HEADER SIGNALING PROTEIN 24-MAY-02 1GZM TITLE STRUCTURE OF BOVINE RHODOPSIN IN A TRIGONAL CRYSTAL FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: RHODOPSIN; COMPND 3 CHAIN: A, B; COMPND 4 OTHER_DETAILS: DISULFIDE LINK BETWEEN A110 AND A187, AND B110 AND COMPND 5 B187 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 KEYWDS SIGNALING PROTEIN, PHOTORECEPTOR, RETINAL PROTEIN, VISUAL PIGMENT, G- KEYWDS 2 PROTEIN COUPLED RECEPTOR, INTEGRAL MEMBRANE PROTEIN, PALMITATE, KEYWDS 3 PHOSPHORYLATION EXPDTA X-RAY DIFFRACTION AUTHOR J.LI REVDAT 9 23-OCT-24 1GZM 1 REMARK REVDAT 8 13-DEC-23 1GZM 1 HETSYN REVDAT 7 29-JUL-20 1GZM 1 COMPND REMARK HETNAM LINK REVDAT 7 2 1 SITE ATOM REVDAT 6 08-MAY-19 1GZM 1 REMARK LINK REVDAT 5 19-OCT-11 1GZM 1 REMARK HETSYN FORMUL LINK REVDAT 5 2 1 SITE VERSN REVDAT 4 24-FEB-09 1GZM 1 VERSN REVDAT 3 08-JUL-08 1GZM 1 VERSN REMARK REVDAT 2 27-OCT-04 1GZM 1 JRNL REMARK REVDAT 1 20-NOV-03 1GZM 0 JRNL AUTH J.LI,P.EDWARDS,M.BURGHAMMER,C.VILLA,G.F.X.SCHERTLER JRNL TITL STRUCTURE OF BOVINE RHODOPSIN IN A TRIGONAL CRYSTAL FORM JRNL REF J.MOL.BIOL. V. 343 1409 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 15491621 JRNL DOI 10.1016/J.JMB.2004.08.090 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.EDWARDS,J.LI,M.BURGHAMMER,J.H.MCDOWELL,C.VILLA, REMARK 1 AUTH 2 P.A.HARGRAVE,G.F.X.SCHERTLER REMARK 1 TITL CRYSTALS OF NATIVE AND MODIFIED BOVINE RHODOPSINS AND THEIR REMARK 1 TITL 2 HEAVY ATOM DERIVATIVES REMARK 1 REF J.MOL.BIOL. V. 343 1439 2004 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 15491622 REMARK 1 DOI 10.1016/J.JMB.2004.08.089 REMARK 2 REMARK 2 RESOLUTION. 2.65 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 24704 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) : 0.202 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1322 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.74 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2165 REMARK 3 BIN R VALUE (WORKING SET) : 0.3089 REMARK 3 BIN FREE R VALUE : 0.3146 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 130 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.028 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5212 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 540 REMARK 3 SOLVENT ATOMS : 40 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 58.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.45400 REMARK 3 B22 (A**2) : -4.45400 REMARK 3 B33 (A**2) : 8.90700 REMARK 3 B12 (A**2) : -8.52600 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) : 0.31 REMARK 3 ESD FROM SIGMAA (A) : 0.42 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) : 0.37 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.46 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 19.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.880 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 : FLAT MODEL 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) : 0.515 ; 5 REMARK 3 GROUP 1 B-FACTOR (A**2) : 1 ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP_LYR7_CYP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 4 : LIPID-DETG3.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN_LYR2_CYP.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 4 : LIPID-DETG.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE FOLLOWING HOH RESIDUES ARE REMARK 3 EQUIVALENT BY NON- CRYSTALLOGRAPHIC SYMMETRY AND ARE EQUIVALENT REMARK 3 TO THESE RESIDUES IN THE PRIMARY REFERENCE: U1 == V1, AND WATER REMARK 3 RESIDUE 7 IN REFERENCE U2 == V3, AND WATER RESIDUE 16 IN REMARK 3 REFERENCE U3 == V4, AND WATER RESIDUE 8 IN REFERENCE U4 == V5, REMARK 3 AND WATER RESIDUE 11 IN REFERENCE U5 == V6, AND WATER RESIDUE 4 REMARK 3 IN REFERENCE U6 == V7, AND WATER RESIDUE 13 IN REFERENCE U7 == REMARK 3 V11, AND WATER RESIDUE 6 IN REFERENCE U8 == V9, AND WATER REMARK 3 RESIDUE 3 IN REFERENCE U9 == V19, AND WATER RESIDUE 15 IN REMARK 3 REFERENCE U10 == V3, AND WATER RESIDUE 18 IN REFERENCE U11 == REMARK 3 V13, AND WATER RESIDUE 5 IN REFERENCE U12 == V14, AND WATER REMARK 3 RESIDUE 14 IN REFERENCE U13 == V15, AND WATER RESIDUE 19 IN REMARK 3 REFERENCE U14 == V16, AND WATER RESIDUE 9 IN REFERENCE U15 == REMARK 3 V17, AND WATER RESIDUE 1 IN REFERENCE U16 == V12, AND WATER REMARK 3 RESIDUE 17 IN REFERENCE U17 == V18, AND WATER RESIDUE 20 IN REMARK 3 REFERENCE U18 == V2, AND WATER RESIDUE 12 IN REFERENCE U19 == REMARK 3 V19, AND WATER RESIDUE 2 IN REFERENCE U20 == V20, AND WATER REMARK 3 RESIDUE 10 IN REFERENCE THE FOLLOWING CARBOHYDRATE RESIDUES ARE REMARK 3 EQUIVALENT BY NON- CRYSTALLOGRAPHIC SYMMETRY: A1335 IS REMARK 3 EQUIVALENT TO B1335 A1336 IS EQUIVALENT TO B1336 A1337 IS REMARK 3 EQUIVALENT TO B1350 A1338 IS EQUIVALENT TO B1337 A1339 IS REMARK 3 EQUIVALENT TO B1338 A1340 IS EQUIVALENT TO B1339 REMARK 4 REMARK 4 1GZM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-MAY-02. REMARK 100 THE DEPOSITION ID IS D_1290009872. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-OCT-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 4 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) : 0.782 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26026 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.650 REMARK 200 RESOLUTION RANGE LOW (A) : 46.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.11900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.60 REMARK 200 R MERGE FOR SHELL (I) : 0.43400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1F88 REMARK 200 REMARK 200 REMARK: DATA WERE COLLECTED USING MICROFOCUSED SYNCHROTRON SOURCE. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOUR DIFFUSION IN SITTING DROPS OF REMARK 280 15 MG/ML PROTEIN AND 0.2% C8E4, 0.05%LDAO AGAINST 0.8M LI2SO4, REMARK 280 1.6% PEG8000 AND 20% GLYCEROL, PH 8.5, VAPOR DIFFUSION, SITTING REMARK 280 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 25.53000 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 51.06000 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: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 35620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, 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 400 REMARK 400 COMPOUND REMARK 400 LIGHT-ABSORBING MOLECULES THAT MEDIATE VISION. CONSIST OF AN REMARK 400 APOPROTEIN, OPSIN, COVALENTLY BOUND TO 11-CIS-RETINAL. 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 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 PRO B 327 REMARK 465 LEU B 328 REMARK 465 GLY B 329 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 ASP A 330 CG OD1 OD2 REMARK 470 ASP A 331 CG OD1 OD2 REMARK 470 GLU A 332 CA C O CB CG CD OE1 REMARK 470 GLU A 332 OE2 REMARK 470 ASP B 330 CG OD1 OD2 REMARK 470 ASP B 331 CG OD1 OD2 REMARK 470 GLU B 332 CA C O CB CG CD OE1 REMARK 470 GLU B 332 OE2 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 LYS A 141 59.16 32.02 REMARK 500 SER A 144 -157.34 -55.53 REMARK 500 ASN A 145 78.62 -67.93 REMARK 500 SER A 176 -171.00 69.08 REMARK 500 HIS A 195 69.06 20.89 REMARK 500 PHE A 212 -69.40 -151.08 REMARK 500 LYS A 231 -67.19 -99.18 REMARK 500 GLU A 239 106.23 -55.84 REMARK 500 HIS A 278 37.32 -149.14 REMARK 500 CYS A 323 107.88 61.14 REMARK 500 ASP A 331 -54.30 176.39 REMARK 500 PRO B 142 -87.10 -58.82 REMARK 500 MET B 143 -91.69 -14.04 REMARK 500 SER B 144 -136.40 -153.72 REMARK 500 ASN B 145 54.90 -111.83 REMARK 500 SER B 176 -172.55 71.38 REMARK 500 HIS B 195 67.47 24.77 REMARK 500 PHE B 212 -70.53 -150.55 REMARK 500 VAL B 230 -6.71 -58.64 REMARK 500 GLN B 238 85.15 30.86 REMARK 500 HIS B 278 37.49 -150.64 REMARK 500 CYS B 323 91.59 56.51 REMARK 500 ASP B 331 -55.19 178.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PEF A 1341 REMARK 610 C8E A 1343 REMARK 610 C8E A 1344 REMARK 610 C8E A 1345 REMARK 610 C8E A 1346 REMARK 610 C8E A 1348 REMARK 610 C8E B 1341 REMARK 610 PEF B 1342 REMARK 610 C8E B 1344 REMARK 610 C8E B 1345 REMARK 610 C8E B 1346 REMARK 610 C8E B 1347 REMARK 900 REMARK 900 RELATED ENTRIES 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: 1BOK RELATED DB: PDB REMARK 900 BOVINE RHODOPSIN (7-HELIX BUNDLE) WITH 11- CIS RETINAL, THEORETICAL REMARK 900 MODEL 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: 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) DBREF 1GZM A 1 348 UNP P02699 OPSD_BOVIN 1 348 DBREF 1GZM B 1 348 UNP P02699 OPSD_BOVIN 1 348 SEQRES 1 A 349 ACE MET ASN 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 ASP 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 ASN 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 ASP 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 1GZM ASN A 2 ASN GLYCOSYLATION SITE MODRES 1GZM ASN A 15 ASN GLYCOSYLATION SITE MODRES 1GZM ASN B 2 ASN GLYCOSYLATION SITE MODRES 1GZM ASN B 15 ASN GLYCOSYLATION SITE HET ACE A 0 3 HET ACE B 0 3 HET NAG C 1 14 HET NAG C 2 14 HET BMA C 3 11 HET NAG D 1 14 HET NAG D 2 14 HET BMA D 3 11 HET NAG E 1 14 HET NAG E 2 14 HET BMA E 3 11 HET NAG F 1 14 HET NAG F 2 14 HET BMA F 3 11 HET RET A1332 20 HET PLM A1333 17 HET PLM A1334 17 HET PEF A1341 20 HET LDA A1342 16 HET C8E A1343 17 HET C8E A1344 15 HET C8E A1345 10 HET C8E A1346 18 HET C8E A1347 21 HET C8E A1348 12 HET ZN A1349 1 HET RET B1332 20 HET PLM B1333 17 HET PLM B1334 17 HET C8E B1340 21 HET C8E B1341 12 HET PEF B1342 24 HET LDA B1343 16 HET C8E B1344 14 HET C8E B1345 14 HET C8E B1346 10 HET C8E B1347 18 HET LDA B1348 16 HET ZN B1349 1 HETNAM ACE ACETYL GROUP HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM RET RETINAL HETNAM PLM PALMITIC ACID HETNAM PEF DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE HETNAM LDA LAURYL DIMETHYLAMINE-N-OXIDE HETNAM C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE HETNAM ZN ZINC ION 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 BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN PEF 3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL FORMUL 1 ACE 2(C2 H4 O) FORMUL 3 NAG 8(C8 H15 N O6) FORMUL 3 BMA 4(C6 H12 O6) FORMUL 7 RET 2(C20 H28 O) FORMUL 8 PLM 4(C16 H32 O2) FORMUL 10 PEF 2(C37 H74 N O8 P) FORMUL 11 LDA 3(C14 H31 N O) FORMUL 12 C8E 12(C16 H34 O5) FORMUL 18 ZN 2(ZN 2+) FORMUL 32 HOH *40(H2 O) HELIX 1 1 GLU A 33 HIS A 65 1 33 HELIX 2 2 THR A 70 GLY A 90 1 21 HELIX 3 3 GLY A 90 GLY A 101 1 12 HELIX 4 4 PHE A 105 LYS A 141 1 37 HELIX 5 5 GLY A 149 ALA A 169 1 21 HELIX 6 6 PRO A 170 VAL A 173 5 4 HELIX 7 7 HIS A 195 THR A 198 5 4 HELIX 8 8 ASN A 199 HIS A 211 1 13 HELIX 9 9 PHE A 212 ALA A 233 1 22 HELIX 10 10 SER A 240 THR A 277 1 38 HELIX 11 11 PRO A 285 ALA A 295 1 11 HELIX 12 12 VAL A 300 ASN A 310 1 11 HELIX 13 13 ASN A 310 LEU A 321 1 12 HELIX 14 14 GLU B 33 HIS B 65 1 33 HELIX 15 15 THR B 70 GLY B 90 1 21 HELIX 16 16 GLY B 90 GLY B 101 1 12 HELIX 17 17 PHE B 105 LYS B 141 1 37 HELIX 18 18 GLY B 149 ALA B 169 1 21 HELIX 19 19 PRO B 170 VAL B 173 5 4 HELIX 20 20 HIS B 195 THR B 198 5 4 HELIX 21 21 ASN B 199 HIS B 211 1 13 HELIX 22 22 PHE B 212 VAL B 230 1 19 HELIX 23 23 SER B 240 THR B 277 1 38 HELIX 24 24 PRO B 285 ALA B 295 1 11 HELIX 25 25 VAL B 300 ASN B 310 1 11 HELIX 26 26 ASN B 310 LEU B 321 1 12 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 PRO A 180 0 SHEET 2 AB 2 CYS A 187 ILE A 189 -1 O GLY A 188 N ILE A 179 SHEET 1 BA 2 THR B 4 GLY B 6 0 SHEET 2 BA 2 PHE B 9 VAL B 11 -1 O PHE B 9 N GLY B 6 SHEET 1 BB 2 TYR B 178 PRO B 180 0 SHEET 2 BB 2 CYS B 187 ILE B 189 -1 O GLY B 188 N ILE B 179 SSBOND 1 CYS A 110 CYS A 187 1555 1555 2.04 SSBOND 2 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 2 C1 NAG D 1 1555 1555 1.45 LINK ND2 ASN A 15 C1 NAG C 1 1555 1555 1.46 LINK NZ LYS A 296 C15 RET A1332 1555 1555 1.33 LINK SG CYS A 322 C1 PLM A1333 1555 1555 1.79 LINK SG CYS A 323 C1 PLM A1334 1555 1555 1.81 LINK C ACE B 0 N MET B 1 1555 1555 1.33 LINK ND2 ASN B 2 C1 NAG F 1 1555 1555 1.45 LINK ND2 ASN B 15 C1 NAG E 1 1555 1555 1.46 LINK NZ LYS B 296 C15 RET B1332 1555 1555 1.32 LINK SG CYS B 322 C1 PLM B1333 1555 1555 1.80 LINK SG CYS B 323 C1 PLM B1334 1555 1555 1.82 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.39 LINK O4 NAG C 2 C1 BMA C 3 1555 1555 1.39 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.39 LINK O4 NAG D 2 C1 BMA D 3 1555 1555 1.39 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.39 LINK O4 NAG E 2 C1 BMA E 3 1555 1555 1.39 LINK O4 NAG F 1 C1 NAG F 2 1555 1555 1.39 LINK O4 NAG F 2 C1 BMA F 3 1555 1555 1.39 LINK ND2 ASN B 151 ZN ZN B1349 1555 1555 2.62 CRYST1 103.820 103.820 76.590 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 0.009632 0.005561 0.000000 0.00000 SCALE2 0.000000 0.011122 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013057 0.00000 MTRIX1 1 -1.000000 -0.000560 0.000190 51.91986 1 MTRIX2 1 0.000560 -1.000000 -0.000300 29.94182 1 MTRIX3 1 0.000190 -0.000300 1.000000 0.00307 1 MTRIX1 2 -1.000000 -0.000560 0.000190 51.91986 1 MTRIX2 2 0.000560 -1.000000 -0.000300 29.94182 1 MTRIX3 2 0.000190 -0.000300 1.000000 0.00307 1 MTRIX1 3 -0.999990 -0.003080 0.001870 52.03257 1 MTRIX2 3 0.003090 -0.999990 0.000940 29.86744 1 MTRIX3 3 0.001860 0.000950 1.000000 -0.09026 1 HETATM 1 C ACE A 0 17.248 42.781 12.346 1.00 83.12 C HETATM 2 O ACE A 0 17.272 41.557 12.496 1.00 83.33 O HETATM 3 CH3 ACE A 0 16.255 43.618 13.128 1.00 84.47 C