HEADER SIGNALING PROTEIN 17-OCT-11 4A4M TITLE CRYSTAL STRUCTURE OF THE LIGHT-ACTIVATED CONSTITUTIVELY ACTIVE N2C, TITLE 2 M257Y,D282C RHODOPSIN MUTANT IN COMPLEX WITH A PEPTIDE RESEMBLING THE TITLE 3 C-TERMINUS OF THE GALPHA-PROTEIN SUBUNIT (GACT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RHODOPSIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CONSTITUTIVELY ACTIVE RHODOPSIN MUTANT; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: GUANINE NUCLEOTIDE-BINDING PROTEIN G(T) SUBUNIT ALPHA-3; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: RESIDUES 344-354; COMPND 11 SYNONYM: GACT PEPTIDE, GUSTDUCIN ALPHA-3 CHAIN; COMPND 12 ENGINEERED: YES; COMPND 13 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: BOVINE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 ORGAN: EYE; SOURCE 6 TISSUE: RETINA; SOURCE 7 CELL: ROD PHOTORECEPTOR; SOURCE 8 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 9 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 11 EXPRESSION_SYSTEM_CELL_LINE: HEK293S GNTI-; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 15 ORGANISM_COMMON: BOVINE; SOURCE 16 ORGANISM_TAXID: 9913 KEYWDS SIGNALING PROTEIN, G-PROTEIN, G-PROTEIN-COUPLED RECEPTORS, SIGNAL KEYWDS 2 TANSDUCTION, VISUAL SYSTEM, METARHODOPSIN-II EXPDTA X-RAY DIFFRACTION AUTHOR X.DEUPI,P.EDWARDS,A.SINGHAL,B.NICKLE,D.D.OPRIAN,G.F.X.SCHERTLER, AUTHOR 2 J.STANDFUSS REVDAT 5 16-OCT-24 4A4M 1 REMARK REVDAT 4 20-DEC-23 4A4M 1 HETSYN REVDAT 3 29-JUL-20 4A4M 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 23-OCT-19 4A4M 1 SEQADV LINK REVDAT 1 25-JAN-12 4A4M 0 JRNL AUTH X.DEUPI,P.EDWARDS,A.SINGHAL,B.NICKLE,D.OPRIAN,G.SCHERTLER, JRNL AUTH 2 J.STANDFUSS JRNL TITL STABILIZED G PROTEIN BINDING SITE IN THE STRUCTURE OF JRNL TITL 2 CONSTITUTIVELY ACTIVE METARHODOPSIN-II. JRNL REF PROC.NATL.ACAD.SCI.USA V. 109 119 2012 JRNL REFN ISSN 0027-8424 JRNL PMID 22198838 JRNL DOI 10.1073/PNAS.1114089108 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.STANDFUSS,G.XIE,P.C.EDWARDS,M.BURGHAMMER,D.D.OPRIAN, REMARK 1 AUTH 2 G.F.X.SCHERTLER REMARK 1 TITL CRYSTAL STRUCTURE OF A THERMALLY STABLE RHODOPSIN MUTANT. REMARK 1 REF J.MOL.BIOL. V. 372 1179 2007 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 17825322 REMARK 1 DOI 10.1016/J.JMB.2007.03.007 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.STANDFUSS,P.C.EDWARDS,A.D'ANTONA,M.FRANSEN,G.XIE, REMARK 1 AUTH 2 D.D.OPRIAN,G.F.X.SCHERTLER REMARK 1 TITL THE STRUCTURAL BASIS OF AGONIST-INDUCED ACTIVATION IN REMARK 1 TITL 2 CONSTITUTIVELY ACTIVE RHODOPSIN. REMARK 1 REF NATURE V. 471 656 2011 REMARK 1 REFN ISSN 0028-0836 REMARK 1 PMID 21389983 REMARK 1 DOI 10.1038/NATURE09795 REMARK 2 REMARK 2 RESOLUTION. 3.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.1_357) 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) : 3.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 3 NUMBER OF REFLECTIONS : 17632 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 901 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 45.7740 - 5.9928 0.99 3006 151 0.2346 0.2878 REMARK 3 2 5.9928 - 4.7582 1.00 2969 144 0.1827 0.2235 REMARK 3 3 4.7582 - 4.1572 1.00 2928 158 0.1600 0.2018 REMARK 3 4 4.1572 - 3.7773 1.00 2917 167 0.1942 0.2495 REMARK 3 5 3.7773 - 3.5067 1.00 2905 169 0.2509 0.2785 REMARK 3 6 3.5067 - 3.3000 0.69 2006 112 0.3011 0.3730 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.28 REMARK 3 B_SOL : 40.90 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.420 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.860 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 75.56 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -19.65260 REMARK 3 B22 (A**2) : -19.65260 REMARK 3 B33 (A**2) : 39.30520 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 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 : 0.011 2859 REMARK 3 ANGLE : 1.450 3881 REMARK 3 CHIRALITY : 0.084 434 REMARK 3 PLANARITY : 0.010 476 REMARK 3 DIHEDRAL : 17.669 1015 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 4A4M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-OCT-11. REMARK 100 THE DEPOSITION ID IS D_1290048823. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 3 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA 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 : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17649 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.300 REMARK 200 RESOLUTION RANGE LOW (A) : 45.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.18000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 65.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.66000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2X72 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 84.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 7.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.0-3.4 M AMMONIUM SULPHATE, 100 MM REMARK 280 SODIUM ACETATE PH 4.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 121.09500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 69.91423 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 36.60967 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 121.09500 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 69.91423 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 36.60967 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 121.09500 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 69.91423 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 36.60967 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 121.09500 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 69.91423 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 36.60967 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 121.09500 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 69.91423 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 36.60967 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 121.09500 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 69.91423 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 36.60967 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 139.82846 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 73.21933 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 139.82846 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 73.21933 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 139.82846 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 73.21933 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 139.82846 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 73.21933 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 139.82846 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 73.21933 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 139.82846 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 73.21933 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.9 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 109.82900 REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ASN 2 TO CYS REMARK 400 ENGINEERED RESIDUE IN CHAIN A, MET 257 TO TYR REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ASP 282 TO CYS REMARK 400 ENGINEERED RESIDUE IN CHAIN B, LYS 345 TO LEU 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 PRO A 327 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 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 ND1 HIS A 65 OE1 GLU A 239 3555 2.12 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 ACE A 0 O - C - N ANGL. DEV. = -12.2 DEGREES REMARK 500 MET A 1 C - N - CA ANGL. DEV. = 37.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PRO A 12 52.29 -69.47 REMARK 500 GLN A 28 48.20 -99.82 REMARK 500 ALA A 32 142.05 -174.75 REMARK 500 GLU A 33 160.06 -49.88 REMARK 500 LEU A 128 -36.49 -38.32 REMARK 500 VAL A 129 -71.56 -70.82 REMARK 500 LEU A 131 -70.12 -46.34 REMARK 500 LYS A 141 53.80 38.93 REMARK 500 ASN A 145 16.00 58.25 REMARK 500 ALA A 166 -7.54 -55.62 REMARK 500 SER A 176 -168.94 56.68 REMARK 500 ASN A 199 33.98 73.93 REMARK 500 PHE A 212 -64.22 -127.18 REMARK 500 PHE A 228 -70.36 -73.78 REMARK 500 GLN A 237 58.76 -149.94 REMARK 500 ILE A 307 -54.63 -131.33 REMARK 500 CYS A 322 34.79 -90.83 REMARK 500 CYS A 323 37.46 75.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES 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: 1N3M RELATED DB: PDB REMARK 900 THEORETICAL MODEL OF RHODOPSIN OLIGOMER REMARK 900 RELATED ID: 2I37 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A PHOTOACTIVATED RHODOPSIN REMARK 900 RELATED ID: 1BOK RELATED DB: PDB REMARK 900 BOVINE RHODOPSIN (7-HELIX BUNDLE) WITH 11-CIS RETINAL , THEORETICAL REMARK 900 MODEL REMARK 900 RELATED ID: 2I36 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF TRIGONAL CRYSTAL FORM OF GROUND- STATERHODOPSIN 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: 2J4Y RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A RHODOPSIN STABILIZING MUTANT EXPRESSED IN REMARK 900 MAMMALIAN CELLS 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 REMARK 900 RELATED ID: 1LN6 RELATED DB: PDB REMARK 900 STRUCTURE OF BOVINE RHODOPSIN (METARHODOPSIN II) REMARK 900 RELATED ID: 1JFP RELATED DB: PDB REMARK 900 STRUCTURE OF BOVINE RHODOPSIN (DARK ADAPTED) REMARK 900 RELATED ID: 1OV1 RELATED DB: PDB REMARK 900 CALCULATED 3D MODEL OF AN ACTIVATED "STRAITJACKED" RHODOPSIN REMARK 900 RELATED ID: 1F88 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BOVINE RHODOPSIN REMARK 900 RELATED ID: 1BOJ RELATED DB: PDB REMARK 900 BOVINE RHODOPSIN (7-HELIX BUNDLE) WITH ALL-TRANS RETINAL, REMARK 900 METARHODOPSIN II MODEL, THEORETICAL MODEL 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: 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: 2X72 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CONSTITUTIVELY ACTIVE E113Q,N2C ,D282C REMARK 900 RHODOPSIN MUTANT WITH BOUND GALPHACT PEPTIDE. REMARK 900 RELATED ID: 1U19 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BOVINE RHODOPSIN AT 2.2 ANGSTROMSRESOLUTION REMARK 900 RELATED ID: 1FDF RELATED DB: PDB REMARK 900 HELIX 7 BOVINE RHODOPSIN 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: 1HZX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BOVINE RHODOPSIN REMARK 900 RELATED ID: 2I35 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RHOMBOHEDRAL CRYSTAL FORM OF GROUND -STATE REMARK 900 RHODOPSIN REMARK 900 RELATED ID: 1L9H RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BOVINE RHODOPSIN AT 2.6 ANGSTROMSRESOLUTION REMARK 900 RELATED ID: 1GZM RELATED DB: PDB REMARK 900 STRUCTURE OF BOVINE RHODOPSIN IN A TRIGONAL CRYSTAL FORM REMARK 900 RELATED ID: 1EDV RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF 2ND INTRADISKAL LOOP OF BOVINE RHODOPSIN REMARK 900 (RESIDUES 172-205) DBREF 4A4M A 1 348 UNP P02699 OPSD_BOVIN 1 348 DBREF 4A4M B 340 350 UNP P0C7Q4 GNAT3_BOVIN 344 354 SEQADV 4A4M ACE A 0 UNP P02699 ACETYLATION SEQADV 4A4M CYS A 2 UNP P02699 ASN 2 ENGINEERED MUTATION SEQADV 4A4M TYR A 257 UNP P02699 MET 257 ENGINEERED MUTATION SEQADV 4A4M CYS A 282 UNP P02699 ASP 282 ENGINEERED MUTATION SEQADV 4A4M LEU B 341 UNP P0C7Q4 LYS 345 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 TYR 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 11 ILE LEU GLU ASN LEU LYS ASP CYS GLY LEU PHE MODRES 4A4M ASN A 15 ASN GLYCOSYLATION SITE HET ACE A 0 3 HET NAG C 1 14 HET NAG C 2 14 HET RET A 401 20 HET ACT A1402 4 HET BOG A1403 20 HET PLM A1404 17 HETNAM ACE ACETYL GROUP HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM RET RETINAL HETNAM ACT ACETATE ION HETNAM BOG OCTYL BETA-D-GLUCOPYRANOSIDE HETNAM PLM PALMITIC ACID 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 HETSYN BOG BETA-OCTYLGLUCOSIDE; OCTYL BETA-D-GLUCOSIDE; OCTYL D- HETSYN 2 BOG GLUCOSIDE; OCTYL GLUCOSIDE FORMUL 1 ACE C2 H4 O FORMUL 3 NAG 2(C8 H15 N O6) FORMUL 4 RET C20 H28 O FORMUL 5 ACT C2 H3 O2 1- FORMUL 6 BOG C14 H28 O6 FORMUL 7 PLM C16 H32 O2 FORMUL 8 HOH *9(H2 O) HELIX 1 1 SER A 14 GLY A 18 5 5 HELIX 2 2 GLU A 33 HIS A 65 1 33 HELIX 3 3 THR A 70 LEU A 72 5 3 HELIX 4 4 ASN A 73 GLY A 89 1 17 HELIX 5 5 GLY A 90 LEU A 99 1 10 HELIX 6 6 PHE A 105 LYS A 141 1 37 HELIX 7 7 GLY A 149 ALA A 169 1 21 HELIX 8 8 PRO A 170 VAL A 173 5 4 HELIX 9 9 ASN A 199 HIS A 211 1 13 HELIX 10 10 PHE A 212 GLN A 236 1 25 HELIX 11 11 ALA A 241 THR A 277 1 37 HELIX 12 12 THR A 289 ILE A 307 1 19 HELIX 13 13 ASN A 310 CYS A 322 1 13 HELIX 14 14 ILE B 340 CYS B 347 1 8 SHEET 1 AA 2 THR A 4 GLY A 6 0 SHEET 2 AA 2 PHE A 9 VAL A 11 -1 O PHE A 9 N GLY A 6 SHEET 1 AB 2 TYR A 178 GLU A 181 0 SHEET 2 AB 2 SER A 186 ILE A 189 -1 O SER A 186 N GLU A 181 SSBOND 1 CYS A 2 CYS A 282 1555 1555 2.05 SSBOND 2 CYS A 110 CYS A 187 1555 1555 2.01 LINK C ACE A 0 N MET A 1 1555 1555 1.35 LINK ND2 ASN A 15 C1 NAG C 1 1555 1555 1.45 LINK NZ LYS A 296 C15 RET A 401 1555 1555 1.34 LINK SG CYS A 323 C1 PLM A1404 1555 1555 1.69 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.44 CRYST1 242.190 242.190 109.829 90.00 90.00 120.00 H 3 2 18 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 0.004129 0.002384 0.000000 0.00000 SCALE2 0.000000 0.004768 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009105 0.00000 HETATM 1 C ACE A 0 10.091 71.640 39.488 1.00109.31 C HETATM 2 O ACE A 0 9.299 70.679 39.426 1.00107.21 O HETATM 3 CH3 ACE A 0 9.723 73.018 39.989 1.00 87.92 C