2ZZL - Header Asymmetric Unit

HEADER PROTON TRANSPORT 18-FEB-09 2ZZL

TITLE STRUCTURE OF BACTERIORHODOPSIN'S M INTERMEDIATE AT PH 7

COMPND MOL_ID: 1; COMPND 2 MOLECULE: BACTERIORHODOPSIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BR

SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HALOBACTERIUM SALINARUM; SOURCE 3 ORGANISM_TAXID: 2242; SOURCE 4 STRAIN: JW3

KEYWDS RETINAL, PROTEIN-LIPID COMPLEX, REACTION INTERMEDIATE, CELL KEYWDS 2 MEMBRANE, CHROMOPHORE, HYDROGEN ION TRANSPORT, ION KEYWDS 3 TRANSPORT, MEMBRANE, PHOTORECEPTOR PROTEIN, PYRROLIDONE KEYWDS 4 CARBOXYLIC ACID, RECEPTOR, RETINAL PROTEIN, SENSORY KEYWDS 5 TRANSDUCTION, TRANSMEMBRANE, TRANSPORT, PROTON TRANSPORT

EXPDTA X-RAY DIFFRACTION

AUTHOR M.YAMAMOTO,T.KOUYAMA

REVDAT 1 06-OCT-09 2ZZL 0

JRNL AUTH M.YAMAMOTO,N.HAYAKAWA,M.MURAKAMI,T.KOUYAMA JRNL TITL CRYSTAL STRUCTURES OF DIFFERENT SUBSTATES OF JRNL TITL 2 BACTERIORHODOPSIN'S M INTERMEDIATE AT VARIOUS PH JRNL TITL 3 LEVELS. JRNL REF J.MOL.BIOL. 2009 JRNL REFN ESSN 1089-8638 JRNL PMID 19712684 JRNL DOI 10.1016/J.JMB.2009.08.047

REMARK 1

REMARK 2 REMARK 2 RESOLUTION. 2.03 ANGSTROMS.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 2.03 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) (%) : 88.3 REMARK 3 NUMBER OF REFLECTIONS : 18197 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) : 0.207 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 18197 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 1765 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 322 REMARK 3 SOLVENT ATOMS : 40 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.68 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.47 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.46900 REMARK 3 B22 (A**2) : -4.46900 REMARK 3 B33 (A**2) : 8.93700 REMARK 3 B12 (A**2) : -5.34500 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) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.07 REMARK 3 LOW RESOLUTION CUTOFF (A) : 15.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.27 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.13 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.18 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 17.57 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.77 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : OVERALL 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 : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE AUTHOR DIDN'T USE THE REMARK 3 DIFFRACTION DATA AT LOW RESOLUTIONS IN THE STRUCTRAL ANALYSIS. REMARK 3 BECAUSE THE CRYSTAL CONTAINS NATIVE LIPIDS, THE R-FACTOR TENDS REMARK 3 TO BECOME VERY HIGH AT A LOW RESOLUTION (THAN 15 ANGSTROM). REMARK 3 THIS IS PARTLY BECAUSE ALL THE NATIVE LIPIDS THAT MIGHT EXIST REMARK 3 IN THE CRYSTAL ARE NOT INCLUDED IN THE MODEL.

REMARK 4 REMARK 4 2ZZL COMPLIES WITH FORMAT V. 3.20, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-FEB-09. REMARK 100 THE RCSB ID CODE IS RCSB028624.

REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JAN-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.912 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21621 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.030 REMARK 200 RESOLUTION RANGE LOW (A) : 44.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 200 DATA REDUNDANCY : 14.400 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : 0.08400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.03 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 71.4 REMARK 200 DATA REDUNDANCY IN SHELL : 14.00 REMARK 200 R MERGE FOR SHELL (I) : 0.52100 REMARK 200 R SYM FOR SHELL (I) : 0.52100 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.500 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 1IW9 REMARK 200 REMARK 200 REMARK: NULL

REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.2M AMMONIUM SULFATE, 0.1M SODIUM REMARK 280 CITRATE, 0.16M POTASIUM CHLORIDE, 3M AMMONIUM SULFATE, 0.1M REMARK 280 HEPES PH 7, LIQUID PROPANE, MEMBRANE FUSION METHOD, REMARK 280 TEMPERATURE 293K

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 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: 3890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -52.0 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 102.21000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 51.10500 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 88.51646 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 MET A -12 REMARK 465 LEU A -11 REMARK 465 GLU A -10 REMARK 465 LEU A -9 REMARK 465 LEU A -8 REMARK 465 PRO A -7 REMARK 465 THR A -6 REMARK 465 ALA A -5 REMARK 465 VAL A -4 REMARK 465 GLU A -3 REMARK 465 GLY A -2 REMARK 465 VAL A -1 REMARK 465 SER A 0 REMARK 465 GLN A 1 REMARK 465 ALA A 2 REMARK 465 GLN A 3 REMARK 465 ILE A 4 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 465 ASP A 249

REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NZ LYS A 216 C15 RET A 250 1.33 REMARK 500 O3 L2P A 270 C1 GLC A 400 1.44 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 ARG A 7 -51.07 -146.45 REMARK 500 PHE A 71 147.86 -177.42 REMARK 500 VAL A 217 -49.82 -131.99 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 RET A 250 REMARK 610 L1P A 280

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 250 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE L3P A 260 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE L2P A 270 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE L1P A 280 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE L1P A 290 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE L1P A 300 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLC A 400 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MAN A 410 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SGA A 420 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SOG A 430

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1IW6 RELATED DB: PDB REMARK 900 LIGHT-ADAPTED STATE OF BACTERIORHODOPSIN IN THE P622 CRYSTAL REMARK 900 RELATED ID: 1IW9 RELATED DB: PDB REMARK 900 THE M INTERMEDIATE OF BACTERIORHODOPSIN GENERATED AT PH 5.2

DBREF 2ZZL A -12 249 UNP P02945 BACR_HALSA 1 262

SEQRES 1 A 262 MET LEU GLU LEU LEU PRO THR ALA VAL GLU GLY VAL SER SEQRES 2 A 262 GLN ALA GLN ILE THR GLY ARG PRO GLU TRP ILE TRP LEU SEQRES 3 A 262 ALA LEU GLY THR ALA LEU MET GLY LEU GLY THR LEU TYR SEQRES 4 A 262 PHE LEU VAL LYS GLY MET GLY VAL SER ASP PRO ASP ALA SEQRES 5 A 262 LYS LYS PHE TYR ALA ILE THR THR LEU VAL PRO ALA ILE SEQRES 6 A 262 ALA PHE THR MET TYR LEU SER MET LEU LEU GLY TYR GLY SEQRES 7 A 262 LEU THR MET VAL PRO PHE GLY GLY GLU GLN ASN PRO ILE SEQRES 8 A 262 TYR TRP ALA ARG TYR ALA ASP TRP LEU PHE THR THR PRO SEQRES 9 A 262 LEU LEU LEU LEU ASP LEU ALA LEU LEU VAL ASP ALA ASP SEQRES 10 A 262 GLN GLY THR ILE LEU ALA LEU VAL GLY ALA ASP GLY ILE SEQRES 11 A 262 MET ILE GLY THR GLY LEU VAL GLY ALA LEU THR LYS VAL SEQRES 12 A 262 TYR SER TYR ARG PHE VAL TRP TRP ALA ILE SER THR ALA SEQRES 13 A 262 ALA MET LEU TYR ILE LEU TYR VAL LEU PHE PHE GLY PHE SEQRES 14 A 262 THR SER LYS ALA GLU SER MET ARG PRO GLU VAL ALA SER SEQRES 15 A 262 THR PHE LYS VAL LEU ARG ASN VAL THR VAL VAL LEU TRP SEQRES 16 A 262 SER ALA TYR PRO VAL VAL TRP LEU ILE GLY SER GLU GLY SEQRES 17 A 262 ALA GLY ILE VAL PRO LEU ASN ILE GLU THR LEU LEU PHE SEQRES 18 A 262 MET VAL LEU ASP VAL SER ALA LYS VAL GLY PHE GLY LEU SEQRES 19 A 262 ILE LEU LEU ARG SER ARG ALA ILE PHE GLY GLU ALA GLU SEQRES 20 A 262 ALA PRO GLU PRO SER ALA GLY ASP GLY ALA ALA ALA THR SEQRES 21 A 262 SER ASP

HET RET A 250 20 HET L3P A 260 59 HET L2P A 270 46 HET L1P A 280 40 HET L1P A 290 50 HET L1P A 300 50 HET GLC A 400 11 HET MAN A 410 11 HET SGA A 420 15 HET SOG A 430 20

HETNAM RET RETINAL HETNAM L3P 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN- HETNAM 2 L3P GLYCEROL-1'-PHOSPHATE HETNAM L2P 2,3-DI-PHYTANYL-GLYCEROL HETNAM L1P 3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL HETNAM GLC ALPHA-D-GLUCOSE HETNAM MAN ALPHA-D-MANNOSE HETNAM SGA O3-SULFONYLGALACTOSE HETNAM SOG 2-HYDROXYMETHYL-6-OCTYLSULFANYL-TETRAHYDRO-PYRAN-3,4,5- HETNAM 2 SOG TRIOL

HETSYN L2P 1,2-DI-1-(3,7,11,15-TETRAMETHYL-HEXADECANE)-SN-GLYCEROL HETSYN L1P 1,2-DI-1-(3,7,11,15-TETRAMETHYL-HEXADECANE)-SN-GLYCERO- HETSYN 2 L1P 3-PHOSPHATE HETSYN SOG 1-S-OCTYL-BETA-D-THIOGLUCOSIDE

FORMUL 2 RET C20 H28 O FORMUL 3 L3P C46 H94 O11 P2 2- FORMUL 4 L2P C43 H88 O3 FORMUL 5 L1P 3(C43 H89 O6 P) FORMUL 8 GLC C6 H12 O6 FORMUL 8 MAN C6 H12 O6 FORMUL 8 SGA C6 H12 O9 S FORMUL 9 SOG C14 H28 O5 S FORMUL 10 HOH *40(H2 O)

HELIX 1 1 GLU A 9 MET A 32 1 24 HELIX 2 2 ASP A 36 GLY A 63 1 28 HELIX 3 3 TYR A 79 ASP A 102 1 24 HELIX 4 4 ASP A 104 LEU A 127 1 24 HELIX 5 5 VAL A 130 GLU A 161 1 32 HELIX 6 6 ARG A 164 GLY A 192 1 29 HELIX 7 7 PRO A 200 VAL A 217 1 18 HELIX 8 8 VAL A 217 ARG A 225 1 9 HELIX 9 9 SER A 226 PHE A 230 5 5

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

LINK O2 GLC A 400 C1 MAN A 410 1555 1555 1.43 LINK O6 MAN A 410 C1 SGA A 420 1555 1555 1.45

SITE 1 AC1 13 TRP A 86 THR A 89 THR A 90 MET A 118 SITE 2 AC1 13 TRP A 138 SER A 141 THR A 142 TRP A 182 SITE 3 AC1 13 TYR A 185 PRO A 186 ASP A 212 ALA A 215 SITE 4 AC1 13 LYS A 216 SITE 1 AC2 12 GLY A 21 LYS A 40 ALA A 44 LEU A 48 SITE 2 AC2 12 ALA A 51 ASP A 104 THR A 107 ILE A 117 SITE 3 AC2 12 TYR A 147 GLY A 155 SER A 158 HOH A 620 SITE 1 AC3 11 THR A 55 TYR A 64 TRP A 80 ALA A 84 SITE 2 AC3 11 LEU A 87 PHE A 88 GLY A 116 GLY A 120 SITE 3 AC3 11 LEU A 127 GLC A 400 HOH A 628 SITE 1 AC4 6 ARG A 7 TRP A 10 ALA A 14 ALA A 18 SITE 2 AC4 6 LEU A 61 TYR A 133 SITE 1 AC5 2 TYR A 131 ILE A 198 SITE 1 AC6 7 LEU A 22 TYR A 26 VAL A 29 LYS A 30 SITE 2 AC6 7 TYR A 150 PHE A 154 ARG A 225 SITE 1 AC7 8 TYR A 64 THR A 67 LEU A 127 L2P A 270 SITE 2 AC7 8 MAN A 410 HOH A 629 HOH A 631 HOH A 640 SITE 1 AC8 9 TYR A 64 LEU A 66 THR A 67 TRP A 80 SITE 2 AC8 9 LYS A 129 GLC A 400 SGA A 420 SOG A 430 SITE 3 AC8 9 HOH A 630 SITE 1 AC9 3 PRO A 70 LYS A 129 MAN A 410 SITE 1 BC1 9 LEU A 62 TYR A 64 LEU A 127 THR A 128 SITE 2 BC1 9 LYS A 129 TYR A 133 MAN A 410 HOH A 615 SITE 3 BC1 9 HOH A 625

CRYST1 102.210 102.210 112.480 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 0.009784 0.005649 0.000000 0.00000

SCALE2 0.000000 0.011297 0.000000 0.00000

SCALE3 0.000000 0.000000 0.008890 0.00000