HEADER SIGNALING PROTEIN 25-JUN-01 1JGJ TITLE CRYSTAL STRUCTURE OF SENSORY RHODOPSIN II AT 2.4 ANGSTROMS: INSIGHTS TITLE 2 INTO COLOR TUNING AND TRANSDUCER INTERACTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: SENSORY RHODOPSIN II; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NATRONOMONAS PHARAONIS; SOURCE 3 ORGANISM_TAXID: 2257; SOURCE 4 EXPRESSION_SYSTEM: NATRONOMONAS PHARAONIS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 2257 KEYWDS SENSORY RHODOPSIN, MEMBRANE PROTEIN, PHOTOTAXIS RECEPTOR, SIGNALING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.LUECKE REVDAT 6 16-OCT-24 1JGJ 1 REMARK REVDAT 5 16-AUG-23 1JGJ 1 HETSYN REVDAT 4 29-JUL-20 1JGJ 1 COMPND REMARK SEQADV HETNAM REVDAT 4 2 1 LINK SITE REVDAT 3 24-FEB-09 1JGJ 1 VERSN REVDAT 2 12-SEP-01 1JGJ 1 JRNL REVDAT 1 18-JUL-01 1JGJ 0 JRNL AUTH H.LUECKE,B.SCHOBERT,J.K.LANYI,E.N.SPUDICH,J.L.SPUDICH JRNL TITL CRYSTAL STRUCTURE OF SENSORY RHODOPSIN II AT 2.4 ANGSTROMS: JRNL TITL 2 INSIGHTS INTO COLOR TUNING AND TRANSDUCER INTERACTION. JRNL REF SCIENCE V. 293 1499 2001 JRNL REFN ISSN 0036-8075 JRNL PMID 11452084 JRNL DOI 10.1126/SCIENCE.1062977 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.LUECKE,B.SCHOBERT,H.T.RICHTER,J.P.CARTAILLER,J.K.LANYI REMARK 1 TITL STRUCTURE OF BACTERIORHODOPSIN AT 1.55 ANGSTROM RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 291 899 1999 REMARK 1 REFN ISSN 0022-2836 REMARK 1 DOI 10.1006/JMBI.1999.3027 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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, CSD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 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) (%) : 92.2 REMARK 3 NUMBER OF REFLECTIONS : 10704 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.233 REMARK 3 FREE R VALUE : 0.280 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 901 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.45 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2900 REMARK 3 BIN FREE R VALUE : 0.3020 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 23 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 : 1638 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 11 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) : -4.69000 REMARK 3 B22 (A**2) : -3.96200 REMARK 3 B33 (A**2) : 8.65100 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 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) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.297 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) : 1.253 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.735 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.078 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.498 ; 2.500 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1JGJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-JUL-01. REMARK 100 THE DEPOSITION ID IS D_1000013744. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-APR-01 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID13 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9755 REMARK 200 MONOCHROMATOR : DOUBLE-XTAL MONO REMARK 200 OPTICS : ID13 REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10704 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08500 REMARK 200 FOR THE DATA SET : 5.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.44000 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: X-PLOR REMARK 200 STARTING MODEL: 1C3W REMARK 200 REMARK 200 REMARK: USED PROTEIN WITHOUT RETINAL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CUBIC LIPID PHASE WITH MO, PRECIPITANT REMARK 280 KCL, PH 5.3, CUBIC LIPID PHASE, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 -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 25.43500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 25.43500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 43.67000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 65.40500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 43.67000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 65.40500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 25.43500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 43.67000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 65.40500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 25.43500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 43.67000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 65.40500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 ASP A 28 66.75 62.35 REMARK 500 SER A 31 29.51 -71.72 REMARK 500 GLU A 33 -18.93 -167.32 REMARK 500 VAL A 63 -66.87 -120.14 REMARK 500 ALA A 64 -88.66 -112.55 REMARK 500 ARG A 96 -70.14 -41.47 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 BOG A 701 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1C3W RELATED DB: PDB REMARK 900 1.55 A STRUCTURE OF BACTERIORHODOPSIN DBREF 1JGJ A 1 217 UNP P42196 BACS2_NATPH 1 217 SEQADV 1JGJ ALA A 52 UNP P42196 VAL 52 CONFLICT SEQADV 1JGJ VAL A 70 UNP P42196 ALA 70 CONFLICT SEQADV 1JGJ ILE A 135 UNP P42196 LEU 135 CONFLICT SEQADV 1JGJ VAL A 169 UNP P42196 ILE 169 CONFLICT SEQRES 1 A 217 MET VAL GLY LEU THR THR LEU PHE TRP LEU GLY ALA ILE SEQRES 2 A 217 GLY MET LEU VAL GLY THR LEU ALA PHE ALA TRP ALA GLY SEQRES 3 A 217 ARG ASP ALA GLY SER GLY GLU ARG ARG TYR TYR VAL THR SEQRES 4 A 217 LEU VAL GLY ILE SER GLY ILE ALA ALA VAL ALA TYR ALA SEQRES 5 A 217 VAL MET ALA LEU GLY VAL GLY TRP VAL PRO VAL ALA GLU SEQRES 6 A 217 ARG THR VAL PHE VAL PRO ARG TYR ILE ASP TRP ILE LEU SEQRES 7 A 217 THR THR PRO LEU ILE VAL TYR PHE LEU GLY LEU LEU ALA SEQRES 8 A 217 GLY LEU ASP SER ARG GLU PHE GLY ILE VAL ILE THR LEU SEQRES 9 A 217 ASN THR VAL VAL MET LEU ALA GLY PHE ALA GLY ALA MET SEQRES 10 A 217 VAL PRO GLY ILE GLU ARG TYR ALA LEU PHE GLY MET GLY SEQRES 11 A 217 ALA VAL ALA PHE ILE GLY LEU VAL TYR TYR LEU VAL GLY SEQRES 12 A 217 PRO MET THR GLU SER ALA SER GLN ARG SER SER GLY ILE SEQRES 13 A 217 LYS SER LEU TYR VAL ARG LEU ARG ASN LEU THR VAL VAL SEQRES 14 A 217 LEU TRP ALA ILE TYR PRO PHE ILE TRP LEU LEU GLY PRO SEQRES 15 A 217 PRO GLY VAL ALA LEU LEU THR PRO THR VAL ASP VAL ALA SEQRES 16 A 217 LEU ILE VAL TYR LEU ASP LEU VAL THR LYS VAL GLY PHE SEQRES 17 A 217 GLY PHE ILE ALA LEU ASP ALA ALA ALA HET BOG A 701 14 HET RET A 301 20 HETNAM BOG OCTYL BETA-D-GLUCOPYRANOSIDE HETNAM RET RETINAL HETSYN BOG BETA-OCTYLGLUCOSIDE; OCTYL BETA-D-GLUCOSIDE; OCTYL D- HETSYN 2 BOG GLUCOSIDE; OCTYL GLUCOSIDE FORMUL 2 BOG C14 H28 O6 FORMUL 3 RET C20 H28 O FORMUL 4 HOH *11(H2 O) HELIX 1 1 MET A 1 ARG A 27 1 27 HELIX 2 2 GLU A 33 LEU A 56 1 24 HELIX 3 3 VAL A 70 GLY A 92 1 23 HELIX 4 4 ASP A 94 VAL A 118 1 25 HELIX 5 5 ILE A 121 SER A 150 1 30 HELIX 6 6 SER A 153 GLY A 181 1 29 HELIX 7 7 THR A 189 ALA A 216 1 28 SHEET 1 A 2 TRP A 60 PRO A 62 0 SHEET 2 A 2 THR A 67 PHE A 69 -1 N VAL A 68 O VAL A 61 LINK NZ LYS A 205 C15 RET A 301 1555 1555 1.27 CRYST1 87.340 130.810 50.870 90.00 90.00 90.00 C 2 2 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 0.011450 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007645 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019658 0.00000