HEADER SIGNALING PROTEIN 18-JUL-06 2HPY TITLE CRYSTALLOGRAPHIC MODEL OF LUMIRHODOPSIN 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 G PROTEIN-COUPLED RECEPTOR, VISUAL PIGMENT, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.NAKAMICHI,T.OKADA REVDAT 6 30-OCT-24 2HPY 1 HETSYN REVDAT 5 29-JUL-20 2HPY 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE ATOM REVDAT 4 13-JUL-11 2HPY 1 VERSN REVDAT 3 24-FEB-09 2HPY 1 VERSN REVDAT 2 05-SEP-06 2HPY 1 JRNL REVDAT 1 22-AUG-06 2HPY 0 JRNL AUTH H.NAKAMICHI,T.OKADA JRNL TITL LOCAL PEPTIDE MOVEMENT IN THE PHOTOREACTION INTERMEDIATE OF JRNL TITL 2 RHODOPSIN JRNL REF PROC.NATL.ACAD.SCI.USA V. 103 12729 2006 JRNL REFN ISSN 0027-8424 JRNL PMID 16908857 JRNL DOI 10.1073/PNAS.0601765103 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 28564 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1089 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5498 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 384 REMARK 3 SOLVENT ATOMS : 66 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.410 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2HPY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-JUL-06. REMARK 100 THE DEPOSITION ID IS D_1000038622. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUN-04 REMARK 200 TEMPERATURE (KELVIN) : 160 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 : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29920 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 43.5 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 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: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 72.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.9M AMMONIUM SULFATE, 0.05M MES, PH REMARK 280 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 283K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 75.20000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.60000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 112.80000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 13940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -265.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -284.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, E, F 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: A, C, D REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 96.72000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 -75.20000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NE2 GLN A 344 O6 HTG B 1509 4564 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 LYS A 66 -19.01 -49.94 REMARK 500 VAL A 87 -74.43 -44.14 REMARK 500 THR A 93 -77.97 -43.45 REMARK 500 THR A 94 -34.22 -33.45 REMARK 500 PHE A 115 -84.30 -67.50 REMARK 500 LEU A 119 -82.62 -63.22 REMARK 500 LYS A 141 87.24 15.81 REMARK 500 ASN A 145 34.93 -166.16 REMARK 500 ALA A 166 31.95 -73.53 REMARK 500 CYS A 167 -14.87 -167.74 REMARK 500 PRO A 171 -0.74 -55.52 REMARK 500 SER A 176 -175.18 72.15 REMARK 500 GLN A 184 48.60 76.60 REMARK 500 HIS A 195 85.65 20.88 REMARK 500 ASN A 199 40.38 71.79 REMARK 500 GLU A 201 -73.17 -45.98 REMARK 500 PHE A 212 -75.89 -157.52 REMARK 500 LEU A 226 36.08 -81.06 REMARK 500 THR A 229 -130.90 -77.65 REMARK 500 ALA A 233 94.89 -63.17 REMARK 500 ALA A 235 -155.64 -91.76 REMARK 500 GLN A 236 -159.56 -89.06 REMARK 500 GLN A 238 144.35 77.41 REMARK 500 SER A 240 17.49 176.23 REMARK 500 ALA A 241 135.75 152.20 REMARK 500 ALA A 260 4.72 -66.93 REMARK 500 HIS A 278 42.67 -152.30 REMARK 500 GLN A 279 81.69 -58.10 REMARK 500 SER A 281 -168.52 -60.89 REMARK 500 VAL A 300 -42.39 -135.39 REMARK 500 TYR A 301 2.82 -49.10 REMARK 500 CYS A 322 39.65 -75.87 REMARK 500 CYS A 323 -72.76 36.65 REMARK 500 LYS A 325 -112.90 -149.79 REMARK 500 ASN A 326 77.97 50.87 REMARK 500 PRO A 327 22.64 -76.07 REMARK 500 LEU A 328 -97.32 15.53 REMARK 500 ASP A 331 -154.62 61.05 REMARK 500 ALA A 333 -14.29 62.04 REMARK 500 SER A 334 -165.25 -122.17 REMARK 500 THR A 335 156.73 -36.52 REMARK 500 VAL A 337 147.63 178.16 REMARK 500 SER A 338 -145.34 -175.42 REMARK 500 LYS A 339 -67.42 -106.88 REMARK 500 GLU A 341 -123.10 -69.36 REMARK 500 THR A 342 40.25 -92.25 REMARK 500 PRO A 347 -122.95 -81.69 REMARK 500 TYR B 10 93.25 -160.69 REMARK 500 LEU B 50 -75.29 -104.41 REMARK 500 PHE B 52 -72.01 -79.56 REMARK 500 REMARK 500 THIS ENTRY HAS 97 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR B 306 0.08 SIDE CHAIN 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 1410 REMARK 610 PLM B 1407 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 958 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 196 OE2 REMARK 620 2 GLU A 196 OE1 69.0 REMARK 620 3 GLU B 201 OE2 95.8 154.9 REMARK 620 4 GLN B 279 NE2 99.7 96.2 106.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 957 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 201 OE1 REMARK 620 2 GLN A 279 OE1 110.9 REMARK 620 3 GLN A 279 NE2 152.1 70.2 REMARK 620 4 GLU B 196 OE2 101.5 61.6 102.9 REMARK 620 5 GLU B 196 OE1 127.0 106.5 76.1 65.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HG A 903 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 222 O REMARK 620 2 CYS A 222 SG 58.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HG A 901 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 264 SG REMARK 620 2 THR A 297 OG1 70.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 959 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 311 NZ REMARK 620 2 ASP A 330 N 110.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HG A 905 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 312 O REMARK 620 2 CYS A 316 SG 69.5 REMARK 620 3 CYS A 316 N 49.5 65.3 REMARK 620 4 HOH A2061 O 160.0 105.3 110.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HG B 906 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 65 ND1 REMARK 620 2 CYS B 316 SG 110.4 REMARK 620 3 THR B 336 O 113.6 60.5 REMARK 620 4 VAL B 337 O 83.2 105.7 48.4 REMARK 620 5 SER B 338 OG 70.6 164.5 104.5 58.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 956 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 195 NE2 REMARK 620 2 GLU B 197 OE1 66.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HG B 904 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 222 SG REMARK 620 2 CYS B 222 O 62.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HG B 902 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA B 260 O REMARK 620 2 CYS B 264 SG 83.0 REMARK 620 3 THR B 297 OG1 146.4 72.2 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1U19 RELATED DB: PDB REMARK 900 RELATED ID: 2G87 RELATED DB: PDB DBREF 2HPY A 1 348 UNP P02699 OPSD_BOVIN 1 348 DBREF 2HPY B 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 MODRES 2HPY ASN A 2 ASN GLYCOSYLATION SITE MODRES 2HPY ASN A 15 ASN GLYCOSYLATION SITE MODRES 2HPY ASN B 2 ASN GLYCOSYLATION SITE MODRES 2HPY ASN B 15 ASN GLYCOSYLATION SITE HET ACE A 0 3 HET ACE B 0 3 HET NAG C 1 14 HET NAG C 2 14 HET MAN C 3 11 HET NAG D 1 14 HET NAG D 2 14 HET NAG E 1 14 HET NAG E 2 14 HET BMA E 3 11 HET BMA E 4 11 HET NAG F 1 14 HET NAG F 2 14 HET HG A 901 1 HET HG A 903 1 HET HG A 905 1 HET ZN A 957 1 HET ZN A 959 1 HET ZN A 962 1 HET ZN A2011 1 HET RET A1296 20 HET PLM A1322 17 HET PLM A1323 17 HET PLM A1410 16 HET HTG A1507 19 HET HTG A1508 19 HET HG B 902 1 HET HG B 904 1 HET HG B 906 1 HET ZN B 956 1 HET ZN B 958 1 HET ZN B 963 1 HET RET B1296 20 HET PLM B1322 17 HET PLM B1323 17 HET HTO B1401 10 HET PLM B1407 16 HET HTG B1506 19 HET HTG B1509 19 HETNAM ACE ACETYL GROUP HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM HG MERCURY (II) ION HETNAM ZN ZINC ION HETNAM RET RETINAL HETNAM PLM PALMITIC ACID HETNAM HTG HEPTYL 1-THIO-BETA-D-GLUCOPYRANOSIDE HETNAM HTO HEPTANE-1,2,3-TRIOL 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 HETSYN HTG HEPTYL 1-THIOHEXOPYRANOSIDE; HEPTYL 1-THIO-BETA-D- HETSYN 2 HTG GLUCOSIDE; HEPTYL 1-THIO-D-GLUCOSIDE; HEPTYL 1-THIO- HETSYN 3 HTG GLUCOSIDE FORMUL 1 ACE 2(C2 H4 O) FORMUL 3 NAG 8(C8 H15 N O6) FORMUL 3 MAN C6 H12 O6 FORMUL 5 BMA 2(C6 H12 O6) FORMUL 7 HG 6(HG 2+) FORMUL 10 ZN 7(ZN 2+) FORMUL 14 RET 2(C20 H28 O) FORMUL 15 PLM 6(C16 H32 O2) FORMUL 18 HTG 4(C13 H26 O5 S) FORMUL 29 HTO C7 H16 O3 FORMUL 33 HOH *66(H2 O) HELIX 1 1 GLU A 33 HIS A 65 1 33 HELIX 2 2 PRO A 71 LEU A 76 1 6 HELIX 3 3 LEU A 76 GLY A 90 1 15 HELIX 4 4 GLY A 90 HIS A 100 1 11 HELIX 5 5 PHE A 105 CYS A 140 1 36 HELIX 6 6 GLY A 149 ALA A 169 1 21 HELIX 7 7 PRO A 170 VAL A 173 5 4 HELIX 8 8 ASN A 199 HIS A 211 1 13 HELIX 9 9 LEU A 216 LEU A 226 1 11 HELIX 10 10 ALA A 241 THR A 277 1 37 HELIX 11 11 GLY A 284 LYS A 296 1 13 HELIX 12 12 THR A 297 VAL A 300 5 4 HELIX 13 13 ASN A 302 ILE A 307 1 6 HELIX 14 14 ASN A 310 CYS A 322 1 13 HELIX 15 15 GLU B 33 HIS B 65 1 33 HELIX 16 16 THR B 70 GLY B 90 1 21 HELIX 17 17 GLY B 90 GLY B 101 1 12 HELIX 18 18 PHE B 105 CYS B 140 1 36 HELIX 19 19 GLY B 149 ALA B 164 1 16 HELIX 20 20 ALA B 164 ALA B 169 1 6 HELIX 21 21 PRO B 170 VAL B 173 5 4 HELIX 22 22 HIS B 195 THR B 198 5 4 HELIX 23 23 ASN B 199 HIS B 211 1 13 HELIX 24 24 PHE B 212 LEU B 226 1 15 HELIX 25 25 ALA B 241 ALA B 260 1 20 HELIX 26 26 TRP B 265 THR B 277 1 13 HELIX 27 27 GLY B 284 LYS B 296 1 13 HELIX 28 28 THR B 297 ALA B 299 5 3 HELIX 29 29 VAL B 300 ILE B 307 1 8 HELIX 30 30 ASN B 310 CYS B 322 1 13 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 ILE A 179 PRO A 180 0 SHEET 2 B 2 CYS A 187 GLY A 188 -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 GLU B 181 0 SHEET 2 D 2 SER B 186 ILE B 189 -1 O SER B 186 N GLU B 181 SSBOND 1 CYS A 110 CYS A 187 1555 1555 2.04 SSBOND 2 CYS B 110 CYS B 187 1555 1555 2.04 LINK C ACE A 0 N MET A 1 1555 1555 1.35 LINK ND2 ASN A 2 C1 NAG D 1 1555 1555 1.44 LINK ND2 ASN A 15 C1 NAG C 1 1555 1555 1.45 LINK NZ LYS A 296 C15 RET A1296 1555 1555 1.30 LINK SG CYS A 322 C1 PLM A1322 1555 1555 1.85 LINK SG CYS A 323 C1 PLM A1323 1555 1555 1.89 LINK C ACE B 0 N MET B 1 1555 1555 1.36 LINK ND2 ASN B 2 C1 NAG F 1 1555 1555 1.45 LINK ND2 ASN B 15 C1 NAG E 1 1555 1555 1.44 LINK NZ LYS B 296 C15 RET B1296 1555 1555 1.32 LINK SG CYS B 322 C1 PLM B1322 1555 1555 1.87 LINK SG CYS B 323 C1 PLM B1323 1555 1555 1.90 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.40 LINK O4 NAG C 2 C1 MAN C 3 1555 1555 1.40 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.38 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.39 LINK O4 NAG E 2 C1 BMA E 3 1555 1555 1.39 LINK O3 BMA E 3 C1 BMA E 4 1555 1555 1.41 LINK O4 NAG F 1 C1 NAG F 2 1555 1555 1.39 LINK OE1 GLU A 122 ZN ZN A 962 1555 1555 2.19 LINK NE2 HIS A 195 ZN ZN A2011 1555 1555 2.24 LINK OE2 GLU A 196 ZN ZN B 958 2654 1555 1.41 LINK OE1 GLU A 196 ZN ZN B 958 2654 1555 2.29 LINK OE1 GLU A 201 ZN ZN A 957 1555 1555 2.23 LINK O CYS A 222 HG HG A 903 1555 1555 3.51 LINK SG CYS A 222 HG HG A 903 1555 1555 2.56 LINK SG CYS A 264 HG HG A 901 1555 1555 3.41 LINK OE1 GLN A 279 ZN ZN A 957 1555 1555 2.17 LINK NE2 GLN A 279 ZN ZN A 957 1555 1555 1.68 LINK OG1 THR A 297 HG HG A 901 1555 1555 3.23 LINK NZ LYS A 311 ZN ZN A 959 1555 1555 2.05 LINK O GLN A 312 HG HG A 905 1555 1555 3.38 LINK SG CYS A 316 HG HG A 905 1555 1555 2.78 LINK N CYS A 316 HG HG A 905 1555 1555 3.45 LINK N ASP A 330 ZN ZN A 959 1555 1555 2.63 LINK HG HG A 905 O HOH A2061 1555 1555 3.53 LINK ZN ZN A 957 OE2 GLU B 196 1555 2655 1.76 LINK ZN ZN A 957 OE1 GLU B 196 1555 2655 2.25 LINK ND1 HIS B 65 HG HG B 906 1555 1555 2.74 LINK NE2 HIS B 195 ZN ZN B 956 1555 1555 2.34 LINK OE1 GLU B 197 ZN ZN B 956 1555 1555 2.28 LINK OE2 GLU B 201 ZN ZN B 958 1555 1555 2.56 LINK SG CYS B 222 HG HG B 904 1555 1555 2.21 LINK O CYS B 222 HG HG B 904 1555 1555 3.27 LINK O ALA B 260 HG HG B 902 1555 1555 3.22 LINK SG CYS B 264 HG HG B 902 1555 1555 3.39 LINK NE2 GLN B 279 ZN ZN B 958 1555 1555 1.74 LINK OG1 THR B 297 HG HG B 902 1555 1555 3.33 LINK SG CYS B 316 HG HG B 906 1555 1555 2.83 LINK O THR B 336 HG HG B 906 1555 1555 3.11 LINK O VAL B 337 HG HG B 906 1555 1555 2.22 LINK OG SER B 338 HG HG B 906 1555 1555 2.88 CRYST1 96.720 96.720 150.400 90.00 90.00 90.00 P 41 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 0.010339 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010339 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006649 0.00000 HETATM 1 C ACE A 0 53.798 -7.112 35.484 1.00 61.41 C HETATM 2 O ACE A 0 53.206 -7.870 34.685 1.00 59.27 O HETATM 3 CH3 ACE A 0 54.970 -7.624 36.309 1.00 58.71 C