HEADER TRANSPORT PROTEIN 27-JAN-14 3WQJ TITLE CRYSTAL STRUCTURE OF ARCHAERHODOPSIN-2 AT 1.8 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: ARCHAERHODOPSIN-2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: AR 2 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HALOBACTERIUM; SOURCE 3 ORGANISM_TAXID: 29285; SOURCE 4 STRAIN: AUS-2 KEYWDS 7 TRANS-MEMBRANE HELICES, LIGHT-DRIVEN PROTON PUMP, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.KOUYAMA REVDAT 4 06-NOV-24 3WQJ 1 REMARK REVDAT 3 08-NOV-23 3WQJ 1 REMARK REVDAT 2 01-JAN-20 3WQJ 1 JRNL LINK REVDAT 1 15-OCT-14 3WQJ 0 JRNL AUTH T.KOUYAMA,R.FUJII,S.KANADA,T.NAKANISHI,S.K.CHAN,M.MURAKAMI JRNL TITL STRUCTURE OF ARCHAERHODOPSIN-2 AT 1.8 ANGSTROM RESOLUTION. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 70 2692 2014 JRNL REFN ESSN 1399-0047 JRNL PMID 25286853 JRNL DOI 10.1107/S1399004714017313 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.5 REMARK 3 NUMBER OF REFLECTIONS : 21701 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) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1105 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1629 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.26 REMARK 3 BIN R VALUE (WORKING SET) : 0.3050 REMARK 3 BIN FREE R VALUE SET COUNT : 103 REMARK 3 BIN FREE R VALUE : 0.3380 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1810 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 180 REMARK 3 SOLVENT ATOMS : 51 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.15 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.94000 REMARK 3 B22 (A**2) : 0.94000 REMARK 3 B33 (A**2) : -1.41000 REMARK 3 B12 (A**2) : 0.47000 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): 0.162 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.144 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.093 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.996 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2025 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2742 ; 2.033 ; 2.049 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 233 ; 4.917 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 63 ;30.439 ;21.587 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 291 ;17.503 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;19.248 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 339 ; 0.221 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1400 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1152 ; 0.983 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1851 ; 1.704 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 873 ; 2.729 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 891 ; 4.205 ; 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 : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: U VALUES: REFINED INDIVIDUALLY REMARK 4 REMARK 4 3WQJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-FEB-14. REMARK 100 THE DEPOSITION ID IS D_1000096666. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JAN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL38B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI (111) DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21944 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 45.110 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.100 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.3 REMARK 200 DATA REDUNDANCY : 8.800 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : 0.05400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 28.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.00 REMARK 200 R MERGE FOR SHELL (I) : 0.50000 REMARK 200 R SYM FOR SHELL (I) : 0.50000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 2EI4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.8M AMMONIUM SULFATE, 0.1M HEPES, REMARK 280 0.32% NONYLGLUCOSIDE, 8% TREHALOSE, PH 7.0, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 283K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 0.00000 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 0.00000 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 0.00000 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 0.00000 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 SMTRY1 7 1.000000 0.000000 0.000000 31.36950 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 18.11119 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 110.48800 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 31.36950 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 18.11119 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 110.48800 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 31.36950 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 18.11119 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 110.48800 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 31.36950 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 18.11119 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 110.48800 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 31.36950 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 18.11119 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 110.48800 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 31.36950 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 18.11119 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 110.48800 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 36.22238 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 220.97600 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 36.22238 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 220.97600 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 36.22238 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 220.97600 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 36.22238 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 220.97600 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 36.22238 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 220.97600 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 36.22238 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 220.97600 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 23960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -178.0 KCAL/MOL 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 BIOMT1 2 -0.500000 -0.866025 0.000000 31.36950 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 54.33357 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -31.36950 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 54.33357 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 C7 SQL A 308 LIES ON A SPECIAL POSITION. REMARK 375 C12 SQL A 308 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -5 REMARK 465 ASP A -4 REMARK 465 PRO A -3 REMARK 465 ILE A -2 REMARK 465 ALA A -1 REMARK 465 LEU A 0 REMARK 465 LEU A 235 REMARK 465 GLY A 236 REMARK 465 GLU A 237 REMARK 465 THR A 238 REMARK 465 GLU A 239 REMARK 465 ALA A 240 REMARK 465 PRO A 241 REMARK 465 GLU A 242 REMARK 465 PRO A 243 REMARK 465 SER A 244 REMARK 465 ALA A 245 REMARK 465 GLY A 246 REMARK 465 ALA A 247 REMARK 465 ASP A 248 REMARK 465 ALA A 249 REMARK 465 SER A 250 REMARK 465 ALA A 251 REMARK 465 ALA A 252 REMARK 465 ASP A 253 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 ARG A 11 NE - CZ - NH1 ANGL. DEV. = -8.6 DEGREES REMARK 500 ARG A 11 NE - CZ - NH2 ANGL. DEV. = 6.4 DEGREES REMARK 500 LEU A 92 CB - CG - CD1 ANGL. DEV. = 11.1 DEGREES REMARK 500 LEU A 92 CB - CG - CD2 ANGL. DEV. = -15.2 DEGREES REMARK 500 LEU A 98 CB - CG - CD1 ANGL. DEV. = 10.6 DEGREES REMARK 500 LEU A 99 CB - CG - CD1 ANGL. DEV. = 11.3 DEGREES 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 THR A 159 -80.34 -114.57 REMARK 500 ALA A 233 -17.76 -46.42 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 22B A 302 REMARK 610 L3P A 305 REMARK 610 L4P A 306 REMARK 610 L4P A 307 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 22B A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE L2P A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE L3P A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE L4P A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE L4P A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SQL A 308 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2EI4 RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN THE P321 CRYSTAL REMARK 900 RELATED ID: 2Z55 RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN THE P6(3) CRYSTAL REMARK 900 RELATED ID: 1VGO RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN THE P4(3)2(1)2 CRYSTAL REMARK 900 RELATED ID: 1UAZ RELATED DB: PDB REMARK 900 STRUCTURE OF ARCHAERHODOPSIN-1 IN THE C222(1) CRYSTAL REMARK 900 RELATED ID: 1IW6 RELATED DB: PDB REMARK 900 STRUCTURE OF BACTERIORHODOPSIN IN THE P622 CRYSTAL REMARK 900 RELATED ID: 4FBZ RELATED DB: PDB REMARK 900 STRUCTURE OF DELTARHODOPSIN IN THE R32 CRYSTAL DBREF 3WQJ A -5 253 UNP P29563 BACR2_HALS2 1 259 SEQRES 1 A 259 MET ASP PRO ILE ALA LEU GLN ALA GLY PHE ASP LEU LEU SEQRES 2 A 259 ASN ASP GLY ARG PRO GLU THR LEU TRP LEU GLY ILE GLY SEQRES 3 A 259 THR LEU LEU MET LEU ILE GLY THR PHE TYR PHE ILE ALA SEQRES 4 A 259 ARG GLY TRP GLY VAL THR ASP LYS GLU ALA ARG GLU TYR SEQRES 5 A 259 TYR ALA ILE THR ILE LEU VAL PRO GLY ILE ALA SER ALA SEQRES 6 A 259 ALA TYR LEU ALA MET PHE PHE GLY ILE GLY VAL THR GLU SEQRES 7 A 259 VAL GLU LEU ALA SER GLY THR VAL LEU ASP ILE TYR TYR SEQRES 8 A 259 ALA ARG TYR ALA ASP TRP LEU PHE THR THR PRO LEU LEU SEQRES 9 A 259 LEU LEU ASP LEU ALA LEU LEU ALA LYS VAL ASP ARG VAL SEQRES 10 A 259 THR ILE GLY THR LEU ILE GLY VAL ASP ALA LEU MET ILE SEQRES 11 A 259 VAL THR GLY LEU ILE GLY ALA LEU SER LYS THR PRO LEU SEQRES 12 A 259 ALA ARG TYR THR TRP TRP LEU PHE SER THR ILE ALA PHE SEQRES 13 A 259 LEU PHE VAL LEU TYR TYR LEU LEU THR SER LEU ARG SER SEQRES 14 A 259 ALA ALA ALA LYS ARG SER GLU GLU VAL ARG SER THR PHE SEQRES 15 A 259 ASN THR LEU THR ALA LEU VAL ALA VAL LEU TRP THR ALA SEQRES 16 A 259 TYR PRO ILE LEU TRP ILE VAL GLY THR GLU GLY ALA GLY SEQRES 17 A 259 VAL VAL GLY LEU GLY ILE GLU THR LEU ALA PHE MET VAL SEQRES 18 A 259 LEU ASP VAL THR ALA LYS VAL GLY PHE GLY PHE VAL LEU SEQRES 19 A 259 LEU ARG SER ARG ALA ILE LEU GLY GLU THR GLU ALA PRO SEQRES 20 A 259 GLU PRO SER ALA GLY ALA ASP ALA SER ALA ALA ASP HET RET A 301 20 HET 22B A 302 27 HET SO4 A 303 5 HET L2P A 304 46 HET L3P A 305 20 HET L4P A 306 16 HET L4P A 307 16 HET SQL A 308 30 HETNAM RET RETINAL HETNAM 22B BACTERIORUBERIN HETNAM SO4 SULFATE ION HETNAM L2P 2,3-DI-PHYTANYL-GLYCEROL HETNAM L3P 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN- HETNAM 2 L3P GLYCEROL-1'-PHOSPHATE HETNAM L4P 3-[GLYCEROLYLPHOSPHONYL]-[1,2-DI-PHYTANYL]GLYCEROL HETNAM SQL (6E,10E,14E,18E)-2,6,10,15,19,23-HEXAMETHYLTETRACOSA-2, HETNAM 2 SQL 6,10,14,18,22-HEXAENE HETSYN L2P 1,2-DI-1-(3,7,11,15-TETRAMETHYL-HEXADECANE)-SN-GLYCEROL HETSYN L4P 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN- HETSYN 2 L4P GLYCEROL HETSYN SQL SQUALENE FORMUL 2 RET C20 H28 O FORMUL 3 22B C50 H76 O4 FORMUL 4 SO4 O4 S 2- FORMUL 5 L2P C43 H88 O3 FORMUL 6 L3P C46 H94 O11 P2 2- FORMUL 7 L4P 2(C46 H95 O8 P) FORMUL 9 SQL C30 H50 FORMUL 10 HOH *51(H2 O) HELIX 1 1 GLU A 13 TRP A 36 1 24 HELIX 2 2 ASP A 40 GLY A 67 1 28 HELIX 3 3 TYR A 85 LYS A 107 1 23 HELIX 4 4 ASP A 109 SER A 133 1 25 HELIX 5 5 THR A 135 THR A 159 1 25 HELIX 6 6 THR A 159 ALA A 166 1 8 HELIX 7 7 SER A 169 GLY A 197 1 29 HELIX 8 8 GLY A 205 ARG A 230 1 26 SHEET 1 A 2 THR A 71 GLU A 74 0 SHEET 2 A 2 VAL A 80 ILE A 83 -1 O ILE A 83 N THR A 71 LINK NZ LYS A 221 C15 RET A 301 1555 1555 1.46 SITE 1 AC1 12 TRP A 91 THR A 95 MET A 123 TRP A 143 SITE 2 AC1 12 SER A 146 THR A 147 TRP A 187 TYR A 190 SITE 3 AC1 12 PRO A 191 TRP A 194 ASP A 217 LYS A 221 SITE 1 AC2 11 PHE A 29 GLY A 35 ARG A 44 ALA A 48 SITE 2 AC2 11 ILE A 51 THR A 112 THR A 115 VAL A 119 SITE 3 AC2 11 PHE A 145 TYR A 156 SER A 160 SITE 1 AC3 9 PHE A 66 GLY A 67 ILE A 68 SER A 133 SITE 2 AC3 9 LYS A 134 THR A 135 ALA A 138 HOH A 409 SITE 3 AC3 9 HOH A 428 SITE 1 AC4 8 ALA A 59 ALA A 63 TYR A 85 ALA A 89 SITE 2 AC4 8 LEU A 92 VAL A 125 LEU A 128 SQL A 308 SITE 1 AC5 1 ILE A 26 SITE 1 AC6 1 ILE A 113 SITE 1 AC7 4 GLU A 45 ALA A 48 ILE A 49 ARG A 110 SITE 1 AC8 1 L2P A 304 CRYST1 62.739 62.739 331.464 90.00 90.00 120.00 H 3 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 0.015939 0.009202 0.000000 0.00000 SCALE2 0.000000 0.018405 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003017 0.00000