HEADER MEMBRANE PROTEIN 17-AUG-06 2I36 TITLE CRYSTAL STRUCTURE OF TRIGONAL CRYSTAL FORM OF GROUND-STATE RHODOPSIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RHODOPSIN; COMPND 3 CHAIN: A, B, C SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913 KEYWDS TRANS-MEMBRANE PROTEIN, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.E.STENKAMP,I.LE TRONG,D.T.LODOWSKI,D.SALOM,K.PALCZEWSKI REVDAT 7 30-AUG-23 2I36 1 HETSYN REVDAT 6 29-JUL-20 2I36 1 COMPND REMARK HETNAM LINK REVDAT 6 2 1 SITE ATOM REVDAT 5 19-OCT-11 2I36 1 LINK REMARK REVDAT 4 13-JUL-11 2I36 1 VERSN REVDAT 3 24-FEB-09 2I36 1 VERSN REVDAT 2 14-NOV-06 2I36 1 JRNL REVDAT 1 17-OCT-06 2I36 0 JRNL AUTH D.SALOM,D.T.LODOWSKI,R.E.STENKAMP,I.L.TRONG,M.GOLCZAK, JRNL AUTH 2 B.JASTRZEBSKA,T.HARRIS,J.A.BALLESTEROS,K.PALCZEWSKI JRNL TITL CRYSTAL STRUCTURE OF A PHOTOACTIVATED DEPROTONATED JRNL TITL 2 INTERMEDIATE OF RHODOPSIN. JRNL REF PROC.NATL.ACAD.SCI.USA V. 103 16123 2006 JRNL REFN ISSN 0027-8424 JRNL PMID 17060607 JRNL DOI 10.1073/PNAS.0608022103 REMARK 2 REMARK 2 RESOLUTION. 4.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 4.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 16375 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.384 REMARK 3 R VALUE (WORKING SET) : 0.382 REMARK 3 FREE R VALUE : 0.412 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 832 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 4.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 4.20 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1120 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.66 REMARK 3 BIN R VALUE (WORKING SET) : 0.5220 REMARK 3 BIN FREE R VALUE SET COUNT : 60 REMARK 3 BIN FREE R VALUE : 0.5400 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7665 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 218 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 185.0 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 185.0 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -13.16000 REMARK 3 B22 (A**2) : -13.16000 REMARK 3 B33 (A**2) : 19.74000 REMARK 3 B12 (A**2) : -6.58000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 1.223 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 2.000 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 166.899 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.869 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.864 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 8144 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 11108 ; 1.327 ; 1.970 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 958 ; 6.376 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 329 ;40.202 ;23.283 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1208 ;21.531 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;17.059 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1266 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6047 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3750 ; 0.230 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 5513 ; 0.316 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 187 ; 0.169 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 32 ; 0.342 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.170 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 4926 ; 0.000 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 7803 ; 0.000 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3730 ; 0.000 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3305 ; 0.000 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B C REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 1 A 326 1 REMARK 3 1 B 1 B 324 1 REMARK 3 1 C 1 C 322 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 2489 ; 0.03 ; 0.05 REMARK 3 TIGHT POSITIONAL 1 B (A): 2489 ; 0.03 ; 0.05 REMARK 3 TIGHT POSITIONAL 1 C (A): 2489 ; 0.02 ; 0.05 REMARK 3 TIGHT THERMAL 1 A (A**2): 2489 ; 0.00 ; 0.50 REMARK 3 TIGHT THERMAL 1 B (A**2): 2489 ; 0.00 ; 0.50 REMARK 3 TIGHT THERMAL 1 C (A**2): 2489 ; 0.00 ; 0.50 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2I36 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-AUG-06. REMARK 100 THE DEPOSITION ID IS D_1000039078. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-APR-04 REMARK 200 TEMPERATURE (KELVIN) : 77 REMARK 200 PH : 6.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97970 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17705 REMARK 200 RESOLUTION RANGE HIGH (A) : 4.000 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 10.60 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 4.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 4.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1HZX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 72.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 80 MM MES, PH 6.3, 110 MM N-NONYL-BETA REMARK 280 -D-GLUCOSIDE, 200 MM ZINC ACETATE, 0.1% SODIUM AZIDE, 16 MM BETA- REMARK 280 MERCAPTOETHANOL, 2.6% MERPOL HCS, EQUILIBRATED AGAINST 3.1-3.3 M REMARK 280 AMMONIUM SULFATE, VAPOR DIFFUSION, TEMPERATURE 278K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 1 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -Y,-X,-Z+2/3 REMARK 290 5555 -X+Y,Y,-Z+1/3 REMARK 290 6555 X,X-Y,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.38333 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 94.76667 REMARK 290 SMTRY1 4 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 94.76667 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 47.38333 REMARK 290 SMTRY1 6 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, E REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, F, G REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, H, I REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 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 VAL B 137 REMARK 465 VAL B 138 REMARK 465 VAL B 139 REMARK 465 CYS B 140 REMARK 465 LYS B 141 REMARK 465 PRO B 142 REMARK 465 MET B 143 REMARK 465 SER B 144 REMARK 465 ASN B 145 REMARK 465 PHE B 146 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 465 CYS C 323 REMARK 465 GLY C 324 REMARK 465 LYS C 325 REMARK 465 ASN C 326 REMARK 465 PRO C 327 REMARK 465 LEU C 328 REMARK 465 GLY C 329 REMARK 465 ASP C 330 REMARK 465 ASP C 331 REMARK 465 GLU C 332 REMARK 465 ALA C 333 REMARK 465 SER C 334 REMARK 465 THR C 335 REMARK 465 THR C 336 REMARK 465 VAL C 337 REMARK 465 SER C 338 REMARK 465 LYS C 339 REMARK 465 THR C 340 REMARK 465 GLU C 341 REMARK 465 THR C 342 REMARK 465 SER C 343 REMARK 465 GLN C 344 REMARK 465 VAL C 345 REMARK 465 ALA C 346 REMARK 465 PRO C 347 REMARK 465 ALA C 348 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 SG CYS A 323 O2 PLM A 401 1.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 PHE B 148 CG PHE B 148 CD2 0.112 REMARK 500 LYS C 141 CE LYS C 141 NZ 0.430 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 30.96 -77.84 REMARK 500 ARG A 21 -156.05 -134.41 REMARK 500 GLN A 28 49.37 -80.72 REMARK 500 ALA A 32 -145.99 -153.87 REMARK 500 LEU A 47 -71.14 -77.15 REMARK 500 ARG A 69 47.75 -99.74 REMARK 500 PHE A 88 34.17 -94.16 REMARK 500 ASN A 111 10.71 -59.67 REMARK 500 LEU A 112 -62.22 -109.72 REMARK 500 GLU A 122 -35.89 -132.73 REMARK 500 VAL A 139 -37.56 -138.33 REMARK 500 LYS A 141 91.96 59.03 REMARK 500 SER A 144 -93.72 -69.94 REMARK 500 PHE A 146 64.02 -106.25 REMARK 500 PHE A 148 -112.98 -91.77 REMARK 500 SER A 176 -143.58 -151.10 REMARK 500 HIS A 195 68.37 28.34 REMARK 500 ASN A 199 73.31 58.14 REMARK 500 PHE A 212 -61.97 -133.96 REMARK 500 GLN A 244 57.77 -97.64 REMARK 500 GLN A 279 -13.74 40.18 REMARK 500 ASP A 282 58.13 -91.47 REMARK 500 CYS A 323 21.50 84.73 REMARK 500 ASN B 15 31.52 -74.45 REMARK 500 ARG B 21 -154.83 -134.88 REMARK 500 GLN B 28 48.32 -80.78 REMARK 500 ALA B 32 -146.66 -153.41 REMARK 500 LEU B 47 -70.95 -79.46 REMARK 500 PHE B 52 -62.15 -91.12 REMARK 500 ARG B 69 48.29 -101.03 REMARK 500 PHE B 88 33.64 -93.39 REMARK 500 TYR B 102 157.43 179.24 REMARK 500 ASN B 111 6.90 -57.54 REMARK 500 LEU B 112 -64.83 -107.47 REMARK 500 GLU B 122 -38.84 -130.76 REMARK 500 PHE B 148 -113.19 -92.44 REMARK 500 SER B 176 -142.05 -150.80 REMARK 500 HIS B 195 69.34 25.54 REMARK 500 ASN B 199 72.51 59.15 REMARK 500 PHE B 212 -62.21 -132.97 REMARK 500 GLN B 244 59.35 -99.58 REMARK 500 GLN B 279 -12.60 39.92 REMARK 500 ASP B 282 58.78 -92.82 REMARK 500 CYS B 323 3.26 -151.37 REMARK 500 ASN C 15 28.60 -75.76 REMARK 500 ARG C 21 -154.75 -133.75 REMARK 500 GLN C 28 47.71 -79.48 REMARK 500 ALA C 32 -146.48 -152.80 REMARK 500 PHE C 52 -61.93 -90.47 REMARK 500 ARG C 69 47.16 -100.34 REMARK 500 REMARK 500 THIS ENTRY HAS 64 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2I35 RELATED DB: PDB REMARK 900 2I35 IS THE CRYSTAL STRUCTURE OF RHOMBOHEDRAL FORM OF GROUND-STATE REMARK 900 RHODOPSIN DETERMINED AT 3.80 ANGSTROM RESOLUTION REMARK 900 RELATED ID: 2I37 RELATED DB: PDB REMARK 900 2I37 IS THE CRYSTAL STRUCTURE OF PHOTOACTIVATED RHODOPSIN REMARK 900 DETERMINED AT 4.15 ANGSTROM RESOLUTION DBREF 2I36 A 1 348 UNP P02699 OPSD_BOVIN 1 348 DBREF 2I36 B 1 348 UNP P02699 OPSD_BOVIN 1 348 DBREF 2I36 C 1 348 UNP P02699 OPSD_BOVIN 1 348 SEQRES 1 A 349 ACE MET ASN GLY THR GLU GLY PRO ASN PHE TYR VAL PRO SEQRES 2 A 349 PHE SER ASN LYS THR GLY VAL VAL ARG SER PRO PHE GLU SEQRES 3 A 349 ALA PRO GLN TYR TYR LEU ALA GLU PRO TRP GLN PHE SER SEQRES 4 A 349 MET LEU ALA ALA TYR MET PHE LEU LEU ILE MET LEU GLY SEQRES 5 A 349 PHE PRO ILE ASN PHE LEU THR LEU TYR VAL THR VAL GLN SEQRES 6 A 349 HIS LYS LYS LEU ARG THR PRO LEU ASN TYR ILE LEU LEU SEQRES 7 A 349 ASN LEU ALA VAL ALA ASP LEU PHE MET VAL PHE GLY GLY SEQRES 8 A 349 PHE THR THR THR LEU TYR THR SER LEU HIS GLY TYR PHE SEQRES 9 A 349 VAL PHE GLY PRO THR GLY CYS ASN LEU GLU GLY PHE PHE SEQRES 10 A 349 ALA THR LEU GLY GLY GLU ILE ALA LEU TRP SER LEU VAL SEQRES 11 A 349 VAL LEU ALA ILE GLU ARG TYR VAL VAL VAL CYS LYS PRO SEQRES 12 A 349 MET SER ASN PHE ARG PHE GLY GLU ASN HIS ALA ILE MET SEQRES 13 A 349 GLY VAL ALA PHE THR TRP VAL MET ALA LEU ALA CYS ALA SEQRES 14 A 349 ALA PRO PRO LEU VAL GLY TRP SER ARG TYR ILE PRO GLU SEQRES 15 A 349 GLY MET GLN CYS SER CYS GLY ILE ASP TYR TYR THR PRO SEQRES 16 A 349 HIS GLU GLU THR ASN ASN GLU SER PHE VAL ILE TYR MET SEQRES 17 A 349 PHE VAL VAL HIS PHE ILE ILE PRO LEU ILE VAL ILE PHE SEQRES 18 A 349 PHE CYS TYR GLY GLN LEU VAL PHE THR VAL LYS GLU ALA SEQRES 19 A 349 ALA ALA GLN GLN GLN GLU SER ALA THR THR GLN LYS ALA SEQRES 20 A 349 GLU LYS GLU VAL THR ARG MET VAL ILE ILE MET VAL ILE SEQRES 21 A 349 ALA PHE LEU ILE CYS TRP LEU PRO TYR ALA GLY VAL ALA SEQRES 22 A 349 PHE TYR ILE PHE THR HIS GLN GLY SER ASP PHE GLY PRO SEQRES 23 A 349 ILE PHE MET THR ILE PRO ALA PHE PHE ALA LYS THR SER SEQRES 24 A 349 ALA VAL TYR ASN PRO VAL ILE TYR ILE MET MET ASN LYS SEQRES 25 A 349 GLN PHE ARG ASN CYS MET VAL THR THR LEU CYS CYS GLY SEQRES 26 A 349 LYS ASN PRO LEU GLY ASP ASP GLU ALA SER THR THR VAL SEQRES 27 A 349 SER LYS THR GLU THR SER GLN VAL ALA PRO ALA SEQRES 1 B 349 ACE MET ASN GLY THR GLU GLY PRO ASN PHE TYR VAL PRO SEQRES 2 B 349 PHE SER ASN LYS THR GLY VAL VAL ARG SER PRO PHE GLU SEQRES 3 B 349 ALA PRO GLN TYR TYR LEU ALA GLU PRO TRP GLN PHE SER SEQRES 4 B 349 MET LEU ALA ALA TYR MET PHE LEU LEU ILE MET LEU GLY SEQRES 5 B 349 PHE PRO ILE ASN PHE LEU THR LEU TYR VAL THR VAL GLN SEQRES 6 B 349 HIS LYS LYS LEU ARG THR PRO LEU ASN TYR ILE LEU LEU SEQRES 7 B 349 ASN LEU ALA VAL ALA ASP LEU PHE MET VAL PHE GLY GLY SEQRES 8 B 349 PHE THR THR THR LEU TYR THR SER LEU HIS GLY TYR PHE SEQRES 9 B 349 VAL PHE GLY PRO THR GLY CYS ASN LEU GLU GLY PHE PHE SEQRES 10 B 349 ALA THR LEU GLY GLY GLU ILE ALA LEU TRP SER LEU VAL SEQRES 11 B 349 VAL LEU ALA ILE GLU ARG TYR VAL VAL VAL CYS LYS PRO SEQRES 12 B 349 MET SER ASN PHE ARG PHE GLY GLU ASN HIS ALA ILE MET SEQRES 13 B 349 GLY VAL ALA PHE THR TRP VAL MET ALA LEU ALA CYS ALA SEQRES 14 B 349 ALA PRO PRO LEU VAL GLY TRP SER ARG TYR ILE PRO GLU SEQRES 15 B 349 GLY MET GLN CYS SER CYS GLY ILE ASP TYR TYR THR PRO SEQRES 16 B 349 HIS GLU GLU THR ASN ASN GLU SER PHE VAL ILE TYR MET SEQRES 17 B 349 PHE VAL VAL HIS PHE ILE ILE PRO LEU ILE VAL ILE PHE SEQRES 18 B 349 PHE CYS TYR GLY GLN LEU VAL PHE THR VAL LYS GLU ALA SEQRES 19 B 349 ALA ALA GLN GLN GLN GLU SER ALA THR THR GLN LYS ALA SEQRES 20 B 349 GLU LYS GLU VAL THR ARG MET VAL ILE ILE MET VAL ILE SEQRES 21 B 349 ALA PHE LEU ILE CYS TRP LEU PRO TYR ALA GLY VAL ALA SEQRES 22 B 349 PHE TYR ILE PHE THR HIS GLN GLY SER ASP PHE GLY PRO SEQRES 23 B 349 ILE PHE MET THR ILE PRO ALA PHE PHE ALA LYS THR SER SEQRES 24 B 349 ALA VAL TYR ASN PRO VAL ILE TYR ILE MET MET ASN LYS SEQRES 25 B 349 GLN PHE ARG ASN CYS MET VAL THR THR LEU CYS CYS GLY SEQRES 26 B 349 LYS ASN PRO LEU GLY ASP ASP GLU ALA SER THR THR VAL SEQRES 27 B 349 SER LYS THR GLU THR SER GLN VAL ALA PRO ALA SEQRES 1 C 349 ACE MET ASN GLY THR GLU GLY PRO ASN PHE TYR VAL PRO SEQRES 2 C 349 PHE SER ASN LYS THR GLY VAL VAL ARG SER PRO PHE GLU SEQRES 3 C 349 ALA PRO GLN TYR TYR LEU ALA GLU PRO TRP GLN PHE SER SEQRES 4 C 349 MET LEU ALA ALA TYR MET PHE LEU LEU ILE MET LEU GLY SEQRES 5 C 349 PHE PRO ILE ASN PHE LEU THR LEU TYR VAL THR VAL GLN SEQRES 6 C 349 HIS LYS LYS LEU ARG THR PRO LEU ASN TYR ILE LEU LEU SEQRES 7 C 349 ASN LEU ALA VAL ALA ASP LEU PHE MET VAL PHE GLY GLY SEQRES 8 C 349 PHE THR THR THR LEU TYR THR SER LEU HIS GLY TYR PHE SEQRES 9 C 349 VAL PHE GLY PRO THR GLY CYS ASN LEU GLU GLY PHE PHE SEQRES 10 C 349 ALA THR LEU GLY GLY GLU ILE ALA LEU TRP SER LEU VAL SEQRES 11 C 349 VAL LEU ALA ILE GLU ARG TYR VAL VAL VAL CYS LYS PRO SEQRES 12 C 349 MET SER ASN PHE ARG PHE GLY GLU ASN HIS ALA ILE MET SEQRES 13 C 349 GLY VAL ALA PHE THR TRP VAL MET ALA LEU ALA CYS ALA SEQRES 14 C 349 ALA PRO PRO LEU VAL GLY TRP SER ARG TYR ILE PRO GLU SEQRES 15 C 349 GLY MET GLN CYS SER CYS GLY ILE ASP TYR TYR THR PRO SEQRES 16 C 349 HIS GLU GLU THR ASN ASN GLU SER PHE VAL ILE TYR MET SEQRES 17 C 349 PHE VAL VAL HIS PHE ILE ILE PRO LEU ILE VAL ILE PHE SEQRES 18 C 349 PHE CYS TYR GLY GLN LEU VAL PHE THR VAL LYS GLU ALA SEQRES 19 C 349 ALA ALA GLN GLN GLN GLU SER ALA THR THR GLN LYS ALA SEQRES 20 C 349 GLU LYS GLU VAL THR ARG MET VAL ILE ILE MET VAL ILE SEQRES 21 C 349 ALA PHE LEU ILE CYS TRP LEU PRO TYR ALA GLY VAL ALA SEQRES 22 C 349 PHE TYR ILE PHE THR HIS GLN GLY SER ASP PHE GLY PRO SEQRES 23 C 349 ILE PHE MET THR ILE PRO ALA PHE PHE ALA LYS THR SER SEQRES 24 C 349 ALA VAL TYR ASN PRO VAL ILE TYR ILE MET MET ASN LYS SEQRES 25 C 349 GLN PHE ARG ASN CYS MET VAL THR THR LEU CYS CYS GLY SEQRES 26 C 349 LYS ASN PRO LEU GLY ASP ASP GLU ALA SER THR THR VAL SEQRES 27 C 349 SER LYS THR GLU THR SER GLN VAL ALA PRO ALA MODRES 2I36 ASN A 2 ASN GLYCOSYLATION SITE MODRES 2I36 ASN A 15 ASN GLYCOSYLATION SITE MODRES 2I36 ASN B 2 ASN GLYCOSYLATION SITE MODRES 2I36 ASN B 15 ASN GLYCOSYLATION SITE MODRES 2I36 ASN C 2 ASN GLYCOSYLATION SITE MODRES 2I36 ASN C 15 ASN GLYCOSYLATION SITE HET ACE A 0 3 HET ACE B 0 3 HET ACE C 0 3 HET NAG D 1 14 HET NAG D 2 14 HET MAN D 3 11 HET NAG E 1 14 HET NAG E 2 14 HET NAG F 1 14 HET NAG F 2 14 HET MAN F 3 11 HET NAG G 1 14 HET NAG G 2 14 HET NAG H 1 14 HET NAG H 2 14 HET MAN H 3 11 HET NAG I 1 14 HET NAG I 2 14 HET PLM A 401 17 HETNAM ACE ACETYL GROUP HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE 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 MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 1 ACE 3(C2 H4 O) FORMUL 4 NAG 12(C8 H15 N O6) FORMUL 4 MAN 3(C6 H12 O6) FORMUL 10 PLM C16 H32 O2 HELIX 1 1 GLU A 33 GLY A 51 1 19 HELIX 2 2 PHE A 52 HIS A 65 1 14 HELIX 3 3 THR A 70 PHE A 88 1 19 HELIX 4 4 GLY A 89 GLY A 101 1 13 HELIX 5 5 GLY A 109 ALA A 117 1 9 HELIX 6 6 ILE A 133 VAL A 138 1 6 HELIX 7 7 VAL A 157 VAL A 173 1 17 HELIX 8 8 ASN A 199 PHE A 212 1 14 HELIX 9 9 PHE A 212 GLU A 232 1 21 HELIX 10 10 ALA A 233 GLN A 238 1 6 HELIX 11 11 VAL A 250 ILE A 255 1 6 HELIX 12 12 ILE A 256 CYS A 264 1 9 HELIX 13 13 CYS A 264 GLN A 279 1 16 HELIX 14 14 PRO A 285 LYS A 296 1 12 HELIX 15 15 VAL A 300 MET A 309 1 10 HELIX 16 16 PHE A 313 CYS A 323 1 11 HELIX 17 17 GLU B 33 GLY B 51 1 19 HELIX 18 18 PHE B 52 HIS B 65 1 14 HELIX 19 19 THR B 70 PHE B 88 1 19 HELIX 20 20 GLY B 89 GLY B 101 1 13 HELIX 21 21 GLY B 109 ALA B 117 1 9 HELIX 22 22 TRP B 126 LEU B 131 1 6 HELIX 23 23 VAL B 157 VAL B 173 1 17 HELIX 24 24 ASN B 199 PHE B 212 1 14 HELIX 25 25 PHE B 212 GLU B 232 1 21 HELIX 26 26 VAL B 250 ILE B 255 1 6 HELIX 27 27 ILE B 256 CYS B 264 1 9 HELIX 28 28 CYS B 264 GLN B 279 1 16 HELIX 29 29 PRO B 285 LYS B 296 1 12 HELIX 30 30 VAL B 300 MET B 309 1 10 HELIX 31 31 PHE B 313 CYS B 322 1 10 HELIX 32 32 GLU C 33 GLY C 51 1 19 HELIX 33 33 PHE C 52 HIS C 65 1 14 HELIX 34 34 THR C 70 PHE C 88 1 19 HELIX 35 35 GLY C 89 GLY C 101 1 13 HELIX 36 36 GLY C 109 ALA C 117 1 9 HELIX 37 37 ILE C 133 VAL C 138 1 6 HELIX 38 38 VAL C 157 VAL C 173 1 17 HELIX 39 39 ASN C 199 PHE C 212 1 14 HELIX 40 40 PHE C 212 GLU C 232 1 21 HELIX 41 41 VAL C 250 ILE C 255 1 6 HELIX 42 42 ILE C 256 CYS C 264 1 9 HELIX 43 43 CYS C 264 GLN C 279 1 16 HELIX 44 44 PRO C 285 LYS C 296 1 12 HELIX 45 45 VAL C 300 MET C 309 1 10 HELIX 46 46 PHE C 313 CYS C 322 1 10 SHEET 1 A 2 TYR A 178 GLU A 181 0 SHEET 2 A 2 SER A 186 ILE A 189 -1 O GLY A 188 N ILE A 179 SHEET 1 B 2 TYR B 178 GLU B 181 0 SHEET 2 B 2 SER B 186 ILE B 189 -1 O GLY B 188 N ILE B 179 SHEET 1 C 2 TYR C 178 GLU C 181 0 SHEET 2 C 2 SER C 186 ILE C 189 -1 O GLY C 188 N ILE C 179 SSBOND 1 CYS A 110 CYS A 187 1555 1555 2.04 SSBOND 2 CYS B 110 CYS B 187 1555 1555 2.04 SSBOND 3 CYS C 110 CYS C 187 1555 1555 2.04 LINK C ACE A 0 N MET A 1 1555 1555 1.33 LINK ND2 ASN A 2 C1 NAG E 1 1555 1555 1.46 LINK ND2 ASN A 15 C1 NAG D 1 1555 1555 1.43 LINK SG CYS A 323 C1 PLM A 401 1555 1555 1.83 LINK C ACE B 0 N MET B 1 1555 1555 1.33 LINK ND2 ASN B 2 C1 NAG G 1 1555 1555 1.47 LINK ND2 ASN B 15 C1 NAG F 1 1555 1555 1.46 LINK C ACE C 0 N MET C 1 1555 1555 1.33 LINK ND2 ASN C 2 C1 NAG I 1 1555 1555 1.47 LINK ND2 ASN C 15 C1 NAG H 1 1555 1555 1.45 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.44 LINK O4 NAG D 2 C1 MAN D 3 1555 1555 1.45 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.45 LINK O4 NAG F 1 C1 NAG F 2 1555 1555 1.44 LINK O4 NAG F 2 C1 MAN F 3 1555 1555 1.47 LINK O4 NAG G 1 C1 NAG G 2 1555 1555 1.47 LINK O4 NAG H 1 C1 NAG H 2 1555 1555 1.45 LINK O4 NAG H 2 C1 MAN H 3 1555 1555 1.46 LINK O4 NAG I 1 C1 NAG I 2 1555 1555 1.46 CRYST1 159.866 159.866 142.150 90.00 90.00 120.00 P 31 1 2 18 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.006255 0.003611 0.000000 0.00000 SCALE2 0.000000 0.007223 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007035 0.00000 HETATM 1 C ACE A 0 7.858 0.944 76.611 1.00185.00 C HETATM 2 O ACE A 0 8.409 2.054 76.544 1.00185.00 O HETATM 3 CH3 ACE A 0 8.573 -0.282 75.926 1.00185.00 C