PDB Short entry for 2ZIY HEADER SIGNALING PROTEIN 27-FEB-08 2ZIY TITLE CRYSTAL STRUCTURE OF SQUID RHODOPSIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RHODOPSIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TRUNCATION OF C-TERMINAL POLYPRO BY V8-PROTEASE, UNP COMPND 5 RESIDUES 2-373:VAL18ILE CONFIRMED BY MS SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TODARODES PACIFICUS; SOURCE 3 ORGANISM_COMMON: JAPANESE FLYING SQUID KEYWDS TRANSMEMBRANE HELICES, CHROMOPHORE, G-PROTEIN COUPLED RECEPTOR, KEYWDS 2 GLYCOPROTEIN, LIPOPROTEIN, PALMITATE, PHOSPHOPROTEIN, PHOTORECEPTOR KEYWDS 3 PROTEIN, RECEPTOR, RETINAL PROTEIN, SENSORY TRANSDUCTION, KEYWDS 4 TRANSDUCER, VISION, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.MIYANO,T.SHIMAMURA REVDAT 5 01-NOV-23 2ZIY 1 REMARK LINK REVDAT 4 24-FEB-09 2ZIY 1 VERSN REVDAT 3 08-JUL-08 2ZIY 1 JRNL REVDAT 2 27-MAY-08 2ZIY 1 COMPND REVDAT 1 06-MAY-08 2ZIY 0 JRNL AUTH T.SHIMAMURA,K.HIRAKI,N.TAKAHASHI,T.HORI,H.AGO,K.MASUDA, JRNL AUTH 2 K.TAKIO,M.ISHIGURO,M.MIYANO JRNL TITL CRYSTAL STRUCTURE OF SQUID RHODOPSIN WITH INTRACELLULARLY JRNL TITL 2 EXTENDED CYTOPLASMIC REGION JRNL REF J.BIOL.CHEM. V. 283 17753 2008 JRNL REFN ISSN 0021-9258 JRNL PMID 18463093 JRNL DOI 10.1074/JBC.C800040200 REMARK 2 REMARK 2 RESOLUTION. 3.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.20 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) (%) : 93.3 REMARK 3 NUMBER OF REFLECTIONS : 6647 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 SET) : 0.302 REMARK 3 FREE R VALUE : 0.330 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 725 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.87 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 74.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.4141 REMARK 3 BIN FREE R VALUE : 0.4320 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 64 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 : 2926 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 54 REMARK 3 SOLVENT ATOMS : 0 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.017 REMARK 3 BOND ANGLES (DEGREES) : 1.672 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE WAS REFINED ALSO WITH REMARK 3 REFMAC 5.0 REMARK 4 REMARK 4 2ZIY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-FEB-08. REMARK 100 THE DEPOSITION ID IS D_1000028030. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL45XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97950 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6680 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.700 REMARK 200 RESOLUTION RANGE LOW (A) : 43.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.77500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.300 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: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 28% PEG400, 0.1M HEPES, 8% ETHYLENE REMARK 280 GLYCOL, PH7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z 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 71.08250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 71.08250 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 42.15950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 54.37300 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 42.15950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 54.37300 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 71.08250 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 42.15950 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 54.37300 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 71.08250 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 42.15950 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 54.37300 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 36970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.2 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 84.31900 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 71.08250 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 2 REMARK 465 ARG A 3 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 LEU A 98 N LYS A 100 2.17 REMARK 500 O ASP A 80 OG SER A 84 2.18 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 PRO A 15 C - N - CA ANGL. DEV. = 9.5 DEGREES REMARK 500 GLY A 119 N - CA - C ANGL. DEV. = -17.9 DEGREES REMARK 500 ILE A 354 N - CA - C ANGL. DEV. = 22.1 DEGREES REMARK 500 ALA A 366 N - CA - C ANGL. DEV. = 21.6 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 LEU A 5 61.21 78.14 REMARK 500 ARG A 6 60.55 95.10 REMARK 500 GLU A 9 -67.87 -159.02 REMARK 500 TRP A 12 -14.78 -45.28 REMARK 500 PRO A 15 -39.04 -38.16 REMARK 500 ILE A 18 91.98 -69.48 REMARK 500 VAL A 19 174.98 -56.37 REMARK 500 GLU A 25 2.30 -60.92 REMARK 500 ILE A 39 -51.97 -28.70 REMARK 500 ILE A 46 -79.33 -51.36 REMARK 500 ILE A 54 -71.35 -52.02 REMARK 500 LEU A 58 -76.66 -72.39 REMARK 500 PHE A 59 -16.25 -41.27 REMARK 500 SER A 64 4.45 -68.68 REMARK 500 MET A 71 -9.53 -57.01 REMARK 500 PHE A 83 -72.00 -34.53 REMARK 500 LEU A 85 -70.14 -51.58 REMARK 500 LEU A 91 -82.23 -50.18 REMARK 500 LYS A 99 7.36 34.34 REMARK 500 ILE A 114 -73.10 -47.06 REMARK 500 PHE A 118 11.39 -66.90 REMARK 500 ILE A 137 -41.78 -133.26 REMARK 500 HIS A 149 -35.77 -35.44 REMARK 500 ARG A 150 -80.16 -68.95 REMARK 500 ALA A 152 -70.30 -38.49 REMARK 500 VAL A 159 -74.53 -48.80 REMARK 500 TRP A 160 -79.24 -32.92 REMARK 500 LEU A 161 -54.74 -26.55 REMARK 500 TRP A 162 -72.24 -56.92 REMARK 500 SER A 163 -56.16 -28.91 REMARK 500 LEU A 165 -65.27 -27.70 REMARK 500 TRP A 166 1.27 -68.75 REMARK 500 ALA A 176 159.13 167.43 REMARK 500 THR A 178 -159.40 -141.85 REMARK 500 SER A 187 -174.56 -175.27 REMARK 500 ILE A 191 -81.15 -85.92 REMARK 500 SER A 192 121.11 -35.71 REMARK 500 ARG A 193 40.49 -103.20 REMARK 500 PHE A 209 -57.13 -134.96 REMARK 500 TYR A 220 21.13 -55.77 REMARK 500 PHE A 221 -67.55 -122.26 REMARK 500 ALA A 284 -16.87 -48.58 REMARK 500 PRO A 288 76.28 -60.26 REMARK 500 VAL A 292 59.53 -46.74 REMARK 500 ASN A 311 -65.40 -27.07 REMARK 500 SER A 316 15.02 -59.50 REMARK 500 SER A 318 -13.78 -155.72 REMARK 500 PRO A 320 -84.29 -73.59 REMARK 500 LYS A 321 -35.61 -30.18 REMARK 500 PHE A 322 -73.44 -64.76 REMARK 500 REMARK 500 THIS ENTRY HAS 67 RAMACHANDRAN OUTLIERS. 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 RET A 380 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PLM A 381 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PLM A 382 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THERE IS CONFLICTS BETWEEN SEQRES(ILE A 17) REMARK 999 AND SEQUENCE DATABASE (VAL). REMARK 999 THE AUTHORS CONFIRMED EXPERIMENTALLY BY N-TERMINAL REMARK 999 AMINO ACID SEQUENCING, AND THE SEQRES IS CORRECT REMARK 999 AND IS THE TRUE IDENTITY OF THIS RESIDUE REMARK 999 AND IS NATURAL VARIANT. DBREF 2ZIY A 2 373 UNP P31356 OPSD_TODPA 2 373 SEQADV 2ZIY ILE A 18 UNP P31356 VAL 18 SEE REMARK 999 SEQRES 1 A 372 GLY ARG ASP LEU ARG ASP ASN GLU THR TRP TRP TYR ASN SEQRES 2 A 372 PRO SER ILE ILE VAL HIS PRO HIS TRP ARG GLU PHE ASP SEQRES 3 A 372 GLN VAL PRO ASP ALA VAL TYR TYR SER LEU GLY ILE PHE SEQRES 4 A 372 ILE GLY ILE CYS GLY ILE ILE GLY CYS GLY GLY ASN GLY SEQRES 5 A 372 ILE VAL ILE TYR LEU PHE THR LYS THR LYS SER LEU GLN SEQRES 6 A 372 THR PRO ALA ASN MET PHE ILE ILE ASN LEU ALA PHE SER SEQRES 7 A 372 ASP PHE THR PHE SER LEU VAL ASN GLY PHE PRO LEU MET SEQRES 8 A 372 THR ILE SER CYS PHE LEU LYS LYS TRP ILE PHE GLY PHE SEQRES 9 A 372 ALA ALA CYS LYS VAL TYR GLY PHE ILE GLY GLY ILE PHE SEQRES 10 A 372 GLY PHE MET SER ILE MET THR MET ALA MET ILE SER ILE SEQRES 11 A 372 ASP ARG TYR ASN VAL ILE GLY ARG PRO MET ALA ALA SER SEQRES 12 A 372 LYS LYS MET SER HIS ARG ARG ALA PHE ILE MET ILE ILE SEQRES 13 A 372 PHE VAL TRP LEU TRP SER VAL LEU TRP ALA ILE GLY PRO SEQRES 14 A 372 ILE PHE GLY TRP GLY ALA TYR THR LEU GLU GLY VAL LEU SEQRES 15 A 372 CYS ASN CYS SER PHE ASP TYR ILE SER ARG ASP SER THR SEQRES 16 A 372 THR ARG SER ASN ILE LEU CYS MET PHE ILE LEU GLY PHE SEQRES 17 A 372 PHE GLY PRO ILE LEU ILE ILE PHE PHE CYS TYR PHE ASN SEQRES 18 A 372 ILE VAL MET SER VAL SER ASN HIS GLU LYS GLU MET ALA SEQRES 19 A 372 ALA MET ALA LYS ARG LEU ASN ALA LYS GLU LEU ARG LYS SEQRES 20 A 372 ALA GLN ALA GLY ALA ASN ALA GLU MET ARG LEU ALA LYS SEQRES 21 A 372 ILE SER ILE VAL ILE VAL SER GLN PHE LEU LEU SER TRP SEQRES 22 A 372 SER PRO TYR ALA VAL VAL ALA LEU LEU ALA GLN PHE GLY SEQRES 23 A 372 PRO LEU GLU TRP VAL THR PRO TYR ALA ALA GLN LEU PRO SEQRES 24 A 372 VAL MET PHE ALA LYS ALA SER ALA ILE HIS ASN PRO MET SEQRES 25 A 372 ILE TYR SER VAL SER HIS PRO LYS PHE ARG GLU ALA ILE SEQRES 26 A 372 SER GLN THR PHE PRO TRP VAL LEU THR CYS CYS GLN PHE SEQRES 27 A 372 ASP ASP LYS GLU THR GLU ASP ASP LYS ASP ALA GLU THR SEQRES 28 A 372 GLU ILE PRO ALA GLY GLU SER SER ASP ALA ALA PRO SER SEQRES 29 A 372 ALA ASP ALA ALA GLN MET LYS GLU HET RET A 380 20 HET PLM A 381 17 HET PLM A 382 17 HETNAM RET RETINAL HETNAM PLM PALMITIC ACID FORMUL 2 RET C20 H28 O FORMUL 3 PLM 2(C16 H32 O2) HELIX 1 1 HIS A 20 GLU A 25 1 6 HELIX 2 2 PRO A 30 THR A 62 1 33 HELIX 3 3 LYS A 63 GLN A 66 5 4 HELIX 4 4 THR A 67 ALA A 69 5 3 HELIX 5 5 ASN A 70 GLY A 88 1 19 HELIX 6 6 PRO A 90 LEU A 98 1 9 HELIX 7 7 GLY A 104 ILE A 137 1 34 HELIX 8 8 PRO A 140 SER A 144 5 5 HELIX 9 9 SER A 148 GLY A 169 1 22 HELIX 10 10 PRO A 170 GLY A 173 5 4 HELIX 11 11 ASP A 194 GLY A 208 1 15 HELIX 12 12 PHE A 209 ASN A 229 1 21 HELIX 13 13 ASN A 229 MET A 237 1 9 HELIX 14 14 LYS A 244 GLY A 287 1 44 HELIX 15 15 THR A 293 SER A 307 1 15 HELIX 16 16 ILE A 309 SER A 316 1 8 HELIX 17 17 HIS A 319 PHE A 330 1 12 HELIX 18 18 PRO A 331 CYS A 337 5 7 HELIX 19 19 GLU A 343 ASP A 349 1 7 SHEET 1 A 2 TYR A 177 LEU A 179 0 SHEET 2 A 2 CYS A 186 PHE A 188 -1 O SER A 187 N THR A 178 SSBOND 1 CYS A 108 CYS A 186 1555 1555 2.04 LINK NZ LYS A 305 C15 RET A 380 1555 1555 1.30 LINK SG CYS A 336 C1 PLM A 381 1555 1555 1.86 LINK SG CYS A 337 C1 PLM A 382 1555 1555 1.86 CISPEP 1 PHE A 89 PRO A 90 0 0.48 SITE 1 AC1 6 PHE A 120 CYS A 186 MET A 204 PHE A 209 SITE 2 AC1 6 TRP A 274 LYS A 305 SITE 1 AC2 1 CYS A 336 SITE 1 AC3 3 SER A 316 CYS A 336 CYS A 337 CRYST1 84.319 108.746 142.165 90.00 90.00 90.00 C 2 2 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.011860 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009196 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007034 0.00000