HEADER SIGNALING PROTEIN 07-SEP-06 2J4Y TITLE CRYSTAL STRUCTURE OF A RHODOPSIN STABILIZING MUTANT EXPRESSED IN TITLE 2 MAMMALIAN CELLS COMPND MOL_ID: 1; COMPND 2 MOLECULE: RHODOPSIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 ORGAN: EYE; SOURCE 6 TISSUE: RETINA; SOURCE 7 CELL: ROD PHOTORECEPTOR; SOURCE 8 EXPRESSION_SYSTEM: CHLOROCEBUS AETHIOPS; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 9534; SOURCE 10 EXPRESSION_SYSTEM_CELL_LINE: COS-1 MONKEY KIDNEY CELLS; SOURCE 11 EXPRESSION_SYSTEM_ATCC_NUMBER: 1650 KEYWDS CHROMOPHORE, LIPOPROTEIN, GLYCOPROTEIN, SENSORY TRANSDUCTION, KEYWDS 2 PHOTORECEPTOR PROTEIN, INTEGRAL MEMBRANE PROTEIN, G-PROTEIN COUPLED KEYWDS 3 RECEPTOR, VISION, MEMBRANE, RECEPTOR, PALMITATE, TRANSDUCER, RETINAL KEYWDS 4 PROTEIN, PHOSPHORYLATION, SIGNALING PROTEIN, PHOTORECEPTOR, KEYWDS 5 TRANSMEMBRANE, VISUAL PIGMENT EXPDTA X-RAY DIFFRACTION AUTHOR J.STANDFUSS,G.XIE,P.C.EDWARDS,M.BURGHAMMER,D.D.OPRIAN,G.F.X.SCHERTLER REVDAT 7 13-DEC-23 2J4Y 1 HETSYN REVDAT 6 29-JUL-20 2J4Y 1 COMPND REMARK HETNAM LINK REVDAT 6 2 1 SITE REVDAT 5 23-OCT-19 2J4Y 1 SEQADV REVDAT 4 08-MAY-19 2J4Y 1 REMARK LINK REVDAT 3 12-DEC-12 2J4Y 1 SOURCE KEYWDS JRNL REMARK REVDAT 3 2 1 VERSN SEQADV SEQRES HET REVDAT 3 3 1 MODRES HETNAM FORMUL HETSYN REVDAT 3 4 1 HELIX LINK SITE SCALE2 REVDAT 3 5 1 HETATM ATOM TER CONECT REVDAT 3 6 1 MASTER REVDAT 2 24-FEB-09 2J4Y 1 VERSN REVDAT 1 25-SEP-07 2J4Y 0 JRNL AUTH J.STANDFUSS,G.XIE,P.C.EDWARDS,M.BURGHAMMER,D.D.OPRIAN, JRNL AUTH 2 G.F.X.SCHERTLER JRNL TITL CRYSTAL STRUCTURE OF A THERMALLY STABLE RHODOPSIN MUTANT. JRNL REF J.MOL.BIOL. V. 372 1179 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17825322 JRNL DOI 10.1016/J.JMB.2007.03.007 REMARK 2 REMARK 2 RESOLUTION. 3.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 13689 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : 0.325 REMARK 3 R VALUE (WORKING SET) : 0.290 REMARK 3 FREE R VALUE : 0.330 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.000 REMARK 3 FREE R VALUE TEST SET COUNT : 407 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.016 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1610 REMARK 3 BIN R VALUE (WORKING SET) : 0.3775 REMARK 3 BIN FREE R VALUE : 0.3895 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 3.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5184 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 68 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 58.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.49700 REMARK 3 B22 (A**2) : -3.49700 REMARK 3 B33 (A**2) : 6.99400 REMARK 3 B12 (A**2) : -7.21100 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) : 0.50 REMARK 3 ESD FROM SIGMAA (A) : 0.92 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.57 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.88 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 BOND ANGLES (DEGREES) : 1.660 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.114 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.780 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.130 ; 2.500 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.390 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.810 ; 3.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : 0.44 REMARK 3 BSOL : 64.49 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : 0.042 ; 100 REMARK 3 GROUP 1 B-FACTOR (A**2) : 1 ; 10 REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP_LYR9_CYP_AYM2.PARAM REMARK 3 PARAMETER FILE 2 : CARBOHYDRATE2.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN_LYR5_CYP_AYM.TOP REMARK 3 TOPOLOGY FILE 2 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2J4Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-SEP-06. REMARK 100 THE DEPOSITION ID IS D_1290029910. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUN-04 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 : ID13 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 : NULL REMARK 200 OPTICS : MICROFOCUSING REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13689 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 200 DATA REDUNDANCY : 3.030 REMARK 200 R MERGE (I) : 0.24000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.4200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.79 REMARK 200 R MERGE FOR SHELL (I) : 0.70000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.790 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 1GZM REMARK 200 REMARK 200 REMARK: DATA WAS COLLECTED ON 10 POSITION ALONG A MICROCRYSTALLINE REMARK 200 NEEDLE OF 5X5X90 MICRONS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOUR DIFFUSION IN SITTING DROPS OF REMARK 280 10-15 MG/ML PROTEIN AND 0.2% C8E4,0.05%LDAO AGAINST 1.1-1.7M REMARK 280 LITHIUM SULFATE, 0.1M HEPES PH 7.5, VAPOR DIFFUSION, SITTING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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 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 25.90000 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 51.80000 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 DIMER DESCRIBED HERE IN AN ARTIFACT REMARK 300 OF CRYSTALLIZATION AND DOES NOT REPRESENT THE NATURAL REMARK 300 OLIGOMERIC STATE OF THE PROTEIN 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.9 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ASN 2 TO CYS REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ASP 282 TO CYS REMARK 400 ENGINEERED RESIDUE IN CHAIN B, ASN 2 TO CYS REMARK 400 ENGINEERED RESIDUE IN CHAIN B, ASP 282 TO CYS 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 LEU A 328 REMARK 465 GLY A 329 REMARK 465 ASP A 330 REMARK 465 ASP A 331 REMARK 465 GLU A 332 REMARK 465 ALA A 333 REMARK 465 SER A 334 REMARK 465 THR A 335 REMARK 465 THR A 336 REMARK 465 VAL A 337 REMARK 465 SER A 338 REMARK 465 LYS A 339 REMARK 465 THR A 340 REMARK 465 GLU A 341 REMARK 465 THR A 342 REMARK 465 SER A 343 REMARK 465 GLN A 344 REMARK 465 VAL A 345 REMARK 465 ALA A 346 REMARK 465 PRO A 347 REMARK 465 ALA A 348 REMARK 465 LEU B 328 REMARK 465 GLY B 329 REMARK 465 ASP B 330 REMARK 465 ASP B 331 REMARK 465 GLU B 332 REMARK 465 ALA B 333 REMARK 465 SER B 334 REMARK 465 THR B 335 REMARK 465 THR B 336 REMARK 465 VAL B 337 REMARK 465 SER B 338 REMARK 465 LYS B 339 REMARK 465 THR B 340 REMARK 465 GLU B 341 REMARK 465 THR B 342 REMARK 465 SER B 343 REMARK 465 GLN B 344 REMARK 465 VAL B 345 REMARK 465 ALA B 346 REMARK 465 PRO B 347 REMARK 465 ALA B 348 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 PRO A 327 CA C O CB CG CD REMARK 470 PRO B 327 CA C O CB CG CD 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 PRO B 194 O HIS B 195 1.79 REMARK 500 O PRO A 194 O HIS A 195 1.79 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 PRO A 12 49.85 -84.10 REMARK 500 ASN A 15 38.60 -83.22 REMARK 500 PRO A 23 44.14 -70.67 REMARK 500 PHE A 24 4.68 -157.23 REMARK 500 GLU A 25 -50.94 -123.45 REMARK 500 PRO A 34 -5.68 -54.02 REMARK 500 LEU A 50 -39.50 -131.59 REMARK 500 TYR A 60 -26.40 -143.82 REMARK 500 LYS A 67 -2.67 -60.00 REMARK 500 TYR A 102 150.57 178.96 REMARK 500 PHE A 105 -5.48 -51.25 REMARK 500 PRO A 107 -15.74 -48.02 REMARK 500 THR A 108 17.96 -65.62 REMARK 500 CYS A 110 20.81 -67.47 REMARK 500 PHE A 116 12.13 -68.52 REMARK 500 CYS A 140 58.06 -113.57 REMARK 500 LYS A 141 131.50 -36.05 REMARK 500 PRO A 142 -110.36 -79.95 REMARK 500 MET A 143 -148.26 -96.47 REMARK 500 SER A 144 156.97 -34.76 REMARK 500 ARG A 147 131.09 -15.99 REMARK 500 GLU A 150 -28.76 -39.78 REMARK 500 ASN A 151 -71.48 -53.64 REMARK 500 VAL A 162 -72.88 -50.15 REMARK 500 TRP A 175 79.22 -109.27 REMARK 500 SER A 176 -134.56 102.24 REMARK 500 ARG A 177 146.85 155.99 REMARK 500 ILE A 189 135.81 -39.22 REMARK 500 ASP A 190 70.31 -63.16 REMARK 500 TYR A 192 -70.46 -89.63 REMARK 500 HIS A 195 162.90 0.72 REMARK 500 THR A 198 7.63 -152.10 REMARK 500 ASN A 200 -48.94 -24.41 REMARK 500 PHE A 212 -71.49 -152.88 REMARK 500 ILE A 213 -77.60 -56.92 REMARK 500 PRO A 215 -34.58 -39.95 REMARK 500 TYR A 223 -70.40 -80.34 REMARK 500 GLN A 225 -37.14 -30.55 REMARK 500 LEU A 226 33.60 -73.17 REMARK 500 VAL A 227 -28.13 -150.70 REMARK 500 VAL A 230 36.02 -65.01 REMARK 500 LYS A 231 -99.98 -158.93 REMARK 500 ALA A 233 18.12 -67.79 REMARK 500 GLN A 238 107.38 14.97 REMARK 500 GLN A 244 29.35 -79.16 REMARK 500 PRO A 285 30.43 -84.91 REMARK 500 LYS A 296 5.27 -66.53 REMARK 500 SER A 298 5.26 -63.70 REMARK 500 VAL A 300 -51.76 -149.25 REMARK 500 CYS A 322 2.96 -62.45 REMARK 500 REMARK 500 THIS ENTRY HAS 96 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 306 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EDS RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF INTRADISKAL LOOP 1 OF BOVINE RHODOPSIN REMARK 900 (RHODOPSIN RESIDUES 92-123) REMARK 900 RELATED ID: 1EDV RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF 2ND INTRADISKAL LOOP OF BOVINE RHODOPSIN REMARK 900 (RESIDUES 172-205) REMARK 900 RELATED ID: 1EDW RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THIRD INTRADISKAL LOOP OF BOVINE RHODOPSIN REMARK 900 (RESIDUES 268-293) REMARK 900 RELATED ID: 1EDX RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF AMINO TERMINUS OF BOVINE RHODOPSIN (RESIDUES REMARK 900 1- 40) REMARK 900 RELATED ID: 1F88 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BOVINE RHODOPSIN REMARK 900 RELATED ID: 1FDF RELATED DB: PDB REMARK 900 HELIX 7 BOVINE RHODOPSIN REMARK 900 RELATED ID: 1GZM RELATED DB: PDB REMARK 900 STRUCTURE OF BOVINE RHODOPSIN IN A TRIGONAL CRYSTAL FORM REMARK 900 RELATED ID: 1HZX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BOVINE RHODOPSIN REMARK 900 RELATED ID: 1JFP RELATED DB: PDB REMARK 900 STRUCTURE OF BOVINE RHODOPSIN (DARK ADAPTED) REMARK 900 RELATED ID: 1L9H RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BOVINE RHODOPSIN AT 2. 6 ANGSTROMSRESOLUTION REMARK 900 RELATED ID: 1LN6 RELATED DB: PDB REMARK 900 STRUCTURE OF BOVINE RHODOPSIN (METARHODOPSIN II) REMARK 900 RELATED ID: 1N3M RELATED DB: PDB REMARK 900 THEORETICAL MODEL OF RHODOPSIN OLIGOMER REMARK 900 RELATED ID: 1NZS RELATED DB: PDB REMARK 900 NMR STRUCTURES OF PHOSPHORYLATED CARBOXY TERMINUS OF REMARK 900 BOVINERHODOPSIN IN ARRESTIN-BOUND STATE REMARK 900 RELATED ID: 1OV0 RELATED DB: PDB REMARK 900 CALCULATED 3D MODEL OF META-II RHODOPSIN BASED ON LIMITEDDATA OF REMARK 900 SITE-DIRECTED SPIN- LABELING REMARK 900 RELATED ID: 1OV1 RELATED DB: PDB REMARK 900 CALCULATED 3D MODEL OF AN ACTIVATED "STRAITJACKED" RHODOPSIN REMARK 900 RELATED ID: 1U19 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BOVINE RHODOPSIN AT 2.2 ANGSTROMS RESOLUTION REMARK 900 RELATED ID: 1VQX RELATED DB: PDB REMARK 900 ARRESTIN-BOUND NMR STRUCTURES OF THE PHOSPHORYLATED CARBOXY- REMARK 900 TERMINAL DOMAIN OF RHODOPSIN, REFINED DBREF 2J4Y A 1 348 UNP P02699 OPSD_BOVIN 1 348 DBREF 2J4Y B 1 348 UNP P02699 OPSD_BOVIN 1 348 SEQADV 2J4Y ACE A 0 UNP P02699 ACETYLATION SEQADV 2J4Y CYS A 2 UNP P02699 ASN 2 ENGINEERED MUTATION SEQADV 2J4Y CYS A 282 UNP P02699 ASP 282 ENGINEERED MUTATION SEQADV 2J4Y ACE B 0 UNP P02699 ACETYLATION SEQADV 2J4Y CYS B 2 UNP P02699 ASN 2 ENGINEERED MUTATION SEQADV 2J4Y CYS B 282 UNP P02699 ASP 282 ENGINEERED MUTATION SEQRES 1 A 349 ACE MET CYS GLY THR GLU GLY PRO ASN PHE TYR VAL PRO SEQRES 2 A 349 PHE SER ASN LYS THR GLY VAL VAL ARG SER PRO PHE GLU SEQRES 3 A 349 ALA PRO GLN TYR TYR LEU ALA GLU PRO TRP GLN PHE SER SEQRES 4 A 349 MET LEU ALA ALA TYR MET PHE LEU LEU ILE MET LEU GLY SEQRES 5 A 349 PHE PRO ILE ASN PHE LEU THR LEU TYR VAL THR VAL GLN SEQRES 6 A 349 HIS LYS LYS LEU ARG THR PRO LEU ASN TYR ILE LEU LEU SEQRES 7 A 349 ASN LEU ALA VAL ALA ASP LEU PHE MET VAL PHE GLY GLY SEQRES 8 A 349 PHE THR THR THR LEU TYR THR SER LEU HIS GLY TYR PHE SEQRES 9 A 349 VAL PHE GLY PRO THR GLY CYS ASN LEU GLU GLY PHE PHE SEQRES 10 A 349 ALA THR LEU GLY GLY GLU ILE ALA LEU TRP SER LEU VAL SEQRES 11 A 349 VAL LEU ALA ILE GLU ARG TYR VAL VAL VAL CYS LYS PRO SEQRES 12 A 349 MET SER ASN PHE ARG PHE GLY GLU ASN HIS ALA ILE MET SEQRES 13 A 349 GLY VAL ALA PHE THR TRP VAL MET ALA LEU ALA CYS ALA SEQRES 14 A 349 ALA PRO PRO LEU VAL GLY TRP SER ARG TYR ILE PRO GLU SEQRES 15 A 349 GLY MET GLN CYS SER CYS GLY ILE ASP TYR TYR THR PRO SEQRES 16 A 349 HIS GLU GLU THR ASN ASN GLU SER PHE VAL ILE TYR MET SEQRES 17 A 349 PHE VAL VAL HIS PHE ILE ILE PRO LEU ILE VAL ILE PHE SEQRES 18 A 349 PHE CYS TYR GLY GLN LEU VAL PHE THR VAL LYS GLU ALA SEQRES 19 A 349 ALA ALA GLN GLN GLN GLU SER ALA THR THR GLN LYS ALA SEQRES 20 A 349 GLU LYS GLU VAL THR ARG MET VAL ILE ILE MET VAL ILE SEQRES 21 A 349 ALA PHE LEU ILE CYS TRP LEU PRO TYR ALA GLY VAL ALA SEQRES 22 A 349 PHE TYR ILE PHE THR HIS GLN GLY SER CYS PHE GLY PRO SEQRES 23 A 349 ILE PHE MET THR ILE PRO ALA PHE PHE ALA LYS THR SER SEQRES 24 A 349 ALA VAL TYR ASN PRO VAL ILE TYR ILE MET MET ASN LYS SEQRES 25 A 349 GLN PHE ARG ASN CYS MET VAL THR THR LEU CYS CYS GLY SEQRES 26 A 349 LYS ASN PRO LEU GLY ASP ASP GLU ALA SER THR THR VAL SEQRES 27 A 349 SER LYS THR GLU THR SER GLN VAL ALA PRO ALA SEQRES 1 B 349 ACE MET CYS GLY THR GLU GLY PRO ASN PHE TYR VAL PRO SEQRES 2 B 349 PHE SER ASN LYS THR GLY VAL VAL ARG SER PRO PHE GLU SEQRES 3 B 349 ALA PRO GLN TYR TYR LEU ALA GLU PRO TRP GLN PHE SER SEQRES 4 B 349 MET LEU ALA ALA TYR MET PHE LEU LEU ILE MET LEU GLY SEQRES 5 B 349 PHE PRO ILE ASN PHE LEU THR LEU TYR VAL THR VAL GLN SEQRES 6 B 349 HIS LYS LYS LEU ARG THR PRO LEU ASN TYR ILE LEU LEU SEQRES 7 B 349 ASN LEU ALA VAL ALA ASP LEU PHE MET VAL PHE GLY GLY SEQRES 8 B 349 PHE THR THR THR LEU TYR THR SER LEU HIS GLY TYR PHE SEQRES 9 B 349 VAL PHE GLY PRO THR GLY CYS ASN LEU GLU GLY PHE PHE SEQRES 10 B 349 ALA THR LEU GLY GLY GLU ILE ALA LEU TRP SER LEU VAL SEQRES 11 B 349 VAL LEU ALA ILE GLU ARG TYR VAL VAL VAL CYS LYS PRO SEQRES 12 B 349 MET SER ASN PHE ARG PHE GLY GLU ASN HIS ALA ILE MET SEQRES 13 B 349 GLY VAL ALA PHE THR TRP VAL MET ALA LEU ALA CYS ALA SEQRES 14 B 349 ALA PRO PRO LEU VAL GLY TRP SER ARG TYR ILE PRO GLU SEQRES 15 B 349 GLY MET GLN CYS SER CYS GLY ILE ASP TYR TYR THR PRO SEQRES 16 B 349 HIS GLU GLU THR ASN ASN GLU SER PHE VAL ILE TYR MET SEQRES 17 B 349 PHE VAL VAL HIS PHE ILE ILE PRO LEU ILE VAL ILE PHE SEQRES 18 B 349 PHE CYS TYR GLY GLN LEU VAL PHE THR VAL LYS GLU ALA SEQRES 19 B 349 ALA ALA GLN GLN GLN GLU SER ALA THR THR GLN LYS ALA SEQRES 20 B 349 GLU LYS GLU VAL THR ARG MET VAL ILE ILE MET VAL ILE SEQRES 21 B 349 ALA PHE LEU ILE CYS TRP LEU PRO TYR ALA GLY VAL ALA SEQRES 22 B 349 PHE TYR ILE PHE THR HIS GLN GLY SER CYS PHE GLY PRO SEQRES 23 B 349 ILE PHE MET THR ILE PRO ALA PHE PHE ALA LYS THR SER SEQRES 24 B 349 ALA VAL TYR ASN PRO VAL ILE TYR ILE MET MET ASN LYS SEQRES 25 B 349 GLN PHE ARG ASN CYS MET VAL THR THR LEU CYS CYS GLY SEQRES 26 B 349 LYS ASN PRO LEU GLY ASP ASP GLU ALA SER THR THR VAL SEQRES 27 B 349 SER LYS THR GLU THR SER GLN VAL ALA PRO ALA MODRES 2J4Y ASN A 15 ASN GLYCOSYLATION SITE MODRES 2J4Y ASN B 15 ASN GLYCOSYLATION SITE HET ACE A 0 3 HET ACE B 0 3 HET RET A1296 20 HET NAG A1327 14 HET RET B1296 20 HET NAG B1327 14 HETNAM ACE ACETYL GROUP HETNAM RET RETINAL HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 1 ACE 2(C2 H4 O) FORMUL 3 RET 2(C20 H28 O) FORMUL 4 NAG 2(C8 H15 N O6) HELIX 1 1 TRP A 35 LEU A 47 1 13 HELIX 2 2 LEU A 47 PHE A 52 1 6 HELIX 3 3 PHE A 52 LEU A 57 1 6 HELIX 4 4 LEU A 57 HIS A 65 1 9 HELIX 5 5 THR A 70 LEU A 76 1 7 HELIX 6 6 ASN A 78 ASP A 83 1 6 HELIX 7 7 ASP A 83 PHE A 88 1 6 HELIX 8 8 PHE A 91 LEU A 99 1 9 HELIX 9 9 ASN A 111 TRP A 126 1 16 HELIX 10 10 LEU A 128 CYS A 140 1 13 HELIX 11 11 GLY A 149 ALA A 169 1 21 HELIX 12 12 PRO A 170 VAL A 173 5 4 HELIX 13 13 ASN A 199 HIS A 211 1 13 HELIX 14 14 PHE A 212 GLN A 225 1 14 HELIX 15 15 LYS A 248 HIS A 278 1 31 HELIX 16 16 MET A 288 LYS A 296 1 9 HELIX 17 17 VAL A 300 MET A 309 1 10 HELIX 18 18 ASN A 310 CYS A 322 1 13 HELIX 19 19 TRP B 35 LEU B 47 1 13 HELIX 20 20 LEU B 47 PHE B 52 1 6 HELIX 21 21 PHE B 52 LEU B 57 1 6 HELIX 22 22 LEU B 57 HIS B 65 1 9 HELIX 23 23 THR B 70 LEU B 76 1 7 HELIX 24 24 ASN B 78 PHE B 88 1 11 HELIX 25 25 PHE B 91 LEU B 99 1 9 HELIX 26 26 ASN B 111 TRP B 126 1 16 HELIX 27 27 LEU B 128 CYS B 140 1 13 HELIX 28 28 GLY B 149 ALA B 169 1 21 HELIX 29 29 ALA B 169 GLY B 174 1 6 HELIX 30 30 ASN B 199 HIS B 211 1 13 HELIX 31 31 PHE B 212 GLN B 225 1 14 HELIX 32 32 ALA B 246 TRP B 265 1 20 HELIX 33 33 TRP B 265 HIS B 278 1 14 HELIX 34 34 MET B 288 LYS B 296 1 9 HELIX 35 35 VAL B 300 MET B 308 1 9 HELIX 36 36 ASN B 310 CYS B 322 1 13 SHEET 1 AA 2 TYR A 178 PRO A 180 0 SHEET 2 AA 2 CYS A 187 ILE A 189 -1 O GLY A 188 N ILE A 179 SHEET 1 BA 2 TYR B 178 PRO B 180 0 SHEET 2 BA 2 CYS B 187 ILE B 189 -1 O GLY B 188 N ILE B 179 SSBOND 1 CYS A 2 CYS A 282 1555 1555 2.04 SSBOND 2 CYS A 110 CYS A 187 1555 1555 2.04 SSBOND 3 CYS B 2 CYS B 282 1555 1555 2.03 SSBOND 4 CYS B 110 CYS B 187 1555 1555 2.04 LINK C ACE A 0 N MET A 1 1555 1555 1.33 LINK ND2 ASN A 15 C1 NAG A1327 1555 1555 1.48 LINK NZ LYS A 296 C15 RET A1296 1555 1555 1.31 LINK C ACE B 0 N MET B 1 1555 1555 1.34 LINK ND2 ASN B 15 C1 NAG B1327 1555 1555 1.50 LINK NZ LYS B 296 C15 RET B1296 1555 1555 1.30 CRYST1 109.300 109.300 77.700 90.00 90.00 120.00 P 31 6 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 0.009149 0.005282 0.000000 0.00000 SCALE2 0.000000 0.010565 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012870 0.00000 MTRIX1 1 -1.000000 0.000570 -0.000350 0.01135 1 MTRIX2 1 -0.000570 -1.000000 -0.000070 63.07932 1 MTRIX3 1 -0.000350 -0.000070 1.000000 0.01048 1 HETATM 1 C ACE A 0 -33.240 16.950 -14.068 1.00 81.71 C HETATM 2 O ACE A 0 -33.689 17.940 -13.484 1.00 81.96 O HETATM 3 CH3 ACE A 0 -34.075 16.275 -15.147 1.00 81.27 C