PDB Short entry for 3ABW HEADER MEMBRANE PROTEIN 24-DEC-09 3ABW TITLE CRYSTAL STRUCTURE OF PHARAONIS HALORHODOPSIN IN COMPLEX WITH AZIDE ION COMPND MOL_ID: 1; COMPND 2 MOLECULE: HALORHODOPSIN; COMPND 3 CHAIN: A, B, D SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NATRONOMONAS PHARAONIS; SOURCE 3 ORGANISM_TAXID: 348780; SOURCE 4 STRAIN: MK-1; SOURCE 5 OTHER_DETAILS: STRAIN MK-1 WAS A HALORHODOPSIN-OVERPRODUCING MUTANT SOURCE 6 GENERATED FROM TYPE STRAIN D2160T. KEYWDS LIGHT-DRIVEN CHLORIDE ION PUMP, TRIMERIC BACTERIORUBERIN-PROTEIN KEYWDS 2 COMPLEX, RETINAL PROTEIN, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.KOUYAMA,S.KANADA REVDAT 2 01-NOV-23 3ABW 1 REMARK LINK REVDAT 1 02-FEB-11 3ABW 0 JRNL AUTH S.KANADA,T.KOUYAMA JRNL TITL BINDING MODE OF AZIDE ION TO PHARAONIS HALORHODOPSIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 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) (%) : 87.9 REMARK 3 NUMBER OF REFLECTIONS : 80687 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) : 0.242 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.400 REMARK 3 FREE R VALUE TEST SET COUNT : 4064 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3718 REMARK 3 BIN FREE R VALUE : 0.3854 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 295 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 : 5889 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 303 REMARK 3 SOLVENT ATOMS : 128 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.91400 REMARK 3 B22 (A**2) : -1.36800 REMARK 3 B33 (A**2) : -1.54600 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -9.53200 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.27 REMARK 3 ESD FROM SIGMAA (A) : 0.29 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) : 0.31 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.27 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL 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) : 1.239 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.809 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.816 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.434 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 99.10 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 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : SO4.PARAM REMARK 3 PARAMETER FILE 5 : TRA.PARAM REMARK 3 PARAMETER FILE 6 : BRU.PARAM REMARK 3 PARAMETER FILE 7 : L1P.PARAM REMARK 3 PARAMETER FILE 8 : L2P.PARAM REMARK 3 PARAMETER FILE 9 : L3P.PARAM REMARK 3 PARAMETER FILE 10 : AZI.PARAM REMARK 3 PARAMETER FILE 11 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 TOPOLOGY FILE 7 : NULL REMARK 3 TOPOLOGY FILE 8 : NULL REMARK 3 TOPOLOGY FILE 9 : NULL REMARK 3 TOPOLOGY FILE 10 : NULL REMARK 3 TOPOLOGY FILE 11 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3ABW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-JAN-10. REMARK 100 THE DEPOSITION ID IS D_1000029062. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-DEC-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 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 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 80799 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 38.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.0 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : 0.07100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.52600 REMARK 200 R SYM FOR SHELL (I) : 0.52600 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200 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 3A7K REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: A DROP CONTAINING 2MG/ML REMARK 280 HALORHODOPSIN, 1M AMMONIUM SULFATE, 0.16M NACL, 0.04M NA-CITRATE, REMARK 280 0.04% NAN3,5MG/ML NONYL GLUCOSIDE WAS CONCENTRATED BY VAPOR REMARK 280 DIFFUSIONAGAINST A RESERVE SOLUTION CONTAINING 2.9 M AMMONIUM REMARK 280 SULFATE, 0.04M NA-CITRATE, PH 6, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 288K. AFTER THE CRYSTAL GREW, THE MOTHER SOLUTION REMARK 280 WAS EXCHANGED WITH A SOLUTION CONTAINING 3M AMMONIUM SULFATE, REMARK 280 200 MM NA-N3, 100 MM HEPES (PH7) AND 30 % TREHALOSE. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 76.04500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.39500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 76.04500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 49.39500 REMARK 290 SMTRY3 4 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 MET A 1 REMARK 465 THR A 2 REMARK 465 GLU A 3 REMARK 465 THR A 4 REMARK 465 LEU A 5 REMARK 465 PRO A 6 REMARK 465 PRO A 7 REMARK 465 VAL A 8 REMARK 465 THR A 9 REMARK 465 GLU A 10 REMARK 465 SER A 11 REMARK 465 ALA A 12 REMARK 465 VAL A 13 REMARK 465 ALA A 14 REMARK 465 LEU A 15 REMARK 465 GLN A 16 REMARK 465 ALA A 17 REMARK 465 ILE A 278 REMARK 465 LEU A 279 REMARK 465 ASP A 280 REMARK 465 VAL A 281 REMARK 465 PRO A 282 REMARK 465 SER A 283 REMARK 465 ALA A 284 REMARK 465 SER A 285 REMARK 465 GLY A 286 REMARK 465 ALA A 287 REMARK 465 PRO A 288 REMARK 465 ALA A 289 REMARK 465 ASP A 290 REMARK 465 ASP A 291 REMARK 465 MET B 1 REMARK 465 THR B 2 REMARK 465 GLU B 3 REMARK 465 THR B 4 REMARK 465 LEU B 5 REMARK 465 PRO B 6 REMARK 465 PRO B 7 REMARK 465 VAL B 8 REMARK 465 THR B 9 REMARK 465 GLU B 10 REMARK 465 SER B 11 REMARK 465 ALA B 12 REMARK 465 VAL B 13 REMARK 465 ALA B 14 REMARK 465 LEU B 15 REMARK 465 GLN B 16 REMARK 465 ALA B 17 REMARK 465 SER B 277 REMARK 465 ILE B 278 REMARK 465 LEU B 279 REMARK 465 ASP B 280 REMARK 465 VAL B 281 REMARK 465 PRO B 282 REMARK 465 SER B 283 REMARK 465 ALA B 284 REMARK 465 SER B 285 REMARK 465 GLY B 286 REMARK 465 ALA B 287 REMARK 465 PRO B 288 REMARK 465 ALA B 289 REMARK 465 ASP B 290 REMARK 465 ASP B 291 REMARK 465 MET D 1 REMARK 465 THR D 2 REMARK 465 GLU D 3 REMARK 465 THR D 4 REMARK 465 LEU D 5 REMARK 465 PRO D 6 REMARK 465 PRO D 7 REMARK 465 VAL D 8 REMARK 465 THR D 9 REMARK 465 GLU D 10 REMARK 465 SER D 11 REMARK 465 ALA D 12 REMARK 465 VAL D 13 REMARK 465 ALA D 14 REMARK 465 LEU D 15 REMARK 465 GLN D 16 REMARK 465 ALA D 17 REMARK 465 SER D 277 REMARK 465 ILE D 278 REMARK 465 LEU D 279 REMARK 465 ASP D 280 REMARK 465 VAL D 281 REMARK 465 PRO D 282 REMARK 465 SER D 283 REMARK 465 ALA D 284 REMARK 465 SER D 285 REMARK 465 GLY D 286 REMARK 465 ALA D 287 REMARK 465 PRO D 288 REMARK 465 ALA D 289 REMARK 465 ASP D 290 REMARK 465 ASP D 291 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 HOH A 600 O HOH A 600 2656 1.79 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 30 -1.00 72.45 REMARK 500 MET A 108 78.19 60.80 REMARK 500 LYS A 256 -69.97 -109.02 REMARK 500 ASN B 30 -17.15 78.08 REMARK 500 MET B 108 107.68 72.18 REMARK 500 VAL B 196 -65.62 -98.93 REMARK 500 ASN D 30 -7.17 69.84 REMARK 500 VAL D 107 -44.06 -134.26 REMARK 500 MET D 108 103.08 64.62 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 300 REMARK 610 L3P A 310 REMARK 610 L3P A 313 REMARK 610 L3P A 317 REMARK 610 L3P B 311 REMARK 610 L3P B 315 REMARK 610 L3P B 318 REMARK 610 22B B 300 REMARK 610 L3P D 312 REMARK 610 L3P D 314 REMARK 610 L3P D 316 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 292 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 22B A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE L3P A 313 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE L3P A 317 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RET B 292 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE L3P B 311 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE L3P B 315 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE L3P B 318 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AZI A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RET D 292 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE L3P D 312 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE L3P D 314 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 22B B 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE L3P D 316 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AZI B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AZI D 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3A7K RELATED DB: PDB REMARK 900 STRUCTURE OF PHARAONIS HALORHODOPSIN WITH CHLORIDE ION DBREF 3ABW A 1 291 UNP Q3ITX1 Q3ITX1_NATPD 1 291 DBREF 3ABW B 1 291 UNP Q3ITX1 Q3ITX1_NATPD 1 291 DBREF 3ABW D 1 291 UNP Q3ITX1 Q3ITX1_NATPD 1 291 SEQRES 1 A 291 MET THR GLU THR LEU PRO PRO VAL THR GLU SER ALA VAL SEQRES 2 A 291 ALA LEU GLN ALA GLU VAL THR GLN ARG GLU LEU PHE GLU SEQRES 3 A 291 PHE VAL LEU ASN ASP PRO LEU LEU ALA SER SER LEU TYR SEQRES 4 A 291 ILE ASN ILE ALA LEU ALA GLY LEU SER ILE LEU LEU PHE SEQRES 5 A 291 VAL PHE MET THR ARG GLY LEU ASP ASP PRO ARG ALA LYS SEQRES 6 A 291 LEU ILE ALA VAL SER THR ILE LEU VAL PRO VAL VAL SER SEQRES 7 A 291 ILE ALA SER TYR THR GLY LEU ALA SER GLY LEU THR ILE SEQRES 8 A 291 SER VAL LEU GLU MET PRO ALA GLY HIS PHE ALA GLU GLY SEQRES 9 A 291 SER SER VAL MET LEU GLY GLY GLU GLU VAL ASP GLY VAL SEQRES 10 A 291 VAL THR MET TRP GLY ARG TYR LEU THR TRP ALA LEU SER SEQRES 11 A 291 THR PRO MET ILE LEU LEU ALA LEU GLY LEU LEU ALA GLY SEQRES 12 A 291 SER ASN ALA THR LYS LEU PHE THR ALA ILE THR PHE ASP SEQRES 13 A 291 ILE ALA MET CYS VAL THR GLY LEU ALA ALA ALA LEU THR SEQRES 14 A 291 THR SER SER HIS LEU MET ARG TRP PHE TRP TYR ALA ILE SEQRES 15 A 291 SER CYS ALA CYS PHE ILE VAL VAL LEU TYR ILE LEU LEU SEQRES 16 A 291 VAL GLU TRP ALA GLN ASP ALA LYS ALA ALA GLY THR ALA SEQRES 17 A 291 ASP ILE PHE SER THR LEU LYS LEU LEU THR VAL VAL MET SEQRES 18 A 291 TRP LEU GLY TYR PRO ILE VAL TRP ALA LEU GLY VAL GLU SEQRES 19 A 291 GLY VAL ALA VAL LEU PRO VAL GLY TYR THR SER TRP ALA SEQRES 20 A 291 TYR SER ALA LEU ASP ILE VAL ALA LYS TYR ILE PHE ALA SEQRES 21 A 291 PHE LEU LEU LEU ASN TYR LEU THR SER ASN GLU GLY VAL SEQRES 22 A 291 VAL SER GLY SER ILE LEU ASP VAL PRO SER ALA SER GLY SEQRES 23 A 291 ALA PRO ALA ASP ASP SEQRES 1 B 291 MET THR GLU THR LEU PRO PRO VAL THR GLU SER ALA VAL SEQRES 2 B 291 ALA LEU GLN ALA GLU VAL THR GLN ARG GLU LEU PHE GLU SEQRES 3 B 291 PHE VAL LEU ASN ASP PRO LEU LEU ALA SER SER LEU TYR SEQRES 4 B 291 ILE ASN ILE ALA LEU ALA GLY LEU SER ILE LEU LEU PHE SEQRES 5 B 291 VAL PHE MET THR ARG GLY LEU ASP ASP PRO ARG ALA LYS SEQRES 6 B 291 LEU ILE ALA VAL SER THR ILE LEU VAL PRO VAL VAL SER SEQRES 7 B 291 ILE ALA SER TYR THR GLY LEU ALA SER GLY LEU THR ILE SEQRES 8 B 291 SER VAL LEU GLU MET PRO ALA GLY HIS PHE ALA GLU GLY SEQRES 9 B 291 SER SER VAL MET LEU GLY GLY GLU GLU VAL ASP GLY VAL SEQRES 10 B 291 VAL THR MET TRP GLY ARG TYR LEU THR TRP ALA LEU SER SEQRES 11 B 291 THR PRO MET ILE LEU LEU ALA LEU GLY LEU LEU ALA GLY SEQRES 12 B 291 SER ASN ALA THR LYS LEU PHE THR ALA ILE THR PHE ASP SEQRES 13 B 291 ILE ALA MET CYS VAL THR GLY LEU ALA ALA ALA LEU THR SEQRES 14 B 291 THR SER SER HIS LEU MET ARG TRP PHE TRP TYR ALA ILE SEQRES 15 B 291 SER CYS ALA CYS PHE ILE VAL VAL LEU TYR ILE LEU LEU SEQRES 16 B 291 VAL GLU TRP ALA GLN ASP ALA LYS ALA ALA GLY THR ALA SEQRES 17 B 291 ASP ILE PHE SER THR LEU LYS LEU LEU THR VAL VAL MET SEQRES 18 B 291 TRP LEU GLY TYR PRO ILE VAL TRP ALA LEU GLY VAL GLU SEQRES 19 B 291 GLY VAL ALA VAL LEU PRO VAL GLY TYR THR SER TRP ALA SEQRES 20 B 291 TYR SER ALA LEU ASP ILE VAL ALA LYS TYR ILE PHE ALA SEQRES 21 B 291 PHE LEU LEU LEU ASN TYR LEU THR SER ASN GLU GLY VAL SEQRES 22 B 291 VAL SER GLY SER ILE LEU ASP VAL PRO SER ALA SER GLY SEQRES 23 B 291 ALA PRO ALA ASP ASP SEQRES 1 D 291 MET THR GLU THR LEU PRO PRO VAL THR GLU SER ALA VAL SEQRES 2 D 291 ALA LEU GLN ALA GLU VAL THR GLN ARG GLU LEU PHE GLU SEQRES 3 D 291 PHE VAL LEU ASN ASP PRO LEU LEU ALA SER SER LEU TYR SEQRES 4 D 291 ILE ASN ILE ALA LEU ALA GLY LEU SER ILE LEU LEU PHE SEQRES 5 D 291 VAL PHE MET THR ARG GLY LEU ASP ASP PRO ARG ALA LYS SEQRES 6 D 291 LEU ILE ALA VAL SER THR ILE LEU VAL PRO VAL VAL SER SEQRES 7 D 291 ILE ALA SER TYR THR GLY LEU ALA SER GLY LEU THR ILE SEQRES 8 D 291 SER VAL LEU GLU MET PRO ALA GLY HIS PHE ALA GLU GLY SEQRES 9 D 291 SER SER VAL MET LEU GLY GLY GLU GLU VAL ASP GLY VAL SEQRES 10 D 291 VAL THR MET TRP GLY ARG TYR LEU THR TRP ALA LEU SER SEQRES 11 D 291 THR PRO MET ILE LEU LEU ALA LEU GLY LEU LEU ALA GLY SEQRES 12 D 291 SER ASN ALA THR LYS LEU PHE THR ALA ILE THR PHE ASP SEQRES 13 D 291 ILE ALA MET CYS VAL THR GLY LEU ALA ALA ALA LEU THR SEQRES 14 D 291 THR SER SER HIS LEU MET ARG TRP PHE TRP TYR ALA ILE SEQRES 15 D 291 SER CYS ALA CYS PHE ILE VAL VAL LEU TYR ILE LEU LEU SEQRES 16 D 291 VAL GLU TRP ALA GLN ASP ALA LYS ALA ALA GLY THR ALA SEQRES 17 D 291 ASP ILE PHE SER THR LEU LYS LEU LEU THR VAL VAL MET SEQRES 18 D 291 TRP LEU GLY TYR PRO ILE VAL TRP ALA LEU GLY VAL GLU SEQRES 19 D 291 GLY VAL ALA VAL LEU PRO VAL GLY TYR THR SER TRP ALA SEQRES 20 D 291 TYR SER ALA LEU ASP ILE VAL ALA LYS TYR ILE PHE ALA SEQRES 21 D 291 PHE LEU LEU LEU ASN TYR LEU THR SER ASN GLU GLY VAL SEQRES 22 D 291 VAL SER GLY SER ILE LEU ASP VAL PRO SER ALA SER GLY SEQRES 23 D 291 ALA PRO ALA ASP ASP HET RET A 292 20 HET 22B A 300 27 HET L3P A 310 20 HET L3P A 313 20 HET L3P A 317 20 HET AZI A 401 3 HET RET B 292 20 HET L3P B 311 20 HET L3P B 315 20 HET L3P B 318 20 HET 22B B 300 27 HET AZI B 401 3 HET RET D 292 20 HET L3P D 312 20 HET L3P D 314 20 HET L3P D 316 20 HET AZI D 401 3 HETNAM RET RETINAL HETNAM 22B BACTERIORUBERIN HETNAM L3P 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN- HETNAM 2 L3P GLYCEROL-1'-PHOSPHATE HETNAM AZI AZIDE ION FORMUL 4 RET 3(C20 H28 O) FORMUL 5 22B 2(C50 H76 O4) FORMUL 6 L3P 9(C46 H94 O11 P2 2-) FORMUL 9 AZI 3(N3 1-) FORMUL 21 HOH *128(H2 O) HELIX 1 1 THR A 20 LEU A 29 1 10 HELIX 2 2 ASP A 31 THR A 56 1 26 HELIX 3 3 ASP A 61 SER A 87 1 27 HELIX 4 4 TRP A 121 ALA A 142 1 22 HELIX 5 5 ASN A 145 THR A 169 1 25 HELIX 6 6 SER A 172 VAL A 196 1 25 HELIX 7 7 VAL A 196 GLY A 206 1 11 HELIX 8 8 THR A 207 GLY A 232 1 26 HELIX 9 9 PRO A 240 LYS A 256 1 17 HELIX 10 10 LYS A 256 THR A 268 1 13 HELIX 11 11 ASN A 270 GLY A 276 1 7 HELIX 12 12 THR B 20 LEU B 29 1 10 HELIX 13 13 ASP B 31 ARG B 57 1 27 HELIX 14 14 ASP B 61 SER B 87 1 27 HELIX 15 15 MET B 120 ALA B 142 1 23 HELIX 16 16 ASN B 145 THR B 169 1 25 HELIX 17 17 SER B 172 VAL B 196 1 25 HELIX 18 18 VAL B 196 ALA B 205 1 10 HELIX 19 19 THR B 207 GLY B 232 1 26 HELIX 20 20 PRO B 240 LYS B 256 1 17 HELIX 21 21 LYS B 256 ASN B 270 1 15 HELIX 22 22 ASN B 270 GLY B 276 1 7 HELIX 23 23 THR D 20 LEU D 29 1 10 HELIX 24 24 ASP D 31 THR D 56 1 26 HELIX 25 25 ASP D 61 SER D 87 1 27 HELIX 26 26 MET D 120 ALA D 142 1 23 HELIX 27 27 ASN D 145 THR D 169 1 25 HELIX 28 28 SER D 172 VAL D 196 1 25 HELIX 29 29 GLU D 197 ALA D 205 1 9 HELIX 30 30 THR D 207 GLY D 232 1 26 HELIX 31 31 PRO D 240 LYS D 256 1 17 HELIX 32 32 LYS D 256 ASN D 270 1 15 HELIX 33 33 ASN D 270 SER D 275 1 6 SHEET 1 A 2 SER A 92 LEU A 94 0 SHEET 2 A 2 VAL A 117 THR A 119 -1 O THR A 119 N SER A 92 SHEET 1 B 2 SER B 92 LEU B 94 0 SHEET 2 B 2 VAL B 117 THR B 119 -1 O THR B 119 N SER B 92 SHEET 1 C 2 SER D 92 LEU D 94 0 SHEET 2 C 2 VAL D 117 THR D 119 -1 O THR D 119 N SER D 92 LINK NZ LYS A 256 C15 RET A 292 1555 1555 1.35 LINK NZ LYS B 256 C15 RET B 292 1555 1555 1.35 LINK NZ LYS D 256 C15 RET D 292 1555 1555 1.35 SITE 1 AC1 11 TRP A 127 THR A 131 MET A 159 TYR A 180 SITE 2 AC1 11 SER A 183 PHE A 187 TRP A 222 TYR A 225 SITE 3 AC1 11 PRO A 226 ASP A 252 LYS A 256 SITE 1 AC2 8 ILE A 49 THR A 56 LYS A 65 ILE A 72 SITE 2 AC2 8 PHE D 155 ALA D 185 VAL D 189 ILE D 193 SITE 1 AC3 5 VAL A 93 TRP A 121 LEU A 164 LEU A 168 SITE 2 AC3 5 L3P B 311 SITE 1 AC4 6 ALA A 80 LEU A 89 THR A 126 VAL D 161 SITE 2 AC4 6 THR D 162 TRP D 179 SITE 1 AC5 11 TRP B 127 THR B 131 MET B 159 TYR B 180 SITE 2 AC5 11 SER B 183 PHE B 187 TRP B 222 TYR B 225 SITE 3 AC5 11 PRO B 226 ASP B 252 LYS B 256 SITE 1 AC6 8 VAL A 161 LEU A 168 L3P A 313 GLN B 21 SITE 2 AC6 8 ALA B 80 LEU B 89 TRP B 121 THR B 126 SITE 1 AC7 4 SER B 92 VAL B 93 TRP B 121 LEU B 164 SITE 1 AC8 2 PHE B 150 VAL D 77 SITE 1 AC9 6 SER A 78 SER A 81 THR A 126 SER A 130 SITE 2 AC9 6 LYS A 256 HOH A 504 SITE 1 BC1 10 TRP D 127 THR D 131 MET D 159 TYR D 180 SITE 2 BC1 10 SER D 183 PHE D 187 TRP D 222 TYR D 225 SITE 3 BC1 10 PRO D 226 LYS D 256 SITE 1 BC2 2 ILE D 153 THR D 154 SITE 1 BC3 10 VAL B 161 LEU B 164 LEU B 168 VAL D 19 SITE 2 BC3 10 GLN D 21 ALA D 80 LEU D 89 TRP D 121 SITE 3 BC3 10 THR D 126 HOH D 521 SITE 1 BC4 7 THR A 147 PHE A 155 VAL A 189 ILE B 49 SITE 2 BC4 7 VAL B 53 THR B 56 ILE B 72 SITE 1 BC5 1 LEU D 125 SITE 1 BC6 5 SER B 78 SER B 81 THR B 126 SER B 130 SITE 2 BC6 5 LYS B 256 SITE 1 BC7 6 SER D 78 SER D 81 THR D 126 TRP D 127 SITE 2 BC7 6 SER D 130 LYS D 256 CRYST1 152.090 98.790 100.140 90.00 127.85 90.00 C 1 2 1 12 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 0.006575 0.000000 0.005109 0.00000 SCALE2 0.000000 0.010122 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012647 0.00000