16.81 82.20 REMARK 500 ASP A 229 -96.29 -37.86 REMARK 500 THR A 230 -59.79 -128.90 REMARK 500 TYR A 231 101.64 101.87 REMARK 500 ASP A 233 164.15 -49.79 REMARK 500 HIS A 262 -16.98 84.19 REMARK 500 ALA A 359 49.23 -86.65 REMARK 500 TYR A 382 46.56 -146.31 REMARK 500 LEU A 394 5.39 -66.01 REMARK 500 ASN B 210 -130.53 -92.91 REMARK 500 MET B 212 76.59 -150.82 REMARK 500 LYS B 236 -167.10 -31.86 REMARK 500 PRO B 261 129.30 -39.19 REMARK 500 HIS B 262 -5.23 71.58 REMARK 500 PRO B 267 121.35 -39.36 REMARK 500 ASP B 296 26.01 41.28 REMARK 500 LEU B 327 -69.52 -127.13 REMARK 500 ASP B 418 -74.60 -75.03 REMARK 500 GLN B 419 106.45 -36.14 REMARK 500 PRO B 420 -85.42 -24.30 REMARK 500 ILE B 421 117.41 64.72 REMARK 500 ILE F 689 -41.32 176.02 REMARK 500 GLU F 696 86.25 -66.22 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 ASP A 233 ALA A 234 137.93 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 9CR A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 9CR B 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FBY RELATED DB: PDB REMARK 900 HUMAN HOMOLOGUE WITH RETINOIC ACID REMARK 900 RELATED ID: 1LBD RELATED DB: PDB REMARK 900 HUMAN HOMOLOGUE WITHOUT RETINOIC ACID (MONOMER) REMARK 900 RELATED ID: 1G1U RELATED DB: PDB REMARK 900 HUMAN HOMOLOGUE WITHOUT RETINOIC ACID (TETRAMER) DBREF 1XIU A 207 436 GB 19386469 AAL86461 207 436 DBREF 1XIU B 207 436 GB 19386469 AAL86461 207 436 DBREF 1XIU E 686 700 UNP Q15788 NCOA1_HUMAN 686 700 DBREF 1XIU F 686 700 UNP Q15788 NCOA1_HUMAN 686 700 SEQRES 1 A 230 GLY ALA ASN ASN ASP MET PRO VAL GLU GLN ILE LEU GLU SEQRES 2 A 230 ALA GLU LEU ALA VAL ASP PRO LYS ILE ASP THR TYR ILE SEQRES 3 A 230 ASP ALA GLN LYS ASP PRO VAL THR ASN ILE CYS GLN ALA SEQRES 4 A 230 ALA ASP LYS GLN LEU PHE THR LEU VAL GLU TRP ALA LYS SEQRES 5 A 230 ARG ILE PRO HIS PHE THR GLU LEU PRO LEU GLU ASP GLN SEQRES 6 A 230 VAL ILE LEU LEU ARG ALA GLY TRP ASN GLU LEU LEU ILE SEQRES 7 A 230 ALA GLY PHE SER HIS ARG SER ILE MET ALA LYS ASP GLY SEQRES 8 A 230 ILE LEU LEU ALA THR GLY LEU HIS VAL HIS ARG SER SER SEQRES 9 A 230 ALA HIS GLN ALA GLY VAL GLY THR ILE PHE ASP ARG VAL SEQRES 10 A 230 LEU THR GLU LEU VAL ALA LYS MET ARG ASP MET LYS MET SEQRES 11 A 230 ASP LYS THR GLU LEU GLY CYS LEU ARG ALA VAL VAL LEU SEQRES 12 A 230 PHE ASN PRO ASP ALA LYS GLY LEU THR ALA VAL GLN GLU SEQRES 13 A 230 VAL GLU GLN LEU ARG GLU LYS VAL TYR ALA SER LEU GLU SEQRES 14 A 230 GLU TYR THR LYS SER ARG TYR PRO GLU GLU PRO GLY ARG SEQRES 15 A 230 PHE ALA LYS LEU LEU LEU ARG LEU PRO ALA LEU ARG SER SEQRES 16 A 230 ILE GLY LEU LYS CYS LEU GLU HIS LEU PHE PHE PHE LYS SEQRES 17 A 230 LEU ILE GLY ASP GLN PRO ILE ASP THR PHE LEU MET GLU SEQRES 18 A 230 MET LEU GLU ASN PRO SER PRO ALA THR SEQRES 1 B 230 GLY ALA ASN ASN ASP MET PRO VAL GLU GLN ILE LEU GLU SEQRES 2 B 230 ALA GLU LEU ALA VAL ASP PRO LYS ILE ASP THR TYR ILE SEQRES 3 B 230 ASP ALA GLN LYS ASP PRO VAL THR ASN ILE CYS GLN ALA SEQRES 4 B 230 ALA ASP LYS GLN LEU PHE THR LEU VAL GLU TRP ALA LYS SEQRES 5 B 230 ARG ILE PRO HIS PHE THR GLU LEU PRO LEU GLU ASP GLN SEQRES 6 B 230 VAL ILE LEU LEU ARG ALA GLY TRP ASN GLU LEU LEU ILE SEQRES 7 B 230 ALA GLY PHE SER HIS ARG SER ILE MET ALA LYS ASP GLY SEQRES 8 B 230 ILE LEU LEU ALA THR GLY LEU HIS VAL HIS ARG SER SER SEQRES 9 B 230 ALA HIS GLN ALA GLY VAL GLY THR ILE PHE ASP ARG VAL SEQRES 10 B 230 LEU THR GLU LEU VAL ALA LYS MET ARG ASP MET LYS MET SEQRES 11 B 230 ASP LYS THR GLU LEU GLY CYS LEU ARG ALA VAL VAL LEU SEQRES 12 B 230 PHE ASN PRO ASP ALA LYS GLY LEU THR ALA VAL GLN GLU SEQRES 13 B 230 VAL GLU GLN LEU ARG GLU LYS VAL TYR ALA SER LEU GLU SEQRES 14 B 230 GLU TYR THR LYS SER ARG TYR PRO GLU GLU PRO GLY ARG SEQRES 15 B 230 PHE ALA LYS LEU LEU LEU ARG LEU PRO ALA LEU ARG SER SEQRES 16 B 230 ILE GLY LEU LYS CYS LEU GLU HIS LEU PHE PHE PHE LYS SEQRES 17 B 230 LEU ILE GLY ASP GLN PRO ILE ASP THR PHE LEU MET GLU SEQRES 18 B 230 MET LEU GLU ASN PRO SER PRO ALA THR SEQRES 1 E 15 ARG HIS LYS ILE LEU HIS ARG LEU LEU GLN GLU GLY SER SEQRES 2 E 15 PRO SER SEQRES 1 F 15 ARG HIS LYS ILE LEU HIS ARG LEU LEU GLN GLU GLY SER SEQRES 2 F 15 PRO SER HET 9CR A 201 22 HET 9CR B 202 22 HETNAM 9CR (9CIS)-RETINOIC ACID FORMUL 5 9CR 2(C20 H28 O2) FORMUL 7 HOH *47(H2 O) HELIX 1 1 PRO A 213 ASP A 225 1 13 HELIX 2 2 ASP A 237 ARG A 259 1 23 HELIX 3 3 HIS A 262 LEU A 266 5 5 HELIX 4 4 PRO A 267 SER A 291 1 25 HELIX 5 5 ILE A 292 ALA A 294 5 3 HELIX 6 6 ARG A 308 ALA A 314 1 7 HELIX 7 7 VAL A 316 LEU A 327 1 12 HELIX 8 8 LEU A 327 MET A 334 1 8 HELIX 9 9 ASP A 337 PHE A 350 1 14 HELIX 10 10 ALA A 359 TYR A 382 1 24 HELIX 11 11 GLY A 387 LEU A 394 1 8 HELIX 12 12 ARG A 395 ASP A 418 1 24 HELIX 13 13 ASP A 422 LEU A 429 1 8 HELIX 14 14 PRO B 213 ASP B 225 1 13 HELIX 15 15 ASP B 237 ARG B 259 1 23 HELIX 16 16 HIS B 262 LEU B 266 5 5 HELIX 17 17 PRO B 267 SER B 291 1 25 HELIX 18 18 ILE B 292 ALA B 294 5 3 HELIX 19 19 ARG B 308 ALA B 314 1 7 HELIX 20 20 VAL B 316 LEU B 327 1 12 HELIX 21 21 LEU B 327 MET B 334 1 8 HELIX 22 22 ASP B 337 PHE B 350 1 14 HELIX 23 23 ALA B 359 TYR B 382 1 24 HELIX 24 24 GLY B 387 LEU B 394 1 8 HELIX 25 25 ARG B 395 GLY B 417 1 23 HELIX 26 26 ASP B 422 ASN B 431 1 10 HELIX 27 27 HIS E 687 GLY E 697 1 11 HELIX 28 28 ILE F 689 GLU F 696 1 8 SHEET 1 A 3 ILE A 232 ALA A 234 0 SHEET 2 A 3 LEU A 304 HIS A 307 1 O HIS A 305 N ILE A 232 SHEET 3 A 3 GLY A 297 LEU A 299 -1 N ILE A 298 O VAL A 306 SHEET 1 B 3 ILE B 232 ASP B 233 0 SHEET 2 B 3 LEU B 304 HIS B 307 1 O HIS B 305 N ILE B 232 SHEET 3 B 3 GLY B 297 LEU B 299 -1 N ILE B 298 O VAL B 306 SITE 1 AC1 10 ALA A 245 ALA A 246 GLN A 249 PHE A 287 SITE 2 AC1 10 ARG A 290 LEU A 300 ALA A 301 VAL A 316 SITE 3 AC1 10 CYS A 406 HIS A 409 SITE 1 AC2 9 ILE B 242 ALA B 246 GLN B 249 PHE B 287 SITE 2 AC2 9 ARG B 290 LEU B 300 ALA B 301 CYS B 406 SITE 3 AC2 9 HIS B 409 CRYST1 87.100 87.100 320.400 90.00 90.00 120.00 P 61 2 2 24 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 0.011481 0.006629 0.000000 0.00000 SCALE2 0.000000 0.013257 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003121 0.00000