1DZE - Header Asymmetric Unit

HEADER BACTERIORHODOPSIN 25-FEB-00 1DZE

TITLE STRUCTURE OF THE M INTERMEDIATE OF BACTERIORHODOPSIN TITLE 2 TRAPPED AT 100K

COMPND MOL_ID: 1; COMPND 2 MOLECULE: BACTERIORHODOPSIN (M INTERMEDIATE); COMPND 3 CHAIN: A; COMPND 4 OTHER_DETAILS: 5 LIPIDS AND 18 WATER MOLECULES

SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HALOBACTERIUM SALINARIUM; SOURCE 3 ORGANISM_TAXID: 2242; SOURCE 4 STRAIN: JW3; SOURCE 5 CELLULAR_LOCATION: CELL MEMBRANE; SOURCE 6 OTHER_DETAILS: HALOBACTERIUM SALINARIUM

KEYWDS BACTERIORHODOPSIN, PROTON PUMP, MEMBRANE PROTEIN, RETINAL KEYWDS 2 PROTEIN, PHOTORECEPTOR, REACTION INTERMEDIATE, KEYWDS 3 HALOBACTERIA, ION PUMP, HELIX, SLIDING

EXPDTA X-RAY DIFFRACTION

AUTHOR K.TAKEDA,Y.MATSUI,H.SATO,T.HINO,E.KANAMORI,H.OKUMURA, AUTHOR 2 T.YAMANE,T.IIZUKA,N.KAMIYA,S.ADACHI,T.KOUYAMA

REVDAT 3 24-FEB-09 1DZE 1 VERSN REVDAT 2 02-SEP-04 1DZE 1 JRNL REVDAT 1 16-AUG-00 1DZE 0

JRNL AUTH K.TAKEDA,Y.MATSUI,N.KAMIYA,S.ADACHI,H.OKUMURA, JRNL AUTH 2 T.KOUYAMA JRNL TITL CRYSTAL STRUCTURE OF THE M INTERMEDIATE OF JRNL TITL 2 BACTERIORHODOPSIN: ALLOSTERIC STRUCTURAL CHANGES JRNL TITL 3 MEDIATED BY SLIDING MOVEMENT OF A TRANSMEMBRANE JRNL TITL 4 HELIX JRNL REF J.MOL.BIOL. V. 341 1023 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 15328615 JRNL DOI 10.1016/J.JMB.2004.06.080

REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.SATO,K.TAKEDA,K.TANI,T.HINO,T.OKADA,M.NAKASAKO, REMARK 1 AUTH 2 N.KAMIYA,T.KOUYAMA REMARK 1 TITL SPECIFIC LIPID-PROTEIN INTERACTIONS IN A NOVEL REMARK 1 TITL 2 HONEYCOMB LATTICE STRUCTURE OF BACTERIORHODOPSIN REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. D55 1251 1999 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 10393291 REMARK 1 DOI 10.1107/S090744499900503X

REMARK 2 REMARK 2 RESOLUTION. 2.5 ANGSTROMS.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.5 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.8 REMARK 3 NUMBER OF REFLECTIONS : 11017 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) : 0.257 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0 REMARK 3 FREE R VALUE TEST SET COUNT : 561 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.61 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 756 REMARK 3 BIN R VALUE (WORKING SET) : 0.371 REMARK 3 BIN FREE R VALUE : 0.437 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 41 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 : 1740 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 247 REMARK 3 SOLVENT ATOMS : 18 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.0 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -19.7 REMARK 3 B22 (A**2) : -19.7 REMARK 3 B33 (A**2) : 13.4 REMARK 3 B12 (A**2) : -9.8 REMARK 3 B13 (A**2) : 0 REMARK 3 B23 (A**2) : 0 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) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.22 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.1 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.22 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) : 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 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : RET_CIS.PAR REMARK 3 PARAMETER FILE 3 : DPG.PAR REMARK 3 PARAMETER FILE 4 : GLC.PAR REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : RET_CIS.TOP REMARK 3 TOPOLOGY FILE 3 : DPG.TOP REMARK 3 TOPOLOGY FILE 4 : GLC.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE C-TERMINAL RESIDUES WERE NOT REMARK 3 SEEN IN THE DENSITY MAPS

REMARK 4 REMARK 4 1DZE COMPLIES WITH FORMAT V. 3.15, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-FEB-00. REMARK 100 THE PDBE ID CODE IS EBI-4664.

REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-NOV-98 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.20 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.70 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11480 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 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 (%) : 91.7 REMARK 200 DATA REDUNDANCY : 14.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 55.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.30400 REMARK 200 <I/SIGMA(I)> 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: PDB ENTRY 1QM8 REMARK 200 REMARK 200 REMARK: DATA WERE COLLECTED USING THE OSCILLATION METHOD

REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE CRYSTALLIZATION CONSISTS OF REMARK 280 TWO STEPS. FIRST, A MIXTURE OF 5 MG/ML PURPLE MEMBRANE, REMARK 280 0.25% OTG, 1 M AMMONIUM SULFATE, 0.16 M NACL, 0.04 M SODIUM REMARK 280 CITRATE (PH5.2) , 0.04% NAN3 WAS INCUBATED AND 15% TREHALOSE REMARK 280 AT 305K FOR 5 DAYS. THIS RESULTED IN THE FORMATION OF SPHERICAL REMARK 280 VESICLES WITH A DIAMETER OF 50 NM. AFTER SEDIMENTAL MATERIALS REMARK 280 WERE REMOVED BY CENTRIFUGATION (4000G X 10 MIN), A SUSPENSION REMARK 280 OF THE SPHERICAL VESICLES WAS COOLED TO 278K AND CONCENTRATED REMARK 280 BY VAPOR DIFFUSION AGAINST A RESERVOIR SOLUTION CONTAINING REMARK 280 2.0 M AMMONIUM SULFATE 0.08M SODIUM CITRATE (PH 5.2) AND REMARK 280 30% TREHALOSE. INCUBATION FOR A COUPLE OF MONTHS YIELDED REMARK 280 HEXAGONAL CRYSTALS.

REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 6 2 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 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z REMARK 290 6555 X-Y,X,Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 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 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 -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 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 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 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 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 GENERATING THE BIOMOLECULE 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 10290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -79.2 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 51.20000 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 88.68100 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 -0.866025 0.000000 102.40000 REMARK 350 BIOMT2 3 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 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 GLN A 1 REMARK 465 ALA A 2 REMARK 465 GLN A 3 REMARK 465 ILE A 4 REMARK 465 THR A 5 REMARK 465 GLY A 231 REMARK 465 GLU A 232 REMARK 465 ALA A 233 REMARK 465 GLU A 234 REMARK 465 ALA A 235 REMARK 465 PRO A 236 REMARK 465 GLU A 237 REMARK 465 PRO A 238 REMARK 465 SER A 239 REMARK 465 ALA A 240 REMARK 465 GLY A 241 REMARK 465 ASP A 242 REMARK 465 GLY A 243 REMARK 465 ALA A 244 REMARK 465 ALA A 245 REMARK 465 ALA A 246 REMARK 465 THR A 247 REMARK 465 SER A 248

REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 227 CG CD NE CZ NH1 NH2 REMARK 470 L1P A 260 C51 C52 C53 C54 C55 C56 C57 REMARK 470 L1P A 260 C58 C59 C60 REMARK 470 L2P A 270 C58 C59 C60 REMARK 470 L3P A 280 C22 C23 C24 C25 C26 C27 C28 REMARK 470 L3P A 280 C29 C30 C51 C52 C53 C54 C55 REMARK 470 L3P A 280 C56 C57 C58 C59 C60 REMARK 470 L4P A 290 O6 C48 C49 C50 C51 C52 C53 REMARK 470 L4P A 290 C54 C55 C56 C57 C58 C59 C60 REMARK 470 L2P A 300 C18 C19 C20 C21 C22 C23 C24 REMARK 470 L2P A 300 C25 C26 C27 C28 C29 C30 C58 REMARK 470 L2P A 300 C59 C60

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 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 ARG A 7 -58.06 -156.68 REMARK 500 SER A 162 31.94 -84.28 REMARK 500 REMARK 500 REMARK: NULL

REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE):

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 L1P A 260 REMARK 610 L2P A 270 REMARK 610 L2P A 300 REMARK 610 L3P A 280 REMARK 610 L4P A 290

REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLC A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MAN A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GAL A 420 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RET A 250 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE L1P A 260 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE L2P A 270 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE L3P A 280 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE L4P A 290 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE L2P A 300

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1C3W RELATED DB: PDB REMARK 900 BACTERIORHODOPSIN/LIPID COMPLEX AT 1.55 A RESOLUTION REMARK 900 (GROUND STATE WILD TYPE "BR") REMARK 900 RELATED ID: 1BRD RELATED DB: PDB REMARK 900 BACTERIORHODOPSIN, HALOBACTERIUM HALOBIUM, ELECTRON DIFFRACTION REMARK 900 RELATED ID: 2BRD RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BACTERIORHODOPSIN IN PURPLE MEMBRANE REMARK 900 RELATED ID: 1BRR RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF THE BACTERIORHODOPSIN TRIMER/LIPID COMPLEX REMARK 900 RELATED ID: 1BAC RELATED DB: PDB REMARK 900 RHODOPSIN (7-HELIX BUNDLE) COMPLEX WITH ALL-TRANS REMARK 900 RETINAL (THEORETICAL MODEL) REMARK 900 RELATED ID: 1BAD RELATED DB: PDB REMARK 900 BACTERIORHODOPSIN (7-HELIX BUNDLE) WITH 13-CIS RETINAL REMARK 900 (THEORETICAL MODEL) REMARK 900 RELATED ID: 1BHA RELATED DB: PDB REMARK 900 BACTERIORHODOPSIN (PROTEOLYTIC FRAGMENT 1 - 71, SOLUBILIZED REMARK 900 IN SDS MICELLES) (NMR, 12 STRUCTURES) REMARK 900 RELATED ID: 1BHB RELATED DB: PDB REMARK 900 BACTERIORHODOPSIN (PROTEOLYTIC FRAGMENT 1 - 71, SOLUBILIZED REMARK 900 IN METHANOL-CHLOROFORM) (NMR, 12 STRUCTURES) REMARK 900 RELATED ID: 1BCT RELATED DB: PDB REMARK 900 BACTERIORHODOPSIN (FRAGMENT 163-231) (NMR, 14 STRUCTURES) REMARK 900 RELATED ID: 1AP9 RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF BACTERIORHODOPSIN FROM MICROCRYSTALS REMARK 900 GROWN IN LIPIDIC CUBIC PHASES REMARK 900 RELATED ID: 1AT9 RELATED DB: PDB REMARK 900 STRUCTURE OF BACTERIORHODOPSIN AT 3.0 ANGSTROM DETERMINED REMARK 900 BY ELECTRON CRYSTALLOGRAPHY REMARK 900 RELATED ID: 1QM8 RELATED DB: PDB REMARK 900 STRUCTURE OF BACTERIORHODOPSIN AT 100 K

DBREF 1DZE A 1 248 UNP P02945 BACR_HALHA 14 261

SEQRES 1 A 248 GLN ALA GLN ILE THR GLY ARG PRO GLU TRP ILE TRP LEU SEQRES 2 A 248 ALA LEU GLY THR ALA LEU MET GLY LEU GLY THR LEU TYR SEQRES 3 A 248 PHE LEU VAL LYS GLY MET GLY VAL SER ASP PRO ASP ALA SEQRES 4 A 248 LYS LYS PHE TYR ALA ILE THR THR LEU VAL PRO ALA ILE SEQRES 5 A 248 ALA PHE THR MET TYR LEU SER MET LEU LEU GLY TYR GLY SEQRES 6 A 248 LEU THR MET VAL PRO PHE GLY GLY GLU GLN ASN PRO ILE SEQRES 7 A 248 TYR TRP ALA ARG TYR ALA ASP TRP LEU PHE THR THR PRO SEQRES 8 A 248 LEU LEU LEU LEU ASP LEU ALA LEU LEU VAL ASP ALA ASP SEQRES 9 A 248 GLN GLY THR ILE LEU ALA LEU VAL GLY ALA ASP GLY ILE SEQRES 10 A 248 MET ILE GLY THR GLY LEU VAL GLY ALA LEU THR LYS VAL SEQRES 11 A 248 TYR SER TYR ARG PHE VAL TRP TRP ALA ILE SER THR ALA SEQRES 12 A 248 ALA MET LEU TYR ILE LEU TYR VAL LEU PHE PHE GLY PHE SEQRES 13 A 248 THR SER LYS ALA GLU SER MET ARG PRO GLU VAL ALA SER SEQRES 14 A 248 THR PHE LYS VAL LEU ARG ASN VAL THR VAL VAL LEU TRP SEQRES 15 A 248 SER ALA TYR PRO VAL VAL TRP LEU ILE GLY SER GLU GLY SEQRES 16 A 248 ALA GLY ILE VAL PRO LEU ASN ILE GLU THR LEU LEU PHE SEQRES 17 A 248 MET VAL LEU ASP VAL SER ALA LYS VAL GLY PHE GLY LEU SEQRES 18 A 248 ILE LEU LEU ARG SER ARG ALA ILE PHE GLY GLU ALA GLU SEQRES 19 A 248 ALA PRO GLU PRO SER ALA GLY ASP GLY ALA ALA ALA THR SEQRES 20 A 248 SER

MODRES 1DZE LYS A 216 LYS RETINAL CHROMOPHORE BINDING

HET GLC A 400 11 HET MAN A 410 11 HET GAL A 420 11 HET RET A 250 20 HET L1P A 260 40 HET L2P A 270 43 HET L3P A 280 40 HET L4P A 290 41 HET L2P A 300 30

HETNAM GLC ALPHA-D-GLUCOSE HETNAM MAN ALPHA-D-MANNOSE HETNAM GAL BETA-D-GALACTOSE HETNAM RET RETINAL HETNAM L1P 3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL HETNAM L2P 2,3-DI-PHYTANYL-GLYCEROL HETNAM L3P 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL- HETNAM 2 L3P 3'-SN-GLYCEROL-1'-PHOSPHATE HETNAM L4P 3-[GLYCEROLYLPHOSPHONYL]-[1,2-DI-PHYTANYL] HETNAM 2 L4P GLYCEROL

FORMUL 2 GLC C6 H12 O6 FORMUL 2 MAN C6 H12 O6 FORMUL 2 GAL C6 H12 O6 FORMUL 3 RET C20 H28 O FORMUL 4 L1P C43 H89 O6 P FORMUL 5 L2P 2(C43 H88 O3) FORMUL 6 L3P C46 H94 O11 P2 2- FORMUL 7 L4P C46 H95 O8 P FORMUL 9 HOH *18(H2 O1)

HELIX 1 1 GLU A 9 MET A 32 1 24 HELIX 2 2 ASP A 38 LEU A 62 1 25 HELIX 3 3 TRP A 80 ASP A 102 1 23 HELIX 4 4 ASP A 104 THR A 128 1 25 HELIX 5 5 TYR A 133 PHE A 154 1 22 HELIX 6 6 GLY A 155 SER A 162 1 8 HELIX 7 7 ARG A 164 SER A 183 1 20 HELIX 8 8 ALA A 184 GLY A 192 1 9 HELIX 9 9 PRO A 200 ARG A 225 1 26

SHEET 1 A 2 LEU A 66 PRO A 70 0 SHEET 2 A 2 GLN A 75 TYR A 79 -1 N ILE A 78 O THR A 67

LINK NZ LYS A 216 C15 RET A 250 1555 1555 1.34 LINK O3 L2P A 270 C1 GLC A 400 1555 1555 1.43 LINK O2 GLC A 400 C1 MAN A 410 1555 1555 1.42 LINK O6 MAN A 410 C1 GAL A 420 1555 1555 1.45

SITE 1 AC1 4 THR A 67 LEU A 127 L2P A 270 MAN A 410 SITE 1 AC2 8 TYR A 64 LEU A 66 THR A 67 TRP A 80 SITE 2 AC2 8 LYS A 129 GLC A 400 GAL A 420 HOH A2018 SITE 1 AC3 1 MAN A 410 SITE 1 AC4 11 TRP A 86 THR A 89 THR A 90 MET A 118 SITE 2 AC4 11 TRP A 138 SER A 141 THR A 142 TRP A 182 SITE 3 AC4 11 TYR A 185 PRO A 186 LYS A 216 SITE 1 AC5 16 THR A 24 LEU A 28 LYS A 40 ALA A 44 SITE 2 AC5 16 ALA A 51 THR A 107 ALA A 110 ALA A 114 SITE 3 AC5 16 ILE A 117 ALA A 144 TYR A 147 TYR A 150 SITE 4 AC5 16 L2P A 300 HOH A2002 HOH A2014 HOH A2015 SITE 1 AC6 13 MET A 56 TYR A 64 TRP A 80 ALA A 84 SITE 2 AC6 13 PHE A 88 LEU A 109 GLY A 113 ILE A 117 SITE 3 AC6 13 GLY A 120 LEU A 123 VAL A 124 LEU A 127 SITE 4 AC6 13 GLC A 400 SITE 1 AC7 12 GLY A 6 TRP A 10 ALA A 14 ALA A 18 SITE 2 AC7 12 MET A 60 LEU A 61 LEU A 62 GLY A 63 SITE 3 AC7 12 TYR A 133 ALA A 139 HOH A2016 HOH A2017 SITE 1 AC8 9 LEU A 22 LEU A 25 TYR A 131 PHE A 135 SITE 2 AC8 9 TRP A 138 ALA A 139 LEU A 190 ALA A 196 SITE 3 AC8 9 GLY A 197 SITE 1 AC9 4 TYR A 26 TYR A 150 LEU A 221 L1P A 260

CRYST1 102.400 102.400 112.300 90.00 90.00 120.00 P 6 2 2 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 0.009766 0.005638 0.000000 0.00000

SCALE2 0.000000 0.011276 0.000000 0.00000

SCALE3 0.000000 0.000000 0.008905 0.00000