HEADER MEMBRANE PROTEIN 17-AUG-06 2I35 TITLE CRYSTAL STRUCTURE OF RHOMBOHEDRAL CRYSTAL FORM OF GROUND-STATE TITLE 2 RHODOPSIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RHODOPSIN; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913 KEYWDS TRANS-MEMBRANE PROTEIN, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.E.STENKAMP,I.LE TRONG,D.T.LODOWSKI,D.SALOM,K.PALCZEWSKI REVDAT 7 30-AUG-23 2I35 1 HETSYN REVDAT 6 29-JUL-20 2I35 1 COMPND REMARK HETNAM LINK REVDAT 6 2 1 SITE ATOM REVDAT 5 18-OCT-17 2I35 1 REMARK REVDAT 4 13-JUL-11 2I35 1 VERSN REVDAT 3 24-FEB-09 2I35 1 VERSN REVDAT 2 14-NOV-06 2I35 1 JRNL REVDAT 1 17-OCT-06 2I35 0 JRNL AUTH D.SALOM,D.T.LODOWSKI,R.E.STENKAMP,I.L.TRONG,M.GOLCZAK, JRNL AUTH 2 B.JASTRZEBSKA,T.HARRIS,J.A.BALLESTEROS,K.PALCZEWSKI JRNL TITL CRYSTAL STRUCTURE OF A PHOTOACTIVATED DEPROTONATED JRNL TITL 2 INTERMEDIATE OF RHODOPSIN. JRNL REF PROC.NATL.ACAD.SCI.USA V. 103 16123 2006 JRNL REFN ISSN 0027-8424 JRNL PMID 17060607 JRNL DOI 10.1073/PNAS.0608022103 REMARK 2 REMARK 2 RESOLUTION. 3.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 84.5 REMARK 3 NUMBER OF REFLECTIONS : 8168 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.375 REMARK 3 R VALUE (WORKING SET) : 0.373 REMARK 3 FREE R VALUE : 0.418 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 401 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 372 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 56.81 REMARK 3 BIN R VALUE (WORKING SET) : 0.6040 REMARK 3 BIN FREE R VALUE SET COUNT : 24 REMARK 3 BIN FREE R VALUE : 0.3930 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2606 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 121 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 227.0 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 225.8 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -22.65000 REMARK 3 B22 (A**2) : -22.65000 REMARK 3 B33 (A**2) : 33.98000 REMARK 3 B12 (A**2) : -11.33000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 1.013 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 1.444 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 107.468 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.873 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.799 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2812 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3823 ; 1.437 ; 1.986 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 326 ; 6.009 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 111 ;39.196 ;23.333 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 411 ;20.123 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;20.560 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 431 ; 0.126 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2078 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1648 ; 0.244 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1952 ; 0.316 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 108 ; 0.185 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 49 ; 0.313 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.194 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2I35 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-AUG-06. REMARK 100 THE DEPOSITION ID IS D_1000039077. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUN-04 REMARK 200 TEMPERATURE (KELVIN) : 77 REMARK 200 PH : 6.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8204 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 84.5 REMARK 200 DATA REDUNDANCY : 15.90 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 59.2 REMARK 200 DATA REDUNDANCY IN SHELL : 9.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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 1HZX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 81.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 6.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 80 MM MES, PH 6.3, 110 MM N-NONYL-BETA REMARK 280 -D-GLUCOSIDE, 200 MM ZINC ACETATE, 16 MM BETA-MERCAPTOETHANOL, REMARK 280 0.4% MERPOL DA, 0.1% SODIUM AZIDE, EQUILIBRATED AGAINST 3.0 M REMARK 280 AMMONIUM SULFATE, VAPOR DIFFUSION, TEMPERATURE 278K 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 138.76700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 80.11716 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 22.10700 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 138.76700 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 80.11716 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 22.10700 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 138.76700 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 80.11716 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 22.10700 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 138.76700 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 80.11716 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 22.10700 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 138.76700 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 80.11716 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 22.10700 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 138.76700 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 80.11716 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 22.10700 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 160.23433 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 44.21400 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 160.23433 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 44.21400 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 160.23433 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 44.21400 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 160.23433 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 44.21400 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 160.23433 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 44.21400 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 160.23433 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 44.21400 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 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 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 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 ASN A 315 OG1 THR A 319 1.98 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 52.68 -69.69 REMARK 500 SER A 14 107.88 -59.39 REMARK 500 ASN A 15 30.25 -68.58 REMARK 500 ALA A 32 -123.30 -169.52 REMARK 500 SER A 38 7.99 -68.56 REMARK 500 VAL A 63 -70.74 -44.62 REMARK 500 LEU A 95 -71.58 -47.50 REMARK 500 TYR A 102 162.30 173.60 REMARK 500 ASN A 111 -73.39 -65.36 REMARK 500 LEU A 112 -73.68 -40.24 REMARK 500 LYS A 141 60.79 28.31 REMARK 500 SER A 144 -179.38 -63.21 REMARK 500 ASN A 145 104.27 -43.27 REMARK 500 SER A 176 -178.31 62.44 REMARK 500 GLN A 184 -21.74 65.93 REMARK 500 HIS A 195 91.95 31.15 REMARK 500 GLU A 197 1.40 -69.18 REMARK 500 PHE A 212 -65.80 -143.59 REMARK 500 GLN A 238 -6.74 69.43 REMARK 500 GLU A 239 123.48 -32.77 REMARK 500 GLU A 249 -8.11 -58.78 REMARK 500 HIS A 278 55.26 -104.78 REMARK 500 GLN A 279 98.10 -57.94 REMARK 500 ALA A 292 -78.54 -73.24 REMARK 500 VAL A 300 -50.50 -135.09 REMARK 500 CYS A 323 68.22 74.59 REMARK 500 ASP A 331 -68.03 -174.37 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 RET A 1332 REMARK 610 PLM A 1333 REMARK 610 PLM A 1334 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2I36 RELATED DB: PDB REMARK 900 2I36 IS THE CRYSTAL STRUCTURE OF TRIGONAL FORM OF GROUND-STATE REMARK 900 RHODOPSIN DETERMINED AT 4.10 ANGSTROM RESOLUTION REMARK 900 RELATED ID: 2I37 RELATED DB: PDB REMARK 900 2I37 IS THE CRYSTAL STRUCTURE OF PHOTOACTIVATED RHODOPSIN REMARK 900 DETERMINED AT 4.15 ANGSTROM RESOLUTION DBREF 2I35 A 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 MODRES 2I35 ASN A 2 ASN GLYCOSYLATION SITE MODRES 2I35 ASN A 15 ASN GLYCOSYLATION SITE HET ACE A 0 3 HET NAG B 1 14 HET NAG B 2 14 HET BMA B 3 11 HET NAG C 1 14 HET NAG C 2 14 HET RET A1332 20 HET PLM A1333 17 HET PLM A1334 17 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 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 FORMUL 1 ACE C2 H4 O FORMUL 2 NAG 4(C8 H15 N O6) FORMUL 2 BMA C6 H12 O6 FORMUL 4 RET C20 H28 O FORMUL 5 PLM 2(C16 H32 O2) HELIX 1 1 PRO A 27 ALA A 32 5 6 HELIX 2 2 GLU A 33 HIS A 65 1 33 HELIX 3 3 THR A 70 GLY A 89 1 20 HELIX 4 4 GLY A 89 LEU A 99 1 11 HELIX 5 5 PHE A 105 CYS A 140 1 36 HELIX 6 6 ASN A 151 ALA A 169 1 19 HELIX 7 7 ALA A 169 GLY A 174 1 6 HELIX 8 8 ASN A 199 PHE A 212 1 14 HELIX 9 9 PHE A 212 ALA A 233 1 22 HELIX 10 10 SER A 240 HIS A 278 1 39 HELIX 11 11 PRO A 285 LYS A 296 1 12 HELIX 12 12 THR A 297 ALA A 299 5 3 HELIX 13 13 VAL A 300 ASN A 310 1 11 HELIX 14 14 ASN A 310 CYS A 323 1 14 SHEET 1 A 2 TYR A 178 GLU A 181 0 SHEET 2 A 2 SER A 186 ILE A 189 -1 O SER A 186 N GLU A 181 SSBOND 1 CYS A 110 CYS A 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 C 1 1555 1555 1.45 LINK ND2 ASN A 15 C1 NAG B 1 1555 1555 1.45 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.46 LINK O4 NAG B 2 C1 BMA B 3 1555 1555 1.46 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.45 CRYST1 277.534 277.534 66.321 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 0.003603 0.002080 0.000000 0.00000 SCALE2 0.000000 0.004161 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015078 0.00000 HETATM 1 C ACE A 0 17.583 127.070 13.924 1.00227.22 C HETATM 2 O ACE A 0 18.778 126.809 13.735 1.00227.22 O HETATM 3 CH3 ACE A 0 16.854 126.675 15.193 1.00227.22 C