HEADER MEMBRANE PROTEIN 17-JUN-22 8A6E TITLE 100 PICOSECOND LIGHT ACTIVATED CRYSTAL STRUCTURE OF BOVINE RHODOPSIN TITLE 2 IN LIPIDIC CUBIC PHASE (SACLA) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RHODOPSIN; COMPND 3 CHAIN: A, B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913 KEYWDS GPCR, OPSIN, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.GRUHL,T.WEINERT,M.J.RODRIGUES,C.J.MILNE,G.ORTOLANI,K.NASS,E.NANGO, AUTHOR 2 S.SEN,P.J.M.JOHNSON,C.CIRELLI,A.FURRER,S.MOUS,P.SKOPINTSEV,D.JAMES, AUTHOR 3 F.DWORKOWSKI,P.BAATH,D.KEKILLI,D.OSEROV,R.TANAKA,H.GLOVER, AUTHOR 4 C.BACELLAR,S.BRUENLE,C.M.CASADEI,A.D.DIETHELM,D.GASHI,G.GOTTHARD, AUTHOR 5 R.GUIXA-GONZALEZ,Y.JOTI,V.KABANOVA,G.KNOPP,E.LESCA,P.MA,I.MARTIEL, AUTHOR 6 J.MUEHLE,S.OWADA,F.PAMULA,D.SARABI,O.TEJERO,C.J.TSAI,N.VARMA,A.WACH, AUTHOR 7 S.BOUTET,K.TONO,P.NOGLY,X.DEUPI,S.IWATA,R.NEUTZE,J.STANDFUSS, AUTHOR 8 G.F.X.SCHERTLER,V.PANNEELS REVDAT 6 13-NOV-24 8A6E 1 REMARK REVDAT 5 29-MAY-24 8A6E 1 COMPND SOURCE REMARK DBREF REVDAT 5 2 1 SEQADV SEQRES HELIX SHEET REVDAT 5 3 1 SSBOND LINK ATOM REVDAT 4 07-FEB-24 8A6E 1 REMARK REVDAT 3 12-APR-23 8A6E 1 JRNL REVDAT 2 05-APR-23 8A6E 1 JRNL REVDAT 1 29-MAR-23 8A6E 0 JRNL AUTH T.GRUHL,T.WEINERT,M.J.RODRIGUES,C.J.MILNE,G.ORTOLANI,K.NASS, JRNL AUTH 2 E.NANGO,S.SEN,P.J.M.JOHNSON,C.CIRELLI,A.FURRER,S.MOUS, JRNL AUTH 3 P.SKOPINTSEV,D.JAMES,F.DWORKOWSKI,P.BATH,D.KEKILLI,D.OZEROV, JRNL AUTH 4 R.TANAKA,H.GLOVER,C.BACELLAR,S.BRUNLE,C.M.CASADEI, JRNL AUTH 5 A.D.DIETHELM,D.GASHI,G.GOTTHARD,R.GUIXA-GONZALEZ,Y.JOTI, JRNL AUTH 6 V.KABANOVA,G.KNOPP,E.LESCA,P.MA,I.MARTIEL,J.MUHLE,S.OWADA, JRNL AUTH 7 F.PAMULA,D.SARABI,O.TEJERO,C.J.TSAI,N.VARMA,A.WACH,S.BOUTET, JRNL AUTH 8 K.TONO,P.NOGLY,X.DEUPI,S.IWATA,R.NEUTZE,J.STANDFUSS, JRNL AUTH 9 G.SCHERTLER,V.PANNEELS JRNL TITL ULTRAFAST STRUCTURAL CHANGES DIRECT THE FIRST MOLECULAR JRNL TITL 2 EVENTS OF VISION. JRNL REF NATURE V. 615 939 2023 JRNL REFN ESSN 1476-4687 JRNL PMID 36949205 JRNL DOI 10.1038/S41586-023-05863-6 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.GRUHL,T.WEINERT,M.RODRIGUES,C.J.MILNE,G.ORTOLANI,K.NASS, REMARK 1 AUTH 2 E.NANGO,S.SEN,P.J.M.JOHNSON,C.CIRELLI,A.FURRER,S.MOUS, REMARK 1 AUTH 3 P.SKOPINTSEV,D.JAMES,F.DWORKOWSKI,P.BATH,D.KEKILLI,D.OZEROV, REMARK 1 AUTH 4 R.TANAKA,H.GLOVER,C.BACELLAR,S.BRUNLE,C.M.CASADEI, REMARK 1 AUTH 5 A.D.DIETHELM,D.GASHI,G.GOTTHARD,R.GUIXA-GONZALEZ,Y.JOTI, REMARK 1 AUTH 6 V.KABANOVA,G.KNOPP,E.LESCA,P.MA,I.MARTIEL,J.MUHLE,S.OWADA, REMARK 1 AUTH 7 F.PAMULA,D.SARABI,O.TEJERO,C.J.TSAI,N.VARMA,A.WACH,S.BOUTET, REMARK 1 AUTH 8 K.TONO,P.NOGLY,X.DEUPI,S.IWATA,R.NEUTZE,J.STANDFUSS, REMARK 1 AUTH 9 G.F.SCHERTLER,V.PANNEELS REMARK 1 TITL ULTRAFAST STRUCTURAL CHANGES DIRECT THE FIRST MOLECULAR REMARK 1 TITL 2 EVENTS OF VISION REMARK 1 REF BIORXIV 2022 REMARK 1 REFN ISSN 2692-8205 REMARK 1 DOI 10.1101/2022.10.14.511948 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20_4459 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 87.1 REMARK 3 NUMBER OF REFLECTIONS : 68049 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.332 REMARK 3 R VALUE (WORKING SET) : 0.332 REMARK 3 FREE R VALUE : 0.369 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.450 REMARK 3 FREE R VALUE TEST SET COUNT : 989 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 10.4700 - 3.4100 0.93 10615 155 0.2353 0.2610 REMARK 3 2 3.4100 - 2.7200 0.93 10270 153 0.2755 0.3558 REMARK 3 3 2.7200 - 2.3800 0.90 9841 147 0.3443 0.3461 REMARK 3 4 2.3800 - 2.1700 0.87 9524 135 0.4110 0.4498 REMARK 3 5 2.1700 - 2.0100 0.85 9249 133 0.4812 0.5197 REMARK 3 6 2.0100 - 1.8900 0.81 8838 131 0.5542 0.5865 REMARK 3 7 1.8900 - 1.8000 0.80 8723 135 0.6064 0.6854 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.442 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 48.899 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.18 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.003 5497 REMARK 3 ANGLE : 0.623 7453 REMARK 3 CHIRALITY : 0.041 828 REMARK 3 PLANARITY : 0.005 912 REMARK 3 DIHEDRAL : 12.395 2017 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -5.3783 28.2035 37.5163 REMARK 3 T TENSOR REMARK 3 T11: 0.2086 T22: 0.1712 REMARK 3 T33: 0.2088 T12: -0.0168 REMARK 3 T13: 0.0510 T23: -0.0049 REMARK 3 L TENSOR REMARK 3 L11: 0.6236 L22: 0.3140 REMARK 3 L33: 0.3665 L12: -0.2580 REMARK 3 L13: -0.2924 L23: 0.0376 REMARK 3 S TENSOR REMARK 3 S11: -0.0169 S12: -0.0045 S13: 0.0574 REMARK 3 S21: 0.0020 S22: -0.0093 S23: -0.0040 REMARK 3 S31: 0.0049 S32: -0.0172 S33: 0.0000 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8A6E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-JUN-22. REMARK 100 THE DEPOSITION ID IS D_1292121880. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-NOV-18 REMARK 200 TEMPERATURE (KELVIN) : 294 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : FREE ELECTRON LASER REMARK 200 BEAMLINE : BL3 REMARK 200 X-RAY GENERATOR MODEL : SACLA BEAMLINE BL3 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.24 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MPCCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL REMARK 200 DATA SCALING SOFTWARE : CRYSTFEL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 78209 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 10.470 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 679.1 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 487.5 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: PHASER REMARK 200 STARTING MODEL: 1U19 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 36 % PEG 600, 100 MM BICINE PH 9.0, REMARK 280 LIPIDIC CUBIC PHASE, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 X,-Y,-Z REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.40500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 75.25500 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.40500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 75.25500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 6.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 APPLY THE FOLLOWING TO CHAINS: B, D REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 -45.40500 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 75.25500 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 544 REMARK 465 SER A 545 REMARK 465 ASN A 546 REMARK 465 PHE A 547 REMARK 465 VAL A 631 REMARK 465 LYS A 632 REMARK 465 GLU A 633 REMARK 465 ALA A 634 REMARK 465 ALA A 635 REMARK 465 ALA A 636 REMARK 465 GLN A 637 REMARK 465 GLN A 638 REMARK 465 GLN A 639 REMARK 465 GLU A 640 REMARK 465 SER A 641 REMARK 465 ALA A 642 REMARK 465 THR A 643 REMARK 465 THR A 644 REMARK 465 GLN A 645 REMARK 465 CYS A 724 REMARK 465 GLY A 725 REMARK 465 LYS A 726 REMARK 465 ASN A 727 REMARK 465 PRO A 728 REMARK 465 LEU A 729 REMARK 465 GLY A 730 REMARK 465 ASP A 731 REMARK 465 ASP A 732 REMARK 465 GLU A 733 REMARK 465 ALA A 734 REMARK 465 SER A 735 REMARK 465 THR A 736 REMARK 465 THR A 737 REMARK 465 VAL A 738 REMARK 465 SER A 739 REMARK 465 LYS A 740 REMARK 465 THR A 741 REMARK 465 GLU A 742 REMARK 465 THR A 743 REMARK 465 SER A 744 REMARK 465 GLN A 745 REMARK 465 VAL A 746 REMARK 465 ALA A 747 REMARK 465 PRO A 748 REMARK 465 ALA A 749 REMARK 465 MET B 544 REMARK 465 SER B 545 REMARK 465 ASN B 546 REMARK 465 PHE B 547 REMARK 465 VAL B 631 REMARK 465 LYS B 632 REMARK 465 GLU B 633 REMARK 465 ALA B 634 REMARK 465 ALA B 635 REMARK 465 ALA B 636 REMARK 465 GLN B 637 REMARK 465 GLN B 638 REMARK 465 GLN B 639 REMARK 465 GLU B 640 REMARK 465 SER B 641 REMARK 465 ALA B 642 REMARK 465 THR B 643 REMARK 465 THR B 644 REMARK 465 CYS B 724 REMARK 465 GLY B 725 REMARK 465 LYS B 726 REMARK 465 ASN B 727 REMARK 465 PRO B 728 REMARK 465 LEU B 729 REMARK 465 GLY B 730 REMARK 465 ASP B 731 REMARK 465 ASP B 732 REMARK 465 GLU B 733 REMARK 465 ALA B 734 REMARK 465 SER B 735 REMARK 465 THR B 736 REMARK 465 THR B 737 REMARK 465 VAL B 738 REMARK 465 SER B 739 REMARK 465 LYS B 740 REMARK 465 THR B 741 REMARK 465 GLU B 742 REMARK 465 THR B 743 REMARK 465 SER B 744 REMARK 465 GLN B 745 REMARK 465 VAL B 746 REMARK 465 ALA B 747 REMARK 465 PRO B 748 REMARK 465 ALA B 749 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 MET A 402 CG SD CE REMARK 470 LYS A 467 CG CD CE NZ REMARK 470 LYS A 468 CD CE NZ REMARK 470 ARG A 548 CG CD NE CZ NH1 NH2 REMARK 470 PHE A 629 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 646 CE NZ REMARK 470 MET B 402 CG SD CE REMARK 470 LYS B 467 CG CD CE NZ REMARK 470 LYS B 468 CE NZ REMARK 470 ARG B 548 CD NE CZ NH1 NH2 REMARK 470 PHE B 629 CG CD1 CD2 CE1 CE2 CZ REMARK 470 THR B 630 OG1 CG2 REMARK 470 GLN B 645 CG CD OE1 NE2 REMARK 470 LYS B 646 CE NZ REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ILE B 614 CA CB CG1 CG2 CD1 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 GLN A 429 39.13 -97.59 REMARK 500 SER A 577 -161.75 64.29 REMARK 500 PHE A 613 -39.52 -130.56 REMARK 500 PHE A 613 -39.15 -130.56 REMARK 500 PHE A 629 56.43 -98.26 REMARK 500 GLN B 429 35.46 -94.37 REMARK 500 PHE B 506 0.84 -68.57 REMARK 500 SER B 577 -165.37 61.50 REMARK 500 HIS B 596 62.99 39.55 REMARK 500 PHE B 613 -59.14 -125.25 REMARK 500 PHE B 629 49.13 -88.25 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 OLC A 805 REMARK 610 OLC A 806 REMARK 610 OLC A 807 REMARK 610 OLC A 808 REMARK 610 OLC A 810 REMARK 610 OLC A 812 REMARK 610 OLC A 814 REMARK 610 OLC B 803 REMARK 610 OLC B 804 REMARK 610 PLM B 805 REMARK 610 OLC B 806 DBREF 8A6E A 402 749 UNP P02699 OPSD_BOVIN 1 348 DBREF 8A6E B 402 749 UNP P02699 OPSD_BOVIN 1 348 SEQADV 8A6E ACE A 401 UNP P02699 ACETYLATION SEQADV 8A6E ACE B 401 UNP P02699 ACETYLATION 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 HET ACE A 401 3 HET ACE B 401 3 HET NAG C 1 14 HET NAG C 2 14 HET NAG D 1 14 HET NAG D 2 14 HET RET A 801 20 HET NAG A 802 14 HET DAO A 803 14 HET OLC A 804 25 HET OLC A 805 22 HET OLC A 806 7 HET OLC A 807 10 HET OLC A 808 12 HET PLM A 809 17 HET OLC A 810 10 HET OLC A 811 25 HET OLC A 812 10 HET OLC A 813 25 HET OLC A 814 13 HET RET B 801 20 HET NAG B 802 14 HET OLC B 803 19 HET OLC B 804 18 HET PLM B 805 7 HET OLC B 806 7 HETNAM ACE ACETYL GROUP HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM RET RETINAL HETNAM DAO LAURIC ACID HETNAM OLC (2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE 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 OLC 1-OLEOYL-R-GLYCEROL FORMUL 1 ACE 2(C2 H4 O) FORMUL 3 NAG 6(C8 H15 N O6) FORMUL 5 RET 2(C20 H28 O) FORMUL 7 DAO C12 H24 O2 FORMUL 8 OLC 13(C21 H40 O4) FORMUL 13 PLM 2(C16 H32 O2) FORMUL 25 HOH *140(H2 O) HELIX 1 AA1 GLU A 434 HIS A 466 1 33 HELIX 2 AA2 THR A 471 GLY A 491 1 21 HELIX 3 AA3 GLY A 491 GLY A 502 1 12 HELIX 4 AA4 PHE A 506 LYS A 542 1 37 HELIX 5 AA5 GLY A 550 ALA A 570 1 21 HELIX 6 AA6 PRO A 571 VAL A 574 5 4 HELIX 7 AA7 HIS A 596 THR A 599 5 4 HELIX 8 AA8 ASN A 600 HIS A 612 1 13 HELIX 9 AA9 PHE A 613 PHE A 629 1 17 HELIX 10 AB1 ALA A 647 HIS A 679 1 33 HELIX 11 AB2 PRO A 686 ALA A 696 1 11 HELIX 12 AB3 LYS A 697 ALA A 700 5 4 HELIX 13 AB4 VAL A 701 ASN A 711 1 11 HELIX 14 AB5 ASN A 711 CYS A 723 1 13 HELIX 15 AB6 GLU B 434 HIS B 466 1 33 HELIX 16 AB7 THR B 471 GLY B 491 1 21 HELIX 17 AB8 GLY B 491 GLY B 502 1 12 HELIX 18 AB9 PHE B 506 LYS B 542 1 37 HELIX 19 AC1 GLY B 550 ALA B 570 1 21 HELIX 20 AC2 PRO B 571 VAL B 574 5 4 HELIX 21 AC3 HIS B 596 THR B 599 5 4 HELIX 22 AC4 ASN B 600 HIS B 612 1 13 HELIX 23 AC5 PHE B 613 PHE B 629 1 17 HELIX 24 AC6 LYS B 646 HIS B 679 1 34 HELIX 25 AC7 PRO B 686 ALA B 696 1 11 HELIX 26 AC8 LYS B 697 ALA B 700 5 4 HELIX 27 AC9 VAL B 701 ASN B 711 1 11 HELIX 28 AD1 ASN B 711 CYS B 723 1 13 SHEET 1 AA1 2 THR A 405 GLU A 406 0 SHEET 2 AA1 2 TYR A 411 VAL A 412 -1 O VAL A 412 N THR A 405 SHEET 1 AA2 2 TYR A 579 GLU A 582 0 SHEET 2 AA2 2 SER A 587 ILE A 590 -1 O SER A 587 N GLU A 582 SHEET 1 AA3 2 THR B 405 GLU B 406 0 SHEET 2 AA3 2 TYR B 411 VAL B 412 -1 O VAL B 412 N THR B 405 SHEET 1 AA4 2 TYR B 579 PRO B 581 0 SHEET 2 AA4 2 CYS B 588 ILE B 590 -1 O GLY B 589 N ILE B 580 SSBOND 1 CYS A 511 CYS A 588 1555 1555 2.03 SSBOND 2 CYS B 511 CYS B 588 1555 1555 2.03 LINK C ACE A 401 N MET A 402 1555 1555 1.33 LINK ND2 ASN A 403 C1 NAG A 802 1555 1555 1.44 LINK ND2 ASN A 416 C1 NAG C 1 1555 1555 1.45 LINK NZ LYS A 697 C15 RET A 801 1555 1555 1.34 LINK SG CYS A 723 C1 PLM A 809 1555 1555 1.77 LINK C ACE B 401 N MET B 402 1555 1555 1.33 LINK ND2 ASN B 403 C1 NAG B 802 1555 1555 1.44 LINK ND2 ASN B 416 C1 NAG D 1 1555 1555 1.44 LINK NZ LYS B 697 C15 RET B 801 1555 1555 1.34 LINK SG CYS B 723 C1 PLM B 805 1555 1555 1.77 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.45 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.44 CRYST1 61.290 90.810 150.510 90.00 90.00 90.00 P 2 21 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.016316 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011012 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006644 0.00000 HETATM 1 C ACE A 401 17.301 34.909 5.033 1.00 56.54 C ANISOU 1 C ACE A 401 7315 6944 7224 598 1408 1210 C HETATM 2 O ACE A 401 18.249 34.504 5.707 1.00 54.99 O ANISOU 2 O ACE A 401 7100 6715 7080 551 1406 1186 O HETATM 3 CH3 ACE A 401 17.462 35.971 3.986 1.00 50.48 C ANISOU 3 CH3 ACE A 401 6546 6170 6463 660 1479 1301 C