HEADER TRANSPORT PROTEIN 11-MAR-07 2EI4 TITLE TRIMERIC COMPLEX OF ARCHAERHODOPSIN-2 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 SP. AUS-2; SOURCE 3 ORGANISM_TAXID: 29285; SOURCE 4 STRAIN: AUS-2 KEYWDS MEMBRANE PROTEIN, RETINAL, BACTERIORUBERIN, PROTON PUMP, TRANSPORT KEYWDS 2 PROTEIN, STRUCTURAL GENOMICS EXPDTA X-RAY DIFFRACTION AUTHOR T.KOUYAMA REVDAT 7 06-NOV-24 2EI4 1 REMARK REVDAT 6 25-OCT-23 2EI4 1 HETSYN REVDAT 5 29-JUL-20 2EI4 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE REVDAT 4 13-JUL-11 2EI4 1 VERSN REVDAT 3 24-FEB-09 2EI4 1 VERSN REVDAT 2 22-JAN-08 2EI4 1 JRNL REVDAT 1 01-JAN-08 2EI4 0 JRNL AUTH K.YOSHIMURA,T.KOUYAMA JRNL TITL STRUCTURAL ROLE OF BACTERIORUBERIN IN THE TRIMERIC STRUCTURE JRNL TITL 2 OF ARCHAERHODOPSIN-2 JRNL REF J.MOL.BIOL. V. 375 1267 2008 JRNL REFN ISSN 0022-2836 JRNL PMID 18082767 JRNL DOI 10.1016/J.JMB.2007.11.039 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.0 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.188 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1651 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 18468 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1838 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 131 REMARK 3 SOLVENT ATOMS : 11 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 ANGLE DISTANCES (A) : NULL REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE CRYSTAL WAS HEMIHEDRALLY TWINNED. REMARK 3 THE TWINNING FRACTION WAS ESTIMATED TO BE 43-45%. AFTER REMARK 3 AVERAGING THE TWIN-RELATED INTENSITIES, THE REFINEMENT WAS REMARK 3 PERFORMED BY THE DETWIN_PERFECT PROCEDURE OF CNS. REMARK 4 REMARK 4 2EI4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-MAR-07. REMARK 100 THE DEPOSITION ID IS D_1000026693. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-NOV-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU 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 : DOUBLE-CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18116 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 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 (%) : 98.4 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : 0.08500 REMARK 200 FOR THE DATA SET : 6.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.42000 REMARK 200 R SYM FOR SHELL (I) : 0.48400 REMARK 200 FOR SHELL : 3.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: SHELXL-97 REMARK 200 STARTING MODEL: PDB ENTRY 1VGO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.8M AMMONIUM SULFATE, 0.1M HEPES, REMARK 280 0.32% NONYLGLUCOSIDE, PH 8.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 288K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 2 1 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 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 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 18130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -119.0 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 98.16000 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 49.08000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 85.00905 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 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: 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 2 -100.51 -146.17 REMARK 500 THR A 159 -76.23 -119.40 REMARK 500 THR A 178 38.14 -82.21 REMARK 500 LEU A 179 -42.00 -148.22 REMARK 500 LYS A 221 -77.39 -97.62 REMARK 500 GLU A 237 158.38 179.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1VGO RELATED DB: PDB REMARK 900 DIMERIC FORM OF ARCHAERHODOPSIN-2 REMARK 900 RELATED ID: 1UAZ RELATED DB: PDB REMARK 900 DIMERIC FORM OF ARCHAERHODOPSIN-1 DBREF 2EI4 A 1 253 UNP P29563 BACR2_HALS2 7 259 SEQRES 1 A 253 GLN ALA GLY PHE ASP LEU LEU ASN ASP GLY ARG PRO GLU SEQRES 2 A 253 THR LEU TRP LEU GLY ILE GLY THR LEU LEU MET LEU ILE SEQRES 3 A 253 GLY THR PHE TYR PHE ILE ALA ARG GLY TRP GLY VAL THR SEQRES 4 A 253 ASP LYS GLU ALA ARG GLU TYR TYR ALA ILE THR ILE LEU SEQRES 5 A 253 VAL PRO GLY ILE ALA SER ALA ALA TYR LEU ALA MET PHE SEQRES 6 A 253 PHE GLY ILE GLY VAL THR GLU VAL GLU LEU ALA SER GLY SEQRES 7 A 253 THR VAL LEU ASP ILE TYR TYR ALA ARG TYR ALA ASP TRP SEQRES 8 A 253 LEU PHE THR THR PRO LEU LEU LEU LEU ASP LEU ALA LEU SEQRES 9 A 253 LEU ALA LYS VAL ASP ARG VAL THR ILE GLY THR LEU ILE SEQRES 10 A 253 GLY VAL ASP ALA LEU MET ILE VAL THR GLY LEU ILE GLY SEQRES 11 A 253 ALA LEU SER LYS THR PRO LEU ALA ARG TYR THR TRP TRP SEQRES 12 A 253 LEU PHE SER THR ILE ALA PHE LEU PHE VAL LEU TYR TYR SEQRES 13 A 253 LEU LEU THR SER LEU ARG SER ALA ALA ALA LYS ARG SER SEQRES 14 A 253 GLU GLU VAL ARG SER THR PHE ASN THR LEU THR ALA LEU SEQRES 15 A 253 VAL ALA VAL LEU TRP THR ALA TYR PRO ILE LEU TRP ILE SEQRES 16 A 253 VAL GLY THR GLU GLY ALA GLY VAL VAL GLY LEU GLY ILE SEQRES 17 A 253 GLU THR LEU ALA PHE MET VAL LEU ASP VAL THR ALA LYS SEQRES 18 A 253 VAL GLY PHE GLY PHE VAL LEU LEU ARG SER ARG ALA ILE SEQRES 19 A 253 LEU GLY GLU THR GLU ALA PRO GLU PRO SER ALA GLY ALA SEQRES 20 A 253 ASP ALA SER ALA ALA ASP HET GLC A 281 11 HET RET A 260 20 HET 22B A 270 54 HET L2P A 280 46 HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM RET RETINAL HETNAM 22B BACTERIORUBERIN HETNAM L2P 2,3-DI-PHYTANYL-GLYCEROL HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN L2P 1,2-DI-1-(3,7,11,15-TETRAMETHYL-HEXADECANE)-SN-GLYCEROL FORMUL 2 GLC C6 H12 O6 FORMUL 3 RET C20 H28 O FORMUL 4 22B C50 H76 O4 FORMUL 5 L2P C43 H88 O3 FORMUL 6 HOH *11(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 LEU A 132 1 24 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 SER A 231 1 27 HELIX 9 9 ARG A 232 LEU A 235 5 4 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 260 1555 1555 1.35 LINK O3 L2P A 280 C1 GLC A 281 1555 1555 1.45 CRYST1 98.160 98.160 56.160 90.00 90.00 120.00 P 3 2 1 6 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 0.010187 0.005882 0.000000 0.00000 SCALE2 0.000000 0.011763 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017806 0.00000