HEADER TRANSPORT PROTEIN 16-AUG-10 3AM6 TITLE CRYSTAL STRUCTURE OF THE PROTON PUMPING RHODOPSIN AR2 FROM MARINE ALGA TITLE 2 ACETABULARIA ACETABULUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: RHODOPSIN-2; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: AR2; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACETABULARIA ACETABULUM; SOURCE 3 ORGANISM_COMMON: MERMAID'S WINE GLASS; SOURCE 4 ORGANISM_TAXID: 35845; SOURCE 5 EXPRESSION_SYSTEM: CELL-FREE SYNTHESIS; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PCR2.1-TOPO KEYWDS SEVEN TRANS-MEMBRANE, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.WADA,S.YOKOYAMA REVDAT 2 07-DEC-11 3AM6 1 JRNL VERSN REVDAT 1 06-JUL-11 3AM6 0 JRNL AUTH T.WADA,K.SHIMONO,T.KIKUKAWA,M.HATO,N.SHINYA,S.Y.KIM, JRNL AUTH 2 T.KIMURA-SOMEYA,M.SHIROUZU,J.TAMOGAMI,S.MIYAUCHI,K.-H.JUNG, JRNL AUTH 3 N.KAMO,S.YOKOYAMA JRNL TITL CRYSTAL STRUCTURE OF THE EUKARYOTIC LIGHT-DRIVEN JRNL TITL 2 PROTON-PUMPING RHODOPSIN, ACETABULARIA RHODOPSIN II, FROM JRNL TITL 3 MARINE ALGA JRNL REF J.MOL.BIOL. V. 411 986 2011 JRNL REFN ISSN 0022-2836 JRNL PMID 21726566 JRNL DOI 10.1016/J.JMB.2011.06.028 REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 53692.390 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 89.2 REMARK 3 NUMBER OF REFLECTIONS : 18250 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) : 0.290 REMARK 3 FREE R VALUE : 0.324 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 891 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.011 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.40 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 72.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2313 REMARK 3 BIN R VALUE (WORKING SET) : 0.3850 REMARK 3 BIN FREE R VALUE : 0.4070 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 129 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.036 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7024 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 304 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -6.54000 REMARK 3 B22 (A**2) : 17.34000 REMARK 3 B33 (A**2) : -10.80000 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) : 0.52 REMARK 3 ESD FROM SIGMAA (A) : 0.70 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.59 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.59 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.40 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 16.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 2.13 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED 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 : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 39.96 REMARK 3 REMARK 3 NCS MODEL : CONSTR 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 : R+C+O.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : R+C+O.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3AM6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-AUG-10. REMARK 100 THE RCSB ID CODE IS RCSB029421. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-OCT-09 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 7.5 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 : SI REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18284 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.192 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 (%) : 89.5 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11500 REMARK 200 FOR THE DATA SET : 8.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.19 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.25100 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: MRBUMP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL (PH 7.5), 6% 2-METHYL-2, REMARK 280 4-PENTANEDIOL, 14% POLYETHYLENE GLYCOL 400, LIPID MESOPHASE, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 42.06000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 64.55800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 55.24350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 64.55800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 42.06000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 55.24350 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4, 5 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 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: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D 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: 5 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 39570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 SER A 36 REMARK 465 GLU A 37 REMARK 465 LEU A 157 REMARK 465 LYS A 158 REMARK 465 MET A 229 REMARK 465 SER B 36 REMARK 465 GLU B 37 REMARK 465 LEU B 157 REMARK 465 LYS B 158 REMARK 465 MET B 229 REMARK 465 SER C 36 REMARK 465 GLU C 37 REMARK 465 LEU C 157 REMARK 465 LYS C 158 REMARK 465 MET C 229 REMARK 465 SER D 36 REMARK 465 GLU D 37 REMARK 465 LEU D 157 REMARK 465 LYS D 158 REMARK 465 MET D 229 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 O LYS A 159 O LYS D 228 4555 2.14 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 ALA A 30 -65.36 -23.79 REMARK 500 ALA A 77 -33.59 -39.31 REMARK 500 ASP A 125 -70.45 -82.90 REMARK 500 ALA A 142 -70.22 -60.47 REMARK 500 THR A 152 -61.43 -100.41 REMARK 500 ASP A 155 53.67 -57.72 REMARK 500 SER A 169 -80.03 -40.41 REMARK 500 SER A 189 -36.91 -38.60 REMARK 500 VAL A 193 -8.27 -59.63 REMARK 500 LYS A 211 -74.17 -101.42 REMARK 500 ILE B 11 -70.49 -43.65 REMARK 500 ALA B 30 -64.37 -24.48 REMARK 500 TYR B 63 -9.08 -56.60 REMARK 500 GLU B 71 45.31 -109.20 REMARK 500 ALA B 77 -33.77 -39.93 REMARK 500 THR B 152 -60.90 -99.44 REMARK 500 ASP B 155 52.91 -57.46 REMARK 500 SER B 169 -80.84 -40.75 REMARK 500 VAL B 193 -7.91 -57.53 REMARK 500 LYS B 211 -73.60 -101.01 REMARK 500 ILE C 11 -70.18 -44.05 REMARK 500 ALA C 30 -64.82 -25.26 REMARK 500 TYR C 63 -8.65 -56.16 REMARK 500 THR C 152 -61.04 -99.75 REMARK 500 ASP C 155 53.43 -57.59 REMARK 500 SER C 169 -81.67 -39.87 REMARK 500 VAL C 193 -8.13 -58.60 REMARK 500 LYS C 211 -72.99 -102.14 REMARK 500 ALA D 30 -64.20 -24.02 REMARK 500 TYR D 63 -9.84 -55.32 REMARK 500 ALA D 77 -33.41 -39.37 REMARK 500 ALA D 142 -70.83 -59.40 REMARK 500 THR D 152 -61.03 -99.73 REMARK 500 ASP D 155 53.54 -57.96 REMARK 500 SER D 169 -80.97 -40.36 REMARK 500 SER D 189 -36.78 -38.91 REMARK 500 VAL D 193 -7.66 -59.92 REMARK 500 LYS D 211 -73.75 -100.47 REMARK 500 PHE D 226 -32.71 -39.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RET A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CLR A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CLR A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RET B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CLR B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CLR B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RET C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CLR C 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CLR C 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RET D 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CLR D 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CLR D 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1C3W RELATED DB: PDB REMARK 900 BACTERIORHODOPSIN REMARK 900 RELATED ID: 1XIO RELATED DB: PDB REMARK 900 ANABAENA SENSORY RHODOPSIN REMARK 999 REMARK 999 SEQUENCE REMARK 999 THERE IS NO UNP REFERENCE SEQUENCE DATABASE FOR THIS PROTEINS AT REMARK 999 THE TIME OF PROCESSING. THE SEQUENCE HAS BEEN DEPOSITED ON GENBANK REMARK 999 WITH THE ACCESSION CODE, HM070408. DBREF 3AM6 A 1 229 PDB 3AM6 3AM6 1 229 DBREF 3AM6 B 1 229 PDB 3AM6 3AM6 1 229 DBREF 3AM6 C 1 229 PDB 3AM6 3AM6 1 229 DBREF 3AM6 D 1 229 PDB 3AM6 3AM6 1 229 SEQRES 1 A 229 MET ALA ASP VAL GLU THR GLU THR GLY MET ILE ALA GLN SEQRES 2 A 229 TRP ILE VAL PHE ALA ILE MET ALA ALA ALA ALA ILE ALA SEQRES 3 A 229 PHE GLY VAL ALA VAL HIS PHE ARG PRO SER GLU LEU LYS SEQRES 4 A 229 SER ALA TYR TYR ILE ASN ILE ALA ILE CYS THR ILE ALA SEQRES 5 A 229 ALA THR ALA TYR TYR ALA MET ALA VAL ASN TYR GLN ASP SEQRES 6 A 229 LEU THR MET ASN GLY GLU ARG GLN VAL VAL TYR ALA ARG SEQRES 7 A 229 TYR ILE ASP TRP VAL LEU THR THR PRO LEU LEU LEU LEU SEQRES 8 A 229 ASP LEU ILE VAL MET THR LYS MET GLY GLY VAL MET ILE SEQRES 9 A 229 SER TRP VAL ILE GLY ALA ASP ILE PHE MET ILE VAL PHE SEQRES 10 A 229 GLY ILE LEU GLY ALA PHE GLU ASP GLU HIS LYS PHE LYS SEQRES 11 A 229 TRP VAL TYR PHE ILE ALA GLY CYS VAL MET GLN ALA VAL SEQRES 12 A 229 LEU THR TYR GLY MET TYR ASN ALA THR TRP LYS ASP ASP SEQRES 13 A 229 LEU LYS LYS SER PRO GLU TYR HIS SER SER TYR VAL SER SEQRES 14 A 229 LEU LEU VAL PHE LEU SER ILE LEU TRP VAL PHE TYR PRO SEQRES 15 A 229 VAL VAL TRP ALA PHE GLY SER GLY SER GLY VAL LEU SER SEQRES 16 A 229 VAL ASP ASN GLU ALA ILE LEU MET GLY ILE LEU ASP VAL SEQRES 17 A 229 LEU ALA LYS PRO LEU PHE GLY MET GLY CYS LEU ILE ALA SEQRES 18 A 229 HIS GLU THR ILE PHE LYS LYS MET SEQRES 1 B 229 MET ALA ASP VAL GLU THR GLU THR GLY MET ILE ALA GLN SEQRES 2 B 229 TRP ILE VAL PHE ALA ILE MET ALA ALA ALA ALA ILE ALA SEQRES 3 B 229 PHE GLY VAL ALA VAL HIS PHE ARG PRO SER GLU LEU LYS SEQRES 4 B 229 SER ALA TYR TYR ILE ASN ILE ALA ILE CYS THR ILE ALA SEQRES 5 B 229 ALA THR ALA TYR TYR ALA MET ALA VAL ASN TYR GLN ASP SEQRES 6 B 229 LEU THR MET ASN GLY GLU ARG GLN VAL VAL TYR ALA ARG SEQRES 7 B 229 TYR ILE ASP TRP VAL LEU THR THR PRO LEU LEU LEU LEU SEQRES 8 B 229 ASP LEU ILE VAL MET THR LYS MET GLY GLY VAL MET ILE SEQRES 9 B 229 SER TRP VAL ILE GLY ALA ASP ILE PHE MET ILE VAL PHE SEQRES 10 B 229 GLY ILE LEU GLY ALA PHE GLU ASP GLU HIS LYS PHE LYS SEQRES 11 B 229 TRP VAL TYR PHE ILE ALA GLY CYS VAL MET GLN ALA VAL SEQRES 12 B 229 LEU THR TYR GLY MET TYR ASN ALA THR TRP LYS ASP ASP SEQRES 13 B 229 LEU LYS LYS SER PRO GLU TYR HIS SER SER TYR VAL SER SEQRES 14 B 229 LEU LEU VAL PHE LEU SER ILE LEU TRP VAL PHE TYR PRO SEQRES 15 B 229 VAL VAL TRP ALA PHE GLY SER GLY SER GLY VAL LEU SER SEQRES 16 B 229 VAL ASP ASN GLU ALA ILE LEU MET GLY ILE LEU ASP VAL SEQRES 17 B 229 LEU ALA LYS PRO LEU PHE GLY MET GLY CYS LEU ILE ALA SEQRES 18 B 229 HIS GLU THR ILE PHE LYS LYS MET SEQRES 1 C 229 MET ALA ASP VAL GLU THR GLU THR GLY MET ILE ALA GLN SEQRES 2 C 229 TRP ILE VAL PHE ALA ILE MET ALA ALA ALA ALA ILE ALA SEQRES 3 C 229 PHE GLY VAL ALA VAL HIS PHE ARG PRO SER GLU LEU LYS SEQRES 4 C 229 SER ALA TYR TYR ILE ASN ILE ALA ILE CYS THR ILE ALA SEQRES 5 C 229 ALA THR ALA TYR TYR ALA MET ALA VAL ASN TYR GLN ASP SEQRES 6 C 229 LEU THR MET ASN GLY GLU ARG GLN VAL VAL TYR ALA ARG SEQRES 7 C 229 TYR ILE ASP TRP VAL LEU THR THR PRO LEU LEU LEU LEU SEQRES 8 C 229 ASP LEU ILE VAL MET THR LYS MET GLY GLY VAL MET ILE SEQRES 9 C 229 SER TRP VAL ILE GLY ALA ASP ILE PHE MET ILE VAL PHE SEQRES 10 C 229 GLY ILE LEU GLY ALA PHE GLU ASP GLU HIS LYS PHE LYS SEQRES 11 C 229 TRP VAL TYR PHE ILE ALA GLY CYS VAL MET GLN ALA VAL SEQRES 12 C 229 LEU THR TYR GLY MET TYR ASN ALA THR TRP LYS ASP ASP SEQRES 13 C 229 LEU LYS LYS SER PRO GLU TYR HIS SER SER TYR VAL SER SEQRES 14 C 229 LEU LEU VAL PHE LEU SER ILE LEU TRP VAL PHE TYR PRO SEQRES 15 C 229 VAL VAL TRP ALA PHE GLY SER GLY SER GLY VAL LEU SER SEQRES 16 C 229 VAL ASP ASN GLU ALA ILE LEU MET GLY ILE LEU ASP VAL SEQRES 17 C 229 LEU ALA LYS PRO LEU PHE GLY MET GLY CYS LEU ILE ALA SEQRES 18 C 229 HIS GLU THR ILE PHE LYS LYS MET SEQRES 1 D 229 MET ALA ASP VAL GLU THR GLU THR GLY MET ILE ALA GLN SEQRES 2 D 229 TRP ILE VAL PHE ALA ILE MET ALA ALA ALA ALA ILE ALA SEQRES 3 D 229 PHE GLY VAL ALA VAL HIS PHE ARG PRO SER GLU LEU LYS SEQRES 4 D 229 SER ALA TYR TYR ILE ASN ILE ALA ILE CYS THR ILE ALA SEQRES 5 D 229 ALA THR ALA TYR TYR ALA MET ALA VAL ASN TYR GLN ASP SEQRES 6 D 229 LEU THR MET ASN GLY GLU ARG GLN VAL VAL TYR ALA ARG SEQRES 7 D 229 TYR ILE ASP TRP VAL LEU THR THR PRO LEU LEU LEU LEU SEQRES 8 D 229 ASP LEU ILE VAL MET THR LYS MET GLY GLY VAL MET ILE SEQRES 9 D 229 SER TRP VAL ILE GLY ALA ASP ILE PHE MET ILE VAL PHE SEQRES 10 D 229 GLY ILE LEU GLY ALA PHE GLU ASP GLU HIS LYS PHE LYS SEQRES 11 D 229 TRP VAL TYR PHE ILE ALA GLY CYS VAL MET GLN ALA VAL SEQRES 12 D 229 LEU THR TYR GLY MET TYR ASN ALA THR TRP LYS ASP ASP SEQRES 13 D 229 LEU LYS LYS SER PRO GLU TYR HIS SER SER TYR VAL SER SEQRES 14 D 229 LEU LEU VAL PHE LEU SER ILE LEU TRP VAL PHE TYR PRO SEQRES 15 D 229 VAL VAL TRP ALA PHE GLY SER GLY SER GLY VAL LEU SER SEQRES 16 D 229 VAL ASP ASN GLU ALA ILE LEU MET GLY ILE LEU ASP VAL SEQRES 17 D 229 LEU ALA LYS PRO LEU PHE GLY MET GLY CYS LEU ILE ALA SEQRES 18 D 229 HIS GLU THR ILE PHE LYS LYS MET HET RET A 301 20 HET CLR A 401 28 HET CLR A 402 28 HET RET B 301 20 HET CLR B 401 28 HET CLR B 402 28 HET RET C 301 20 HET CLR C 401 28 HET CLR C 402 28 HET RET D 301 20 HET CLR D 401 28 HET CLR D 402 28 HETNAM RET RETINAL HETNAM CLR CHOLESTEROL FORMUL 5 RET 4(C20 H28 O) FORMUL 6 CLR 8(C27 H46 O) HELIX 1 1 THR A 6 VAL A 31 1 26 HELIX 2 2 HIS A 32 ARG A 34 5 3 HELIX 3 3 LEU A 38 ASN A 62 1 25 HELIX 4 4 TYR A 76 VAL A 95 1 20 HELIX 5 5 GLY A 100 PHE A 123 1 24 HELIX 6 6 GLU A 126 LYS A 154 1 29 HELIX 7 7 SER A 160 VAL A 179 1 20 HELIX 8 8 VAL A 179 GLY A 188 1 10 HELIX 9 9 SER A 195 LYS A 211 1 17 HELIX 10 10 LYS A 211 LYS A 227 1 17 HELIX 11 11 THR B 6 VAL B 31 1 26 HELIX 12 12 HIS B 32 ARG B 34 5 3 HELIX 13 13 LEU B 38 ASN B 62 1 25 HELIX 14 14 TYR B 76 VAL B 95 1 20 HELIX 15 15 GLY B 100 PHE B 123 1 24 HELIX 16 16 GLU B 126 LYS B 154 1 29 HELIX 17 17 SER B 160 VAL B 179 1 20 HELIX 18 18 VAL B 179 GLY B 188 1 10 HELIX 19 19 SER B 195 LYS B 211 1 17 HELIX 20 20 LYS B 211 LYS B 227 1 17 HELIX 21 21 THR C 6 VAL C 31 1 26 HELIX 22 22 HIS C 32 ARG C 34 5 3 HELIX 23 23 LEU C 38 ASN C 62 1 25 HELIX 24 24 TYR C 76 VAL C 95 1 20 HELIX 25 25 GLY C 100 PHE C 123 1 24 HELIX 26 26 GLU C 126 LYS C 154 1 29 HELIX 27 27 SER C 160 VAL C 179 1 20 HELIX 28 28 VAL C 179 GLY C 188 1 10 HELIX 29 29 SER C 195 LYS C 211 1 17 HELIX 30 30 LYS C 211 LYS C 227 1 17 HELIX 31 31 THR D 6 VAL D 31 1 26 HELIX 32 32 HIS D 32 ARG D 34 5 3 HELIX 33 33 LEU D 38 ASN D 62 1 25 HELIX 34 34 TYR D 76 VAL D 95 1 20 HELIX 35 35 GLY D 100 PHE D 123 1 24 HELIX 36 36 GLU D 126 LYS D 154 1 29 HELIX 37 37 SER D 160 VAL D 179 1 20 HELIX 38 38 VAL D 179 GLY D 188 1 10 HELIX 39 39 SER D 195 LYS D 211 1 17 HELIX 40 40 LYS D 211 LYS D 227 1 17 LINK NZ LYS A 211 C15 RET A 301 1555 1555 1.36 LINK NZ LYS B 211 C15 RET B 301 1555 1555 1.36 LINK NZ LYS C 211 C15 RET C 301 1555 1555 1.35 LINK NZ LYS D 211 C15 RET D 301 1555 1555 1.36 SITE 1 AC1 14 TRP A 82 THR A 85 THR A 86 LEU A 89 SITE 2 AC1 14 MET A 114 GLY A 118 PHE A 134 GLY A 137 SITE 3 AC1 14 CYS A 138 GLN A 141 TRP A 178 TYR A 181 SITE 4 AC1 14 TRP A 185 LYS A 211 SITE 1 AC2 7 ALA A 26 GLU A 223 CLR A 402 GLU B 7 SITE 2 AC2 7 MET B 10 ILE B 11 ALA B 18 SITE 1 AC3 7 VAL A 29 PHE A 33 CLR A 401 PHE B 17 SITE 2 AC3 7 ALA B 18 ALA B 21 ALA B 22 SITE 1 AC4 15 TRP B 82 THR B 85 THR B 86 LEU B 89 SITE 2 AC4 15 MET B 114 GLY B 118 PHE B 134 GLY B 137 SITE 3 AC4 15 CYS B 138 GLN B 141 TRP B 178 TYR B 181 SITE 4 AC4 15 TRP B 185 ALA B 210 LYS B 211 SITE 1 AC5 7 GLU A 7 MET A 10 ILE A 11 ALA A 18 SITE 2 AC5 7 ALA B 26 GLU B 223 CLR B 402 SITE 1 AC6 7 PHE A 17 ALA A 18 ALA A 21 ALA A 22 SITE 2 AC6 7 VAL B 29 PHE B 33 CLR B 401 SITE 1 AC7 14 TRP C 82 THR C 85 THR C 86 LEU C 89 SITE 2 AC7 14 MET C 114 GLY C 118 PHE C 134 GLY C 137 SITE 3 AC7 14 CYS C 138 GLN C 141 TRP C 178 TYR C 181 SITE 4 AC7 14 TRP C 185 LYS C 211 SITE 1 AC8 7 ALA C 26 GLU C 223 CLR C 402 GLU D 7 SITE 2 AC8 7 MET D 10 ILE D 11 ALA D 18 SITE 1 AC9 8 VAL C 29 PHE C 33 CLR C 401 PHE D 17 SITE 2 AC9 8 ALA D 18 ALA D 21 ALA D 22 CLR D 402 SITE 1 BC1 14 TRP D 82 THR D 85 THR D 86 LEU D 89 SITE 2 BC1 14 MET D 114 GLY D 118 PHE D 134 GLY D 137 SITE 3 BC1 14 CYS D 138 GLN D 141 TRP D 178 TYR D 181 SITE 4 BC1 14 TRP D 185 LYS D 211 SITE 1 BC2 7 GLU C 7 MET C 10 ILE C 11 ALA C 18 SITE 2 BC2 7 ALA D 26 GLU D 223 CLR D 402 SITE 1 BC3 8 PHE C 17 ALA C 18 ALA C 21 ALA C 22 SITE 2 BC3 8 CLR C 402 VAL D 29 PHE D 33 CLR D 401 CRYST1 84.120 110.487 129.116 90.00 90.00 90.00 P 21 21 21 16 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 0.011888 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009051 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007745 0.00000