HEADER MEMBRANE PROTEIN 17-AUG-06 2I37 TITLE CRYSTAL STRUCTURE OF A PHOTOACTIVATED RHODOPSIN CAVEAT 2I37 NAG G 1 HAS WRONG CHIRALITY AT ATOM C1 NAG I 1 HAS WRONG CAVEAT 2 2I37 CHIRALITY AT ATOM C1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RHODOPSIN; COMPND 3 CHAIN: A, B, C SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913 KEYWDS TRANS-MEMBRANE PROTEIN, GPCR, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.T.LODOWSKI,R.E.STENKAMP,D.SALOM,I.LE TRONG,K.PALCZEWSKI REVDAT 7 30-AUG-23 2I37 1 HETSYN REVDAT 6 29-JUL-20 2I37 1 CAVEAT COMPND REMARK HET REVDAT 6 2 1 HETNAM FORMUL LINK SITE REVDAT 6 3 1 ATOM REVDAT 5 18-OCT-17 2I37 1 REMARK REVDAT 4 13-JUL-11 2I37 1 VERSN REVDAT 3 24-FEB-09 2I37 1 VERSN REVDAT 2 14-NOV-06 2I37 1 JRNL REVDAT 1 17-OCT-06 2I37 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. 4.15 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) : 4.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 76.8 REMARK 3 NUMBER OF REFLECTIONS : 12455 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) : 0.378 REMARK 3 R VALUE (WORKING SET) : 0.377 REMARK 3 FREE R VALUE : 0.382 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 645 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) : 4.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 4.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 662 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 60.65 REMARK 3 BIN R VALUE (WORKING SET) : 0.4970 REMARK 3 BIN FREE R VALUE SET COUNT : 33 REMARK 3 BIN FREE R VALUE : 0.4880 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7577 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 237 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) : 177.2 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -14.29000 REMARK 3 B22 (A**2) : -14.29000 REMARK 3 B33 (A**2) : 21.43000 REMARK 3 B12 (A**2) : -7.14000 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): 1.434 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 1.596 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 133.351 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.869 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.867 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 8072 ; 0.007 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 7275 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 11019 ; 1.069 ; 1.982 REMARK 3 BOND ANGLES OTHERS (DEGREES): 16765 ; 0.772 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 944 ; 6.048 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 317 ;33.147 ;23.186 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1189 ;18.005 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;20.403 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1273 ; 0.058 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8611 ; 0.002 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1739 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2054 ; 0.184 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 7300 ; 0.169 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4034 ; 0.184 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 4013 ; 0.084 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 176 ; 0.142 ; 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): 14 ; 0.245 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 25 ; 0.204 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 0.336 ; 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): 6173 ; 0.000 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1918 ; 0.000 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 7733 ; 0.000 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 4044 ; 0.000 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3286 ; 0.000 ; 4.500 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B C REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 0 A 322 1 REMARK 3 1 B 0 B 322 1 REMARK 3 1 C 0 C 322 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 4586 ; 0.010 ; 0.050 REMARK 3 TIGHT POSITIONAL 1 B (A): 4586 ; 0.010 ; 0.050 REMARK 3 TIGHT POSITIONAL 1 C (A): 4586 ; 0.010 ; 0.050 REMARK 3 TIGHT THERMAL 1 A (A**2): 4586 ; NULL ; 0.500 REMARK 3 TIGHT THERMAL 1 B (A**2): 4586 ; NULL ; 0.500 REMARK 3 TIGHT THERMAL 1 C (A**2): 4586 ; NULL ; 0.500 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 2I37 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-AUG-06. REMARK 100 THE DEPOSITION ID IS D_1000039079. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-NOV-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 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) : 0.97620 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 : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12498 REMARK 200 RESOLUTION RANGE HIGH (A) : 4.150 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 (%) : 76.8 REMARK 200 DATA REDUNDANCY : 8.900 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 4.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 4.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 61.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.86000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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 2I36 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 73.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.59 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, 0.1% SODIUM AZIDE, 16 MM BETA- REMARK 280 MERCAPTOETHANOL, 2.6% MERPOL HCS, EQUILIBRATED AGAINST 3.1-3.3 M REMARK 280 AMMONIUM SULFATE, VAPOR DIFFUSION, TEMPERATURE 278K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 1 2 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 4555 -Y,-X,-Z+2/3 REMARK 290 5555 -X+Y,Y,-Z+1/3 REMARK 290 6555 X,X-Y,-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 -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 47.81400 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 95.62800 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 95.62800 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 47.81400 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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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, D, E 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, F, G 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: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, H, I 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 VAL A 230 REMARK 465 LYS A 231 REMARK 465 GLU A 232 REMARK 465 ALA A 233 REMARK 465 ALA A 234 REMARK 465 ALA A 235 REMARK 465 GLN A 236 REMARK 465 GLN A 237 REMARK 465 GLN A 238 REMARK 465 LYS A 311 REMARK 465 GLN A 312 REMARK 465 PHE A 313 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 ASN B 145 REMARK 465 PHE B 146 REMARK 465 ARG B 147 REMARK 465 PHE B 148 REMARK 465 GLY B 149 REMARK 465 ALA B 235 REMARK 465 GLN B 236 REMARK 465 GLN B 237 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 465 GLU C 122 REMARK 465 ILE C 123 REMARK 465 ALA C 124 REMARK 465 LEU C 125 REMARK 465 TRP C 126 REMARK 465 LYS C 231 REMARK 465 GLU C 232 REMARK 465 ALA C 233 REMARK 465 ALA C 234 REMARK 465 GLN C 236 REMARK 465 GLN C 237 REMARK 465 GLN C 238 REMARK 465 GLU C 239 REMARK 465 SER C 240 REMARK 465 ALA C 241 REMARK 465 SER C 334 REMARK 465 THR C 335 REMARK 465 THR C 336 REMARK 465 VAL C 337 REMARK 465 SER C 338 REMARK 465 LYS C 339 REMARK 465 THR C 340 REMARK 465 GLU C 341 REMARK 465 THR C 342 REMARK 465 SER C 343 REMARK 465 GLN C 344 REMARK 465 VAL C 345 REMARK 465 ALA C 346 REMARK 465 PRO C 347 REMARK 465 ALA C 348 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 ND2 ASN A 2 C2 NAG E 1 2.19 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 THR A 17 43.24 -89.85 REMARK 500 VAL A 19 -1.10 -148.13 REMARK 500 GLN A 28 52.98 -96.10 REMARK 500 LEU A 68 43.14 -109.57 REMARK 500 ARG A 69 33.88 -91.95 REMARK 500 TYR A 102 145.55 -173.88 REMARK 500 CYS A 140 49.99 -105.79 REMARK 500 VAL A 173 52.20 -142.98 REMARK 500 TRP A 175 98.22 -65.29 REMARK 500 SER A 176 -160.16 73.60 REMARK 500 CYS A 185 -34.50 -133.76 REMARK 500 HIS A 195 62.96 36.44 REMARK 500 ASN A 199 80.43 51.94 REMARK 500 VAL A 209 -61.75 -91.74 REMARK 500 PHE A 212 -63.61 -155.42 REMARK 500 ALA A 241 64.46 -111.27 REMARK 500 GLN A 279 78.72 -68.78 REMARK 500 ASP A 282 44.15 -81.57 REMARK 500 MET A 309 -42.08 -130.40 REMARK 500 CYS A 322 -132.99 -55.39 REMARK 500 CYS A 323 -51.20 176.99 REMARK 500 THR B 17 44.16 -91.60 REMARK 500 VAL B 19 -0.56 -147.93 REMARK 500 GLN B 28 52.72 -95.62 REMARK 500 LEU B 68 43.56 -109.86 REMARK 500 ARG B 69 33.57 -92.31 REMARK 500 TYR B 102 144.75 -174.09 REMARK 500 CYS B 140 49.33 -105.17 REMARK 500 VAL B 173 52.84 -142.97 REMARK 500 TRP B 175 97.99 -65.33 REMARK 500 SER B 176 -159.58 75.29 REMARK 500 CYS B 185 -34.53 -134.29 REMARK 500 HIS B 195 63.00 36.52 REMARK 500 ASN B 199 78.99 52.55 REMARK 500 VAL B 209 -61.65 -91.76 REMARK 500 PHE B 212 -63.73 -155.33 REMARK 500 LYS B 231 -83.05 -157.84 REMARK 500 ALA B 233 34.16 -156.94 REMARK 500 THR B 242 -52.28 -124.20 REMARK 500 GLN B 279 79.01 -68.99 REMARK 500 ASP B 282 43.78 -81.77 REMARK 500 MET B 309 -42.21 -130.53 REMARK 500 CYS B 322 -79.26 -58.65 REMARK 500 CYS B 323 54.90 74.96 REMARK 500 THR C 17 43.31 -89.87 REMARK 500 VAL C 19 -1.85 -147.30 REMARK 500 GLN C 28 51.84 -95.96 REMARK 500 LEU C 68 43.28 -109.89 REMARK 500 ARG C 69 33.61 -92.39 REMARK 500 TYR C 102 144.88 -174.36 REMARK 500 REMARK 500 THIS ENTRY HAS 64 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2I35 RELATED DB: PDB REMARK 900 2I35 IS THE CRYSTAL STRUCTURE OF RHOMBOHEDRAL FORM OF GROUND-STATE REMARK 900 RHODOPSIN DETERMINED AT 3.80 ANGSTROM RESOLUTION 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 DBREF 2I37 A 1 348 UNP P02699 OPSD_BOVIN 1 348 DBREF 2I37 B 1 348 UNP P02699 OPSD_BOVIN 1 348 DBREF 2I37 C 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 SEQRES 1 C 349 ACE MET ASN GLY THR GLU GLY PRO ASN PHE TYR VAL PRO SEQRES 2 C 349 PHE SER ASN LYS THR GLY VAL VAL ARG SER PRO PHE GLU SEQRES 3 C 349 ALA PRO GLN TYR TYR LEU ALA GLU PRO TRP GLN PHE SER SEQRES 4 C 349 MET LEU ALA ALA TYR MET PHE LEU LEU ILE MET LEU GLY SEQRES 5 C 349 PHE PRO ILE ASN PHE LEU THR LEU TYR VAL THR VAL GLN SEQRES 6 C 349 HIS LYS LYS LEU ARG THR PRO LEU ASN TYR ILE LEU LEU SEQRES 7 C 349 ASN LEU ALA VAL ALA ASP LEU PHE MET VAL PHE GLY GLY SEQRES 8 C 349 PHE THR THR THR LEU TYR THR SER LEU HIS GLY TYR PHE SEQRES 9 C 349 VAL PHE GLY PRO THR GLY CYS ASN LEU GLU GLY PHE PHE SEQRES 10 C 349 ALA THR LEU GLY GLY GLU ILE ALA LEU TRP SER LEU VAL SEQRES 11 C 349 VAL LEU ALA ILE GLU ARG TYR VAL VAL VAL CYS LYS PRO SEQRES 12 C 349 MET SER ASN PHE ARG PHE GLY GLU ASN HIS ALA ILE MET SEQRES 13 C 349 GLY VAL ALA PHE THR TRP VAL MET ALA LEU ALA CYS ALA SEQRES 14 C 349 ALA PRO PRO LEU VAL GLY TRP SER ARG TYR ILE PRO GLU SEQRES 15 C 349 GLY MET GLN CYS SER CYS GLY ILE ASP TYR TYR THR PRO SEQRES 16 C 349 HIS GLU GLU THR ASN ASN GLU SER PHE VAL ILE TYR MET SEQRES 17 C 349 PHE VAL VAL HIS PHE ILE ILE PRO LEU ILE VAL ILE PHE SEQRES 18 C 349 PHE CYS TYR GLY GLN LEU VAL PHE THR VAL LYS GLU ALA SEQRES 19 C 349 ALA ALA GLN GLN GLN GLU SER ALA THR THR GLN LYS ALA SEQRES 20 C 349 GLU LYS GLU VAL THR ARG MET VAL ILE ILE MET VAL ILE SEQRES 21 C 349 ALA PHE LEU ILE CYS TRP LEU PRO TYR ALA GLY VAL ALA SEQRES 22 C 349 PHE TYR ILE PHE THR HIS GLN GLY SER ASP PHE GLY PRO SEQRES 23 C 349 ILE PHE MET THR ILE PRO ALA PHE PHE ALA LYS THR SER SEQRES 24 C 349 ALA VAL TYR ASN PRO VAL ILE TYR ILE MET MET ASN LYS SEQRES 25 C 349 GLN PHE ARG ASN CYS MET VAL THR THR LEU CYS CYS GLY SEQRES 26 C 349 LYS ASN PRO LEU GLY ASP ASP GLU ALA SER THR THR VAL SEQRES 27 C 349 SER LYS THR GLU THR SER GLN VAL ALA PRO ALA MODRES 2I37 ASN A 2 ASN GLYCOSYLATION SITE MODRES 2I37 ASN A 15 ASN GLYCOSYLATION SITE MODRES 2I37 ASN B 2 ASN GLYCOSYLATION SITE MODRES 2I37 ASN C 2 ASN GLYCOSYLATION SITE MODRES 2I37 ASN C 15 ASN GLYCOSYLATION SITE MODRES 2I37 ASN B 15 ASN GLYCOSYLATION SITE HET ACE A 0 3 HET ACE B 0 3 HET ACE C 0 3 HET NAG D 1 14 HET NAG D 2 14 HET MAN D 3 11 HET NAG E 1 14 HET NAG E 2 14 HET NAG F 1 14 HET NAG F 2 14 HET MAN F 3 11 HET BMA F 4 11 HET NAG F 5 14 HET NAG G 1 14 HET NAG G 2 14 HET NAG H 1 14 HET NAG H 2 14 HET MAN H 3 11 HET MAN H 4 11 HET NAG I 1 14 HET NAG I 2 14 HETNAM ACE ACETYL GROUP HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE 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 MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 1 ACE 3(C2 H4 O) FORMUL 4 NAG 13(C8 H15 N O6) FORMUL 4 MAN 4(C6 H12 O6) FORMUL 6 BMA C6 H12 O6 HELIX 1 1 SER A 14 GLY A 18 5 5 HELIX 2 2 GLU A 33 LEU A 50 1 18 HELIX 3 3 LEU A 50 HIS A 65 1 16 HELIX 4 4 THR A 70 LEU A 76 1 7 HELIX 5 5 LEU A 77 GLY A 89 1 13 HELIX 6 6 GLY A 89 GLY A 101 1 13 HELIX 7 7 GLY A 106 SER A 127 1 22 HELIX 8 8 SER A 127 VAL A 137 1 11 HELIX 9 9 VAL A 157 ALA A 169 1 13 HELIX 10 10 PRO A 170 GLY A 174 5 5 HELIX 11 11 HIS A 195 ASN A 199 5 5 HELIX 12 12 ASN A 200 HIS A 211 1 12 HELIX 13 13 PHE A 212 CYS A 222 1 11 HELIX 14 14 TYR A 223 VAL A 227 5 5 HELIX 15 15 THR A 242 GLU A 247 1 6 HELIX 16 16 GLU A 249 HIS A 278 1 30 HELIX 17 17 PRO A 285 LYS A 296 1 12 HELIX 18 18 THR A 297 MET A 309 1 13 HELIX 19 19 ARG A 314 CYS A 322 1 9 HELIX 20 20 SER B 14 GLY B 18 5 5 HELIX 21 21 GLU B 33 LEU B 50 1 18 HELIX 22 22 LEU B 50 HIS B 65 1 16 HELIX 23 23 THR B 70 LEU B 76 1 7 HELIX 24 24 LEU B 77 GLY B 89 1 13 HELIX 25 25 GLY B 89 GLY B 101 1 13 HELIX 26 26 GLY B 106 VAL B 137 1 32 HELIX 27 27 VAL B 157 ALA B 169 1 13 HELIX 28 28 PRO B 170 GLY B 174 5 5 HELIX 29 29 HIS B 195 ASN B 199 5 5 HELIX 30 30 ASN B 200 VAL B 210 1 11 HELIX 31 31 PHE B 212 CYS B 222 1 11 HELIX 32 32 TYR B 223 VAL B 227 5 5 HELIX 33 33 THR B 242 GLU B 247 1 6 HELIX 34 34 GLU B 249 HIS B 278 1 30 HELIX 35 35 PRO B 285 LYS B 296 1 12 HELIX 36 36 THR B 297 MET B 309 1 13 HELIX 37 37 ASN B 310 CYS B 323 1 14 HELIX 38 38 SER C 14 GLY C 18 5 5 HELIX 39 39 GLU C 33 LEU C 50 1 18 HELIX 40 40 LEU C 50 HIS C 65 1 16 HELIX 41 41 THR C 70 LEU C 76 1 7 HELIX 42 42 LEU C 77 GLY C 89 1 13 HELIX 43 43 GLY C 89 GLY C 101 1 13 HELIX 44 44 GLY C 106 GLY C 121 1 16 HELIX 45 45 SER C 127 VAL C 137 1 11 HELIX 46 46 VAL C 157 ALA C 169 1 13 HELIX 47 47 PRO C 170 GLY C 174 5 5 HELIX 48 48 HIS C 195 ASN C 199 5 5 HELIX 49 49 ASN C 200 HIS C 211 1 12 HELIX 50 50 PHE C 212 CYS C 222 1 11 HELIX 51 51 TYR C 223 VAL C 227 5 5 HELIX 52 52 THR C 242 GLU C 247 1 6 HELIX 53 53 GLU C 249 HIS C 278 1 30 HELIX 54 54 PRO C 285 LYS C 296 1 12 HELIX 55 55 THR C 297 MET C 309 1 13 HELIX 56 56 ASN C 310 CYS C 323 1 14 SHEET 1 A 2 THR A 4 GLU A 5 0 SHEET 2 A 2 TYR A 10 VAL A 11 -1 O VAL A 11 N THR A 4 SHEET 1 B 2 TYR A 178 PRO A 180 0 SHEET 2 B 2 CYS A 187 ILE A 189 -1 O GLY A 188 N ILE A 179 SHEET 1 C 2 THR B 4 GLU B 5 0 SHEET 2 C 2 TYR B 10 VAL B 11 -1 O VAL B 11 N THR B 4 SHEET 1 D 2 TYR B 178 PRO B 180 0 SHEET 2 D 2 CYS B 187 ILE B 189 -1 O GLY B 188 N ILE B 179 SHEET 1 E 2 THR C 4 GLU C 5 0 SHEET 2 E 2 TYR C 10 VAL C 11 -1 O VAL C 11 N THR C 4 SHEET 1 F 2 TYR C 178 PRO C 180 0 SHEET 2 F 2 CYS C 187 ILE C 189 -1 O GLY C 188 N ILE C 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 SSBOND 3 CYS C 110 CYS C 187 1555 1555 2.03 LINK C ACE A 0 N MET A 1 1555 1555 1.33 LINK ND2 ASN A 2 C1 NAG E 1 1555 1555 1.45 LINK ND2 ASN A 15 C1 NAG D 1 1555 1555 1.45 LINK C ACE B 0 N MET B 1 1555 1555 1.33 LINK ND2 ASN B 2 C1 NAG G 1 1555 1555 1.45 LINK ND2 ASN B 15 C1 NAG F 1 1555 1555 1.45 LINK C ACE C 0 N MET C 1 1555 1555 1.33 LINK ND2 ASN C 2 C1 NAG I 1 1555 1555 1.46 LINK ND2 ASN C 15 C1 NAG H 1 1555 1555 1.45 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.45 LINK O4 NAG D 2 C1 MAN D 3 1555 1555 1.46 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.45 LINK O4 NAG F 1 C1 NAG F 2 1555 1555 1.45 LINK O4 NAG F 2 C1 MAN F 3 1555 1555 1.46 LINK O3 MAN F 3 C1 BMA F 4 1555 1555 1.46 LINK O2 BMA F 4 C1 NAG F 5 1555 1555 1.46 LINK O4 NAG G 1 C1 NAG G 2 1555 1555 1.45 LINK O4 NAG H 1 C1 NAG H 2 1555 1555 1.44 LINK O4 NAG H 2 C1 MAN H 3 1555 1555 1.45 LINK O3 MAN H 3 C1 MAN H 4 1555 1555 1.45 LINK O4 NAG I 1 C1 NAG I 2 1555 1555 1.46 CRYST1 161.245 161.245 143.442 90.00 90.00 120.00 P 31 1 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 0.006202 0.003581 0.000000 0.00000 SCALE2 0.000000 0.007161 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006971 0.00000 HETATM 1 C ACE A 0 6.708 1.725 77.253 1.00183.00 C HETATM 2 O ACE A 0 7.499 2.669 77.207 1.00183.00 O HETATM 3 CH3 ACE A 0 6.391 1.006 78.529 1.00183.00 C