HEADER MEMBRANE PROTEIN 17-JUN-22 8A6D TITLE 10 PICOSECOND LIGHT ACTIVATED CRYSTAL STRUCTURE OF BOVINE RHODOPSIN IN TITLE 2 LIPIDIC CUBIC PHASE 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 4 07-FEB-24 8A6D 1 REMARK REVDAT 3 12-APR-23 8A6D 1 JRNL REVDAT 2 05-APR-23 8A6D 1 JRNL REVDAT 1 29-MAR-23 8A6D 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) : 9.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 88.2 REMARK 3 NUMBER OF REFLECTIONS : 69531 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.314 REMARK 3 R VALUE (WORKING SET) : 0.314 REMARK 3 FREE R VALUE : 0.347 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.450 REMARK 3 FREE R VALUE TEST SET COUNT : 1011 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 9.9900 - 3.4000 0.97 11074 164 0.2255 0.2452 REMARK 3 2 3.4000 - 2.7200 0.95 10577 154 0.2683 0.3117 REMARK 3 3 2.7200 - 2.3800 0.91 10052 151 0.3354 0.3764 REMARK 3 4 2.3800 - 2.1700 0.87 9652 144 0.4315 0.5068 REMARK 3 5 2.1700 - 2.0100 0.85 9376 137 0.5209 0.5341 REMARK 3 6 2.0100 - 1.8900 0.82 9008 133 0.5937 0.6329 REMARK 3 7 1.8900 - 1.8000 0.80 8781 128 0.6115 0.5990 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) : 0.418 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 51.166 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.44 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.69 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 : 0.005 5458 REMARK 3 ANGLE : 0.728 7405 REMARK 3 CHIRALITY : 0.046 826 REMARK 3 PLANARITY : 0.006 906 REMARK 3 DIHEDRAL : 12.903 1985 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): -5.4237 28.3746 37.7685 REMARK 3 T TENSOR REMARK 3 T11: 0.3181 T22: 0.2954 REMARK 3 T33: 0.3132 T12: -0.0351 REMARK 3 T13: 0.0025 T23: -0.0167 REMARK 3 L TENSOR REMARK 3 L11: 1.0738 L22: 0.6163 REMARK 3 L33: 0.5950 L12: -0.4970 REMARK 3 L13: -0.8352 L23: 0.1716 REMARK 3 S TENSOR REMARK 3 S11: -0.0126 S12: 0.0401 S13: 0.0250 REMARK 3 S21: 0.0193 S22: -0.0017 S23: 0.0192 REMARK 3 S31: 0.0343 S32: -0.0317 S33: 0.0001 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 8A6D 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_1292121940. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUL-20 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 : ESA REMARK 200 X-RAY GENERATOR MODEL : SWISSFEL ARAMIS BEAMLINE ESA REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.38 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI JUNGFRAU 1M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL REMARK 200 DATA SCALING SOFTWARE : CRYSTFEL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 79031 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 16.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 595.9 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.7000 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 (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.720 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 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 45.50500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 75.55500 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.50500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 75.55500 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: 6080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 8.0 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 -45.50500 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 75.55500 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 143 REMARK 465 SER A 144 REMARK 465 ASN A 145 REMARK 465 PHE A 146 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 GLU A 239 REMARK 465 SER A 240 REMARK 465 ALA A 241 REMARK 465 THR A 242 REMARK 465 THR A 243 REMARK 465 GLN A 244 REMARK 465 CYS A 323 REMARK 465 GLY A 324 REMARK 465 LYS A 325 REMARK 465 ASN A 326 REMARK 465 PRO A 327 REMARK 465 LEU A 328 REMARK 465 GLY A 329 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 MET B 143 REMARK 465 SER B 144 REMARK 465 ASN B 145 REMARK 465 PHE B 146 REMARK 465 VAL B 230 REMARK 465 LYS B 231 REMARK 465 GLU B 232 REMARK 465 ALA B 233 REMARK 465 ALA B 234 REMARK 465 ALA B 235 REMARK 465 GLN B 236 REMARK 465 GLN B 237 REMARK 465 GLN B 238 REMARK 465 GLU B 239 REMARK 465 SER B 240 REMARK 465 ALA B 241 REMARK 465 THR B 242 REMARK 465 THR B 243 REMARK 465 CYS B 323 REMARK 465 GLY B 324 REMARK 465 LYS B 325 REMARK 465 ASN B 326 REMARK 465 PRO B 327 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 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 1 CG SD CE REMARK 470 LYS A 66 CG CD CE NZ REMARK 470 LYS A 67 CD CE NZ REMARK 470 ARG A 147 CG CD NE CZ NH1 NH2 REMARK 470 PHE A 228 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 245 CE NZ REMARK 470 LYS A 311 CE NZ REMARK 470 MET B 1 CG SD CE REMARK 470 LYS B 66 CG CD CE NZ REMARK 470 LYS B 67 CE NZ REMARK 470 LYS B 141 CD CE NZ REMARK 470 ARG B 147 CG CD NE CZ NH1 NH2 REMARK 470 PHE B 228 CG CD1 CD2 CE1 CE2 CZ REMARK 470 THR B 229 OG1 CG2 REMARK 470 GLN B 244 CG CD OE1 NE2 REMARK 470 LYS B 245 CE NZ REMARK 470 LYS B 311 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 213 CA CB CG1 CG2 CD1 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 SG CYS B 322 O2 PLM B 407 2.08 REMARK 500 SG CYS A 322 O2 PLM A 410 2.08 REMARK 500 O HOH B 540 O HOH B 551 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 ASN A 15 30.65 -94.13 REMARK 500 GLN A 28 49.31 -91.10 REMARK 500 SER A 176 -160.61 60.80 REMARK 500 PHE A 212 -57.55 -125.74 REMARK 500 PHE A 212 -56.36 -125.74 REMARK 500 PHE A 228 57.50 -97.54 REMARK 500 GLN B 28 39.17 -96.54 REMARK 500 SER B 176 -163.45 59.70 REMARK 500 HIS B 195 66.73 38.09 REMARK 500 PHE B 212 -52.56 -130.31 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 DAO A 404 REMARK 610 OLC A 406 REMARK 610 OLC A 407 REMARK 610 OLC A 408 REMARK 610 OLC A 409 REMARK 610 PLM A 410 REMARK 610 OLC A 411 REMARK 610 OLC A 413 REMARK 610 OLC A 414 REMARK 610 OLC B 404 REMARK 610 OLC B 405 REMARK 610 OLC B 406 REMARK 610 PLM B 407 REMARK 610 OLC B 408 DBREF 8A6D A 1 348 UNP P02699 OPSD_BOVIN 1 348 DBREF 8A6D B 1 348 UNP P02699 OPSD_BOVIN 1 348 SEQRES 1 A 348 MET ASN GLY THR GLU GLY PRO ASN PHE TYR VAL PRO PHE SEQRES 2 A 348 SER ASN LYS THR GLY VAL VAL ARG SER PRO PHE GLU ALA SEQRES 3 A 348 PRO GLN TYR TYR LEU ALA GLU PRO TRP GLN PHE SER MET SEQRES 4 A 348 LEU ALA ALA TYR MET PHE LEU LEU ILE MET LEU GLY PHE SEQRES 5 A 348 PRO ILE ASN PHE LEU THR LEU TYR VAL THR VAL GLN HIS SEQRES 6 A 348 LYS LYS LEU ARG THR PRO LEU ASN TYR ILE LEU LEU ASN SEQRES 7 A 348 LEU ALA VAL ALA ASP LEU PHE MET VAL PHE GLY GLY PHE SEQRES 8 A 348 THR THR THR LEU TYR THR SER LEU HIS GLY TYR PHE VAL SEQRES 9 A 348 PHE GLY PRO THR GLY CYS ASN LEU GLU GLY PHE PHE ALA SEQRES 10 A 348 THR LEU GLY GLY GLU ILE ALA LEU TRP SER LEU VAL VAL SEQRES 11 A 348 LEU ALA ILE GLU ARG TYR VAL VAL VAL CYS LYS PRO MET SEQRES 12 A 348 SER ASN PHE ARG PHE GLY GLU ASN HIS ALA ILE MET GLY SEQRES 13 A 348 VAL ALA PHE THR TRP VAL MET ALA LEU ALA CYS ALA ALA SEQRES 14 A 348 PRO PRO LEU VAL GLY TRP SER ARG TYR ILE PRO GLU GLY SEQRES 15 A 348 MET GLN CYS SER CYS GLY ILE ASP TYR TYR THR PRO HIS SEQRES 16 A 348 GLU GLU THR ASN ASN GLU SER PHE VAL ILE TYR MET PHE SEQRES 17 A 348 VAL VAL HIS PHE ILE ILE PRO LEU ILE VAL ILE PHE PHE SEQRES 18 A 348 CYS TYR GLY GLN LEU VAL PHE THR VAL LYS GLU ALA ALA SEQRES 19 A 348 ALA GLN GLN GLN GLU SER ALA THR THR GLN LYS ALA GLU SEQRES 20 A 348 LYS GLU VAL THR ARG MET VAL ILE ILE MET VAL ILE ALA SEQRES 21 A 348 PHE LEU ILE CYS TRP LEU PRO TYR ALA GLY VAL ALA PHE SEQRES 22 A 348 TYR ILE PHE THR HIS GLN GLY SER ASP PHE GLY PRO ILE SEQRES 23 A 348 PHE MET THR ILE PRO ALA PHE PHE ALA LYS THR SER ALA SEQRES 24 A 348 VAL TYR ASN PRO VAL ILE TYR ILE MET MET ASN LYS GLN SEQRES 25 A 348 PHE ARG ASN CYS MET VAL THR THR LEU CYS CYS GLY LYS SEQRES 26 A 348 ASN PRO LEU GLY ASP ASP GLU ALA SER THR THR VAL SER SEQRES 27 A 348 LYS THR GLU THR SER GLN VAL ALA PRO ALA SEQRES 1 B 348 MET ASN GLY THR GLU GLY PRO ASN PHE TYR VAL PRO PHE SEQRES 2 B 348 SER ASN LYS THR GLY VAL VAL ARG SER PRO PHE GLU ALA SEQRES 3 B 348 PRO GLN TYR TYR LEU ALA GLU PRO TRP GLN PHE SER MET SEQRES 4 B 348 LEU ALA ALA TYR MET PHE LEU LEU ILE MET LEU GLY PHE SEQRES 5 B 348 PRO ILE ASN PHE LEU THR LEU TYR VAL THR VAL GLN HIS SEQRES 6 B 348 LYS LYS LEU ARG THR PRO LEU ASN TYR ILE LEU LEU ASN SEQRES 7 B 348 LEU ALA VAL ALA ASP LEU PHE MET VAL PHE GLY GLY PHE SEQRES 8 B 348 THR THR THR LEU TYR THR SER LEU HIS GLY TYR PHE VAL SEQRES 9 B 348 PHE GLY PRO THR GLY CYS ASN LEU GLU GLY PHE PHE ALA SEQRES 10 B 348 THR LEU GLY GLY GLU ILE ALA LEU TRP SER LEU VAL VAL SEQRES 11 B 348 LEU ALA ILE GLU ARG TYR VAL VAL VAL CYS LYS PRO MET SEQRES 12 B 348 SER ASN PHE ARG PHE GLY GLU ASN HIS ALA ILE MET GLY SEQRES 13 B 348 VAL ALA PHE THR TRP VAL MET ALA LEU ALA CYS ALA ALA SEQRES 14 B 348 PRO PRO LEU VAL GLY TRP SER ARG TYR ILE PRO GLU GLY SEQRES 15 B 348 MET GLN CYS SER CYS GLY ILE ASP TYR TYR THR PRO HIS SEQRES 16 B 348 GLU GLU THR ASN ASN GLU SER PHE VAL ILE TYR MET PHE SEQRES 17 B 348 VAL VAL HIS PHE ILE ILE PRO LEU ILE VAL ILE PHE PHE SEQRES 18 B 348 CYS TYR GLY GLN LEU VAL PHE THR VAL LYS GLU ALA ALA SEQRES 19 B 348 ALA GLN GLN GLN GLU SER ALA THR THR GLN LYS ALA GLU SEQRES 20 B 348 LYS GLU VAL THR ARG MET VAL ILE ILE MET VAL ILE ALA SEQRES 21 B 348 PHE LEU ILE CYS TRP LEU PRO TYR ALA GLY VAL ALA PHE SEQRES 22 B 348 TYR ILE PHE THR HIS GLN GLY SER ASP PHE GLY PRO ILE SEQRES 23 B 348 PHE MET THR ILE PRO ALA PHE PHE ALA LYS THR SER ALA SEQRES 24 B 348 VAL TYR ASN PRO VAL ILE TYR ILE MET MET ASN LYS GLN SEQRES 25 B 348 PHE ARG ASN CYS MET VAL THR THR LEU CYS CYS GLY LYS SEQRES 26 B 348 ASN PRO LEU GLY ASP ASP GLU ALA SER THR THR VAL SER SEQRES 27 B 348 LYS THR GLU THR SER GLN VAL ALA PRO ALA HET NAG C 1 14 HET NAG C 2 14 HET NAG D 1 14 HET NAG D 2 14 HET ACE A 401 3 HET RET A 402 20 HET NAG A 403 14 HET DAO A 404 13 HET OLC A 405 25 HET OLC A 406 17 HET OLC A 407 7 HET OLC A 408 10 HET OLC A 409 12 HET PLM A 410 12 HET OLC A 411 10 HET OLC A 412 25 HET OLC A 413 10 HET OLC A 414 13 HET ACE B 401 3 HET RET B 402 20 HET NAG B 403 14 HET OLC B 404 19 HET OLC B 405 18 HET OLC B 406 17 HET PLM B 407 7 HET OLC B 408 7 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM ACE ACETYL GROUP 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 3 NAG 6(C8 H15 N O6) FORMUL 5 ACE 2(C2 H4 O) FORMUL 6 RET 2(C20 H28 O) FORMUL 8 DAO C12 H24 O2 FORMUL 9 OLC 13(C21 H40 O4) FORMUL 14 PLM 2(C16 H32 O2) FORMUL 27 HOH *114(H2 O) HELIX 1 AA1 GLU A 33 HIS A 65 1 33 HELIX 2 AA2 THR A 70 GLY A 90 1 21 HELIX 3 AA3 GLY A 90 GLY A 101 1 12 HELIX 4 AA4 PHE A 105 LYS A 141 1 37 HELIX 5 AA5 GLY A 149 ALA A 169 1 21 HELIX 6 AA6 PRO A 170 VAL A 173 5 4 HELIX 7 AA7 HIS A 195 THR A 198 5 4 HELIX 8 AA8 ASN A 199 HIS A 211 1 13 HELIX 9 AA9 PHE A 212 PHE A 228 1 17 HELIX 10 AB1 ALA A 246 HIS A 278 1 33 HELIX 11 AB2 PRO A 285 ALA A 295 1 11 HELIX 12 AB3 LYS A 296 ALA A 299 5 4 HELIX 13 AB4 VAL A 300 ASN A 310 1 11 HELIX 14 AB5 ASN A 310 CYS A 322 1 13 HELIX 15 AB6 GLU B 33 HIS B 65 1 33 HELIX 16 AB7 THR B 70 GLY B 90 1 21 HELIX 17 AB8 GLY B 90 GLY B 101 1 12 HELIX 18 AB9 PHE B 105 LYS B 141 1 37 HELIX 19 AC1 GLY B 149 ALA B 169 1 21 HELIX 20 AC2 PRO B 170 VAL B 173 5 4 HELIX 21 AC3 HIS B 195 THR B 198 5 4 HELIX 22 AC4 ASN B 199 HIS B 211 1 13 HELIX 23 AC5 PHE B 212 PHE B 228 1 17 HELIX 24 AC6 LYS B 245 THR B 277 1 33 HELIX 25 AC7 PRO B 285 ALA B 295 1 11 HELIX 26 AC8 LYS B 296 ALA B 299 5 4 HELIX 27 AC9 VAL B 300 ASN B 310 1 11 HELIX 28 AD1 ASN B 310 CYS B 322 1 13 SHEET 1 AA1 2 THR A 4 GLY A 6 0 SHEET 2 AA1 2 PHE A 9 VAL A 11 -1 O VAL A 11 N THR A 4 SHEET 1 AA2 2 TYR A 178 GLU A 181 0 SHEET 2 AA2 2 SER A 186 ILE A 189 -1 O SER A 186 N GLU A 181 SHEET 1 AA3 2 THR B 4 GLU B 5 0 SHEET 2 AA3 2 TYR B 10 VAL B 11 -1 O VAL B 11 N THR B 4 SHEET 1 AA4 2 TYR B 178 GLU B 181 0 SHEET 2 AA4 2 SER B 186 ILE B 189 -1 O GLY B 188 N ILE B 179 SSBOND 1 CYS A 110 CYS A 187 1555 1555 2.04 SSBOND 2 CYS B 110 CYS B 187 1555 1555 2.05 LINK N MET A 1 C ACE A 401 1555 1555 1.34 LINK ND2 ASN A 2 C1 NAG A 403 1555 1555 1.45 LINK ND2 ASN A 15 C1 NAG C 1 1555 1555 1.44 LINK NZ LYS A 296 C15 RET A 402 1555 1555 1.33 LINK SG CYS A 322 C1 PLM A 410 1555 1555 1.77 LINK N MET B 1 C ACE B 401 1555 1555 1.33 LINK ND2 ASN B 2 C1 NAG B 403 1555 1555 1.45 LINK ND2 ASN B 15 C1 NAG D 1 1555 1555 1.45 LINK NZ LYS B 296 C15 RET B 402 1555 1555 1.34 LINK SG CYS B 322 C1 PLM B 407 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 1.45 CRYST1 61.510 91.010 151.110 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 0.016258 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010988 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006618 0.00000