HEADER SIGNALING PROTEIN 09-MAY-11 3AYN TITLE CRYSTAL STRUCTURE OF SQUID ISORHODOPSIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RHODOPSIN; COMPND 3 CHAIN: A, B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TODARODES PACIFICUS; SOURCE 3 ORGANISM_COMMON: JAPANESE FLYING SQUID; SOURCE 4 ORGANISM_TAXID: 6637 KEYWDS TRANSMEMBRANE PROTEIN, PHOTORECEPTOR, CHROMOPHORE, GLYCOPROTEIN, KEYWDS 2 LIPOPROTEIN, GQ-TYPE G-PROTEIN, PHOSPHORYLATION, MEMBRANE, SIGNALING KEYWDS 3 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.MURAKAMI,T.KOUYAMA REVDAT 5 16-OCT-24 3AYN 1 HETSYN REVDAT 4 29-JUL-20 3AYN 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE REVDAT 3 11-OCT-17 3AYN 1 REMARK REVDAT 2 26-OCT-11 3AYN 1 JRNL REVDAT 1 17-AUG-11 3AYN 0 JRNL AUTH M.MURAKAMI,T.KOUYAMA JRNL TITL CRYSTALLOGRAPHIC ANALYSIS OF THE PRIMARY PHOTOCHEMICAL JRNL TITL 2 REACTION OF SQUID RHODOPSIN JRNL REF J.MOL.BIOL. V. 413 615 2011 JRNL REFN ISSN 0022-2836 JRNL PMID 21906602 JRNL DOI 10.1016/J.JMB.2011.08.044 REMARK 2 REMARK 2 RESOLUTION. 2.70 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1907373.420 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.5 REMARK 3 NUMBER OF REFLECTIONS : 33666 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) : 0.180 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.500 REMARK 3 FREE R VALUE TEST SET COUNT : 1674 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5194 REMARK 3 BIN R VALUE (WORKING SET) : 0.2480 REMARK 3 BIN FREE R VALUE : 0.2760 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 273 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.017 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5542 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 155 REMARK 3 SOLVENT ATOMS : 59 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 44.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.96 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.03800 REMARK 3 B22 (A**2) : -0.03800 REMARK 3 B33 (A**2) : 0.07600 REMARK 3 B12 (A**2) : -2.27300 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) : 0.27 REMARK 3 ESD FROM SIGMAA (A) : 0.28 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) : 0.30 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.33 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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) : 1.926 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.030 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.761 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.947 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : NULL REMARK 3 BSOL : 74.96 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : RET-11CIS.PARAM REMARK 3 PARAMETER FILE 5 : BOG.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3AYN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-MAY-11. REMARK 100 THE DEPOSITION ID IS D_1000029858. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JAN-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36893 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 61.260 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.52700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS 1.2 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.2M AMMONIUM SULFATE, 20MM MES, 50MM REMARK 280 EDTA, 10MM BETA-MERCAPTOETHANOL , PH 6.0, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 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 105.68667 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 52.84333 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 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 105.68667 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 52.84333 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 MET A 1 REMARK 465 GLY A 2 REMARK 465 ARG A 3 REMARK 465 ASP A 4 REMARK 465 LEU A 5 REMARK 465 ARG A 6 REMARK 465 ASP A 7 REMARK 465 ASN A 8 REMARK 465 SER A 359 REMARK 465 SER A 360 REMARK 465 ASP A 361 REMARK 465 ALA A 362 REMARK 465 ALA A 363 REMARK 465 PRO A 364 REMARK 465 SER A 365 REMARK 465 ALA A 366 REMARK 465 ASP A 367 REMARK 465 ALA A 368 REMARK 465 ALA A 369 REMARK 465 GLN A 370 REMARK 465 MET A 371 REMARK 465 LYS A 372 REMARK 465 GLU A 373 REMARK 465 MET A 374 REMARK 465 MET A 375 REMARK 465 ALA A 376 REMARK 465 MET A 377 REMARK 465 MET A 378 REMARK 465 GLN A 379 REMARK 465 LYS A 380 REMARK 465 MET A 381 REMARK 465 GLN A 382 REMARK 465 GLN A 383 REMARK 465 GLN A 384 REMARK 465 GLN A 385 REMARK 465 ALA A 386 REMARK 465 ALA A 387 REMARK 465 TYR A 388 REMARK 465 PRO A 389 REMARK 465 PRO A 390 REMARK 465 GLN A 391 REMARK 465 GLY A 392 REMARK 465 TYR A 393 REMARK 465 ALA A 394 REMARK 465 PRO A 395 REMARK 465 PRO A 396 REMARK 465 PRO A 397 REMARK 465 GLN A 398 REMARK 465 GLY A 399 REMARK 465 TYR A 400 REMARK 465 PRO A 401 REMARK 465 PRO A 402 REMARK 465 GLN A 403 REMARK 465 GLY A 404 REMARK 465 TYR A 405 REMARK 465 PRO A 406 REMARK 465 PRO A 407 REMARK 465 GLN A 408 REMARK 465 GLY A 409 REMARK 465 TYR A 410 REMARK 465 PRO A 411 REMARK 465 PRO A 412 REMARK 465 GLN A 413 REMARK 465 GLY A 414 REMARK 465 TYR A 415 REMARK 465 PRO A 416 REMARK 465 PRO A 417 REMARK 465 GLN A 418 REMARK 465 GLY A 419 REMARK 465 TYR A 420 REMARK 465 PRO A 421 REMARK 465 PRO A 422 REMARK 465 PRO A 423 REMARK 465 PRO A 424 REMARK 465 GLN A 425 REMARK 465 GLY A 426 REMARK 465 ALA A 427 REMARK 465 PRO A 428 REMARK 465 PRO A 429 REMARK 465 GLN A 430 REMARK 465 GLY A 431 REMARK 465 ALA A 432 REMARK 465 PRO A 433 REMARK 465 PRO A 434 REMARK 465 ALA A 435 REMARK 465 ALA A 436 REMARK 465 PRO A 437 REMARK 465 PRO A 438 REMARK 465 GLN A 439 REMARK 465 GLY A 440 REMARK 465 VAL A 441 REMARK 465 ASP A 442 REMARK 465 ASN A 443 REMARK 465 GLN A 444 REMARK 465 ALA A 445 REMARK 465 TYR A 446 REMARK 465 GLN A 447 REMARK 465 ALA A 448 REMARK 465 MET B 1 REMARK 465 GLY B 2 REMARK 465 ARG B 3 REMARK 465 ASP B 4 REMARK 465 LEU B 5 REMARK 465 ARG B 6 REMARK 465 ASP B 7 REMARK 465 ASN B 8 REMARK 465 ALA B 356 REMARK 465 GLY B 357 REMARK 465 GLU B 358 REMARK 465 SER B 359 REMARK 465 SER B 360 REMARK 465 ASP B 361 REMARK 465 ALA B 362 REMARK 465 ALA B 363 REMARK 465 PRO B 364 REMARK 465 SER B 365 REMARK 465 ALA B 366 REMARK 465 ASP B 367 REMARK 465 ALA B 368 REMARK 465 ALA B 369 REMARK 465 GLN B 370 REMARK 465 MET B 371 REMARK 465 LYS B 372 REMARK 465 GLU B 373 REMARK 465 MET B 374 REMARK 465 MET B 375 REMARK 465 ALA B 376 REMARK 465 MET B 377 REMARK 465 MET B 378 REMARK 465 GLN B 379 REMARK 465 LYS B 380 REMARK 465 MET B 381 REMARK 465 GLN B 382 REMARK 465 GLN B 383 REMARK 465 GLN B 384 REMARK 465 GLN B 385 REMARK 465 ALA B 386 REMARK 465 ALA B 387 REMARK 465 TYR B 388 REMARK 465 PRO B 389 REMARK 465 PRO B 390 REMARK 465 GLN B 391 REMARK 465 GLY B 392 REMARK 465 TYR B 393 REMARK 465 ALA B 394 REMARK 465 PRO B 395 REMARK 465 PRO B 396 REMARK 465 PRO B 397 REMARK 465 GLN B 398 REMARK 465 GLY B 399 REMARK 465 TYR B 400 REMARK 465 PRO B 401 REMARK 465 PRO B 402 REMARK 465 GLN B 403 REMARK 465 GLY B 404 REMARK 465 TYR B 405 REMARK 465 PRO B 406 REMARK 465 PRO B 407 REMARK 465 GLN B 408 REMARK 465 GLY B 409 REMARK 465 TYR B 410 REMARK 465 PRO B 411 REMARK 465 PRO B 412 REMARK 465 GLN B 413 REMARK 465 GLY B 414 REMARK 465 TYR B 415 REMARK 465 PRO B 416 REMARK 465 PRO B 417 REMARK 465 GLN B 418 REMARK 465 GLY B 419 REMARK 465 TYR B 420 REMARK 465 PRO B 421 REMARK 465 PRO B 422 REMARK 465 PRO B 423 REMARK 465 PRO B 424 REMARK 465 GLN B 425 REMARK 465 GLY B 426 REMARK 465 ALA B 427 REMARK 465 PRO B 428 REMARK 465 PRO B 429 REMARK 465 GLN B 430 REMARK 465 GLY B 431 REMARK 465 ALA B 432 REMARK 465 PRO B 433 REMARK 465 PRO B 434 REMARK 465 ALA B 435 REMARK 465 ALA B 436 REMARK 465 PRO B 437 REMARK 465 PRO B 438 REMARK 465 GLN B 439 REMARK 465 GLY B 440 REMARK 465 VAL B 441 REMARK 465 ASP B 442 REMARK 465 ASN B 443 REMARK 465 GLN B 444 REMARK 465 ALA B 445 REMARK 465 TYR B 446 REMARK 465 GLN B 447 REMARK 465 ALA B 448 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 100 144.27 -171.58 REMARK 500 PHE A 209 -70.18 -100.61 REMARK 500 MET A 225 42.29 -80.01 REMARK 500 SER A 226 -2.79 -159.03 REMARK 500 ARG A 240 47.99 -78.58 REMARK 500 ALA A 243 -165.48 -73.28 REMARK 500 PRO A 288 91.70 -64.15 REMARK 500 VAL A 292 78.13 -69.79 REMARK 500 ALA A 308 3.10 -67.42 REMARK 500 THR A 329 -39.30 -131.29 REMARK 500 THR A 335 -70.61 -52.21 REMARK 500 GLN A 338 133.86 -35.59 REMARK 500 ALA A 356 72.47 61.00 REMARK 500 THR B 62 102.71 -59.81 REMARK 500 SER B 144 134.44 -39.63 REMARK 500 ILE B 223 -74.37 -62.08 REMARK 500 SER B 226 -21.96 -155.64 REMARK 500 ALA B 236 5.98 -66.11 REMARK 500 LEU B 241 31.50 39.27 REMARK 500 SER B 318 -24.37 -149.18 REMARK 500 THR B 329 -50.25 -134.06 REMARK 500 CYS B 337 -30.65 -140.29 REMARK 500 GLN B 338 91.27 34.75 REMARK 500 THR B 352 102.25 -53.89 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 PLM A 1001 REMARK 610 PLM A 1004 REMARK 610 PLM B 1001 REMARK 610 PC1 B 1004 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2Z73 RELATED DB: PDB REMARK 900 RELATED ID: 3AYM RELATED DB: PDB DBREF 3AYN A 1 448 UNP P31356 OPSD_TODPA 1 448 DBREF 3AYN B 1 448 UNP P31356 OPSD_TODPA 1 448 SEQRES 1 A 448 MET GLY ARG ASP LEU ARG ASP ASN GLU THR TRP TRP TYR SEQRES 2 A 448 ASN PRO SER ILE VAL VAL HIS PRO HIS TRP ARG GLU PHE SEQRES 3 A 448 ASP GLN VAL PRO ASP ALA VAL TYR TYR SER LEU GLY ILE SEQRES 4 A 448 PHE ILE GLY ILE CYS GLY ILE ILE GLY CYS GLY GLY ASN SEQRES 5 A 448 GLY ILE VAL ILE TYR LEU PHE THR LYS THR LYS SER LEU SEQRES 6 A 448 GLN THR PRO ALA ASN MET PHE ILE ILE ASN LEU ALA PHE SEQRES 7 A 448 SER ASP PHE THR PHE SER LEU VAL ASN GLY PHE PRO LEU SEQRES 8 A 448 MET THR ILE SER CYS PHE LEU LYS LYS TRP ILE PHE GLY SEQRES 9 A 448 PHE ALA ALA CYS LYS VAL TYR GLY PHE ILE GLY GLY ILE SEQRES 10 A 448 PHE GLY PHE MET SER ILE MET THR MET ALA MET ILE SER SEQRES 11 A 448 ILE ASP ARG TYR ASN VAL ILE GLY ARG PRO MET ALA ALA SEQRES 12 A 448 SER LYS LYS MET SER HIS ARG ARG ALA PHE ILE MET ILE SEQRES 13 A 448 ILE PHE VAL TRP LEU TRP SER VAL LEU TRP ALA ILE GLY SEQRES 14 A 448 PRO ILE PHE GLY TRP GLY ALA TYR THR LEU GLU GLY VAL SEQRES 15 A 448 LEU CYS ASN CYS SER PHE ASP TYR ILE SER ARG ASP SER SEQRES 16 A 448 THR THR ARG SER ASN ILE LEU CYS MET PHE ILE LEU GLY SEQRES 17 A 448 PHE PHE GLY PRO ILE LEU ILE ILE PHE PHE CYS TYR PHE SEQRES 18 A 448 ASN ILE VAL MET SER VAL SER ASN HIS GLU LYS GLU MET SEQRES 19 A 448 ALA ALA MET ALA LYS ARG LEU ASN ALA LYS GLU LEU ARG SEQRES 20 A 448 LYS ALA GLN ALA GLY ALA ASN ALA GLU MET ARG LEU ALA SEQRES 21 A 448 LYS ILE SER ILE VAL ILE VAL SER GLN PHE LEU LEU SER SEQRES 22 A 448 TRP SER PRO TYR ALA VAL VAL ALA LEU LEU ALA GLN PHE SEQRES 23 A 448 GLY PRO LEU GLU TRP VAL THR PRO TYR ALA ALA GLN LEU SEQRES 24 A 448 PRO VAL MET PHE ALA LYS ALA SER ALA ILE HIS ASN PRO SEQRES 25 A 448 MET ILE TYR SER VAL SER HIS PRO LYS PHE ARG GLU ALA SEQRES 26 A 448 ILE SER GLN THR PHE PRO TRP VAL LEU THR CYS CYS GLN SEQRES 27 A 448 PHE ASP ASP LYS GLU THR GLU ASP ASP LYS ASP ALA GLU SEQRES 28 A 448 THR GLU ILE PRO ALA GLY GLU SER SER ASP ALA ALA PRO SEQRES 29 A 448 SER ALA ASP ALA ALA GLN MET LYS GLU MET MET ALA MET SEQRES 30 A 448 MET GLN LYS MET GLN GLN GLN GLN ALA ALA TYR PRO PRO SEQRES 31 A 448 GLN GLY TYR ALA PRO PRO PRO GLN GLY TYR PRO PRO GLN SEQRES 32 A 448 GLY TYR PRO PRO GLN GLY TYR PRO PRO GLN GLY TYR PRO SEQRES 33 A 448 PRO GLN GLY TYR PRO PRO PRO PRO GLN GLY ALA PRO PRO SEQRES 34 A 448 GLN GLY ALA PRO PRO ALA ALA PRO PRO GLN GLY VAL ASP SEQRES 35 A 448 ASN GLN ALA TYR GLN ALA SEQRES 1 B 448 MET GLY ARG ASP LEU ARG ASP ASN GLU THR TRP TRP TYR SEQRES 2 B 448 ASN PRO SER ILE VAL VAL HIS PRO HIS TRP ARG GLU PHE SEQRES 3 B 448 ASP GLN VAL PRO ASP ALA VAL TYR TYR SER LEU GLY ILE SEQRES 4 B 448 PHE ILE GLY ILE CYS GLY ILE ILE GLY CYS GLY GLY ASN SEQRES 5 B 448 GLY ILE VAL ILE TYR LEU PHE THR LYS THR LYS SER LEU SEQRES 6 B 448 GLN THR PRO ALA ASN MET PHE ILE ILE ASN LEU ALA PHE SEQRES 7 B 448 SER ASP PHE THR PHE SER LEU VAL ASN GLY PHE PRO LEU SEQRES 8 B 448 MET THR ILE SER CYS PHE LEU LYS LYS TRP ILE PHE GLY SEQRES 9 B 448 PHE ALA ALA CYS LYS VAL TYR GLY PHE ILE GLY GLY ILE SEQRES 10 B 448 PHE GLY PHE MET SER ILE MET THR MET ALA MET ILE SER SEQRES 11 B 448 ILE ASP ARG TYR ASN VAL ILE GLY ARG PRO MET ALA ALA SEQRES 12 B 448 SER LYS LYS MET SER HIS ARG ARG ALA PHE ILE MET ILE SEQRES 13 B 448 ILE PHE VAL TRP LEU TRP SER VAL LEU TRP ALA ILE GLY SEQRES 14 B 448 PRO ILE PHE GLY TRP GLY ALA TYR THR LEU GLU GLY VAL SEQRES 15 B 448 LEU CYS ASN CYS SER PHE ASP TYR ILE SER ARG ASP SER SEQRES 16 B 448 THR THR ARG SER ASN ILE LEU CYS MET PHE ILE LEU GLY SEQRES 17 B 448 PHE PHE GLY PRO ILE LEU ILE ILE PHE PHE CYS TYR PHE SEQRES 18 B 448 ASN ILE VAL MET SER VAL SER ASN HIS GLU LYS GLU MET SEQRES 19 B 448 ALA ALA MET ALA LYS ARG LEU ASN ALA LYS GLU LEU ARG SEQRES 20 B 448 LYS ALA GLN ALA GLY ALA ASN ALA GLU MET ARG LEU ALA SEQRES 21 B 448 LYS ILE SER ILE VAL ILE VAL SER GLN PHE LEU LEU SER SEQRES 22 B 448 TRP SER PRO TYR ALA VAL VAL ALA LEU LEU ALA GLN PHE SEQRES 23 B 448 GLY PRO LEU GLU TRP VAL THR PRO TYR ALA ALA GLN LEU SEQRES 24 B 448 PRO VAL MET PHE ALA LYS ALA SER ALA ILE HIS ASN PRO SEQRES 25 B 448 MET ILE TYR SER VAL SER HIS PRO LYS PHE ARG GLU ALA SEQRES 26 B 448 ILE SER GLN THR PHE PRO TRP VAL LEU THR CYS CYS GLN SEQRES 27 B 448 PHE ASP ASP LYS GLU THR GLU ASP ASP LYS ASP ALA GLU SEQRES 28 B 448 THR GLU ILE PRO ALA GLY GLU SER SER ASP ALA ALA PRO SEQRES 29 B 448 SER ALA ASP ALA ALA GLN MET LYS GLU MET MET ALA MET SEQRES 30 B 448 MET GLN LYS MET GLN GLN GLN GLN ALA ALA TYR PRO PRO SEQRES 31 B 448 GLN GLY TYR ALA PRO PRO PRO GLN GLY TYR PRO PRO GLN SEQRES 32 B 448 GLY TYR PRO PRO GLN GLY TYR PRO PRO GLN GLY TYR PRO SEQRES 33 B 448 PRO GLN GLY TYR PRO PRO PRO PRO GLN GLY ALA PRO PRO SEQRES 34 B 448 GLN GLY ALA PRO PRO ALA ALA PRO PRO GLN GLY VAL ASP SEQRES 35 B 448 ASN GLN ALA TYR GLN ALA HET RET A1000 20 HET PLM A1001 17 HET PLM A1004 17 HET SO4 B 449 5 HET RET B1000 20 HET PLM B1001 17 HET PC1 B1004 39 HET BOG B1005 20 HETNAM RET RETINAL HETNAM PLM PALMITIC ACID HETNAM SO4 SULFATE ION HETNAM PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE HETNAM BOG OCTYL BETA-D-GLUCOPYRANOSIDE HETSYN PC1 3-SN-PHOSPHATIDYLCHOLINE HETSYN BOG BETA-OCTYLGLUCOSIDE; OCTYL BETA-D-GLUCOSIDE; OCTYL D- HETSYN 2 BOG GLUCOSIDE; OCTYL GLUCOSIDE FORMUL 3 RET 2(C20 H28 O) FORMUL 4 PLM 3(C16 H32 O2) FORMUL 6 SO4 O4 S 2- FORMUL 9 PC1 C44 H88 N O8 P FORMUL 10 BOG C14 H28 O6 FORMUL 11 HOH *59(H2 O) 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 ALA A 69 GLY A 88 1 20 HELIX 4 4 PRO A 90 LEU A 98 1 9 HELIX 5 5 PHE A 103 ILE A 137 1 35 HELIX 6 6 SER A 148 ILE A 168 1 21 HELIX 7 7 GLY A 169 GLY A 173 5 5 HELIX 8 8 ASP A 194 GLY A 208 1 15 HELIX 9 9 PHE A 209 MET A 225 1 17 HELIX 10 10 SER A 226 LYS A 239 1 14 HELIX 11 11 GLU A 245 GLY A 287 1 43 HELIX 12 12 THR A 293 SER A 307 1 15 HELIX 13 13 HIS A 310 HIS A 319 1 10 HELIX 14 14 HIS A 319 PHE A 330 1 12 HELIX 15 15 PRO A 331 THR A 335 5 5 HELIX 16 16 ASP A 340 GLU A 343 5 4 HELIX 17 17 THR A 344 THR A 352 1 9 HELIX 18 18 HIS B 20 GLU B 25 1 6 HELIX 19 19 PRO B 30 THR B 62 1 33 HELIX 20 20 LYS B 63 GLN B 66 5 4 HELIX 21 21 THR B 67 PRO B 68 5 2 HELIX 22 22 ALA B 69 GLY B 88 1 20 HELIX 23 23 PRO B 90 LEU B 98 1 9 HELIX 24 24 PHE B 103 ILE B 137 1 35 HELIX 25 25 SER B 148 GLY B 169 1 22 HELIX 26 26 PRO B 170 GLY B 173 5 4 HELIX 27 27 ASP B 194 PHE B 209 1 16 HELIX 28 28 PHE B 209 MET B 225 1 17 HELIX 29 29 SER B 226 LYS B 239 1 14 HELIX 30 30 LYS B 244 GLY B 287 1 44 HELIX 31 31 PRO B 288 VAL B 292 5 5 HELIX 32 32 THR B 293 SER B 307 1 15 HELIX 33 33 ILE B 309 VAL B 317 1 9 HELIX 34 34 HIS B 319 GLN B 328 1 10 HELIX 35 35 PHE B 330 THR B 335 5 6 HELIX 36 36 ASP B 340 GLU B 343 5 4 HELIX 37 37 THR B 344 THR B 352 1 9 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 SHEET 1 B 2 TYR B 177 LEU B 179 0 SHEET 2 B 2 CYS B 186 PHE B 188 -1 O SER B 187 N THR B 178 SSBOND 1 CYS A 108 CYS A 186 1555 1555 2.04 SSBOND 2 CYS B 108 CYS B 186 1555 1555 2.03 LINK NZ LYS A 305 C15 RET A1000 1555 1555 1.32 LINK NZ LYS B 305 C15 RET B1000 1555 1555 1.30 CISPEP 1 PHE A 89 PRO A 90 0 3.27 CISPEP 2 PHE B 89 PRO B 90 0 2.15 CRYST1 122.540 122.540 158.530 90.00 90.00 120.00 P 62 12 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 0.008161 0.004712 0.000000 0.00000 SCALE2 0.000000 0.009423 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006308 0.00000