HEADER PROTON TRANSPORT 05-JUN-13 4L35 TITLE CRYSTAL STRUCTURE OF CRUXRHODOPSIN-3 AT PH5 FROM HALOARCULA TITLE 2 VALLISMORTIS AT 2.1 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: CRUXRHODOPSIN-3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: COP-3, CR-3; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HALOARCULA VALLISMORTIS; SOURCE 3 ORGANISM_TAXID: 28442; SOURCE 4 GENE: COP3; SOURCE 5 EXPRESSION_SYSTEM: HALOBACTERIUM SALINARUM; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 2242 KEYWDS PROTEIN-BACTERIORUBERIN COMPLEX, SEVEN TRANSMEMBRANE ALPHA HELICES, KEYWDS 2 LIGHT-DRIVEN PROTON PUMP, MEMBRANE, PROTON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR T.KOUYAMA,S.K.CHAN REVDAT 4 30-OCT-24 4L35 1 REMARK REVDAT 3 08-NOV-23 4L35 1 REMARK LINK REVDAT 2 24-DEC-14 4L35 1 JRNL REVDAT 1 11-JUN-14 4L35 0 JRNL AUTH S.K.CHAN,T.KITAJIMA-IHARA,R.FUJII,T.GOTOH,M.MURAKAMI, JRNL AUTH 2 K.IHARA,T.KOUYAMA JRNL TITL CRYSTAL STRUCTURE OF CRUXRHODOPSIN-3 FROM HALOARCULA JRNL TITL 2 VALLISMORTIS JRNL REF PLOS ONE V. 9 08362 2014 JRNL REFN ESSN 1932-6203 JRNL PMID 25268964 JRNL DOI 10.1371/JOURNAL.PONE.0108362 REMARK 2 REMARK 2 RESOLUTION. 2.10 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) : 2.10 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) (%) : 92.5 REMARK 3 NUMBER OF REFLECTIONS : 19593 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) : 0.231 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1929 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 : 1862 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 57 REMARK 3 SOLVENT ATOMS : 26 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.42 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.77300 REMARK 3 B22 (A**2) : 3.77300 REMARK 3 B33 (A**2) : -7.54500 REMARK 3 B12 (A**2) : 0.00000 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) : 0.26 REMARK 3 ESD FROM SIGMAA (A) : 0.14 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) : 0.30 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.22 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.152 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 18.61 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.778 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC 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: NULL REMARK 4 REMARK 4 4L35 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-JUN-13. REMARK 100 THE DEPOSITION ID IS D_1000080121. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-MAY-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.0 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 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19657 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 47.460 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : 0.07900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.8000 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 (%) : 96.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.40 REMARK 200 R MERGE FOR SHELL (I) : 0.49400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.600 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 4JR8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.5M AMMONIUM SULFATE, 0.1M NA REMARK 280 -CITRATE, PH 4.0, VAPOR DIFFUSION, SITTING DROP, 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 REMARK 350 TOTAL BURIED SURFACE AREA: 10910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -51.0 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 -53.00500 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 91.80735 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -106.01000 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 ALA A 245 REMARK 465 THR A 246 REMARK 465 ALA A 247 REMARK 465 THR A 248 REMARK 465 ALA A 249 REMARK 465 ASP A 250 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 TRP A 30 -55.32 -29.75 REMARK 500 SER A 129 -90.43 -115.29 REMARK 500 THR A 241 113.43 52.16 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 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1IW6 RELATED DB: PDB REMARK 900 BACTERIORHDOPSIN REMARK 900 RELATED ID: 4JR8 RELATED DB: PDB REMARK 900 CRUXRHODOPSIN-3 AT PH 7.0 DBREF 4L35 A 1 250 UNP P94854 BACR_HALVA 1 250 SEQRES 1 A 250 MET PRO ALA PRO GLU GLY GLU ALA ILE TRP LEU TRP LEU SEQRES 2 A 250 GLY THR ALA GLY MET PHE LEU GLY MET LEU TYR PHE ILE SEQRES 3 A 250 ALA ARG GLY TRP GLY GLU THR ASP SER ARG ARG GLN LYS SEQRES 4 A 250 PHE TYR ILE ALA THR ILE LEU ILE THR ALA ILE ALA PHE SEQRES 5 A 250 VAL ASN TYR LEU ALA MET ALA LEU GLY PHE GLY LEU THR SEQRES 6 A 250 ILE VAL GLU ILE ALA GLY GLU GLN ARG PRO ILE TYR TRP SEQRES 7 A 250 ALA ARG TYR SER ASP TRP LEU PHE THR THR PRO LEU LEU SEQRES 8 A 250 LEU TYR ASP LEU GLY LEU LEU ALA GLY ALA ASP ARG ASN SEQRES 9 A 250 THR ILE SER SER LEU VAL SER LEU ASP VAL LEU MET ILE SEQRES 10 A 250 GLY THR GLY LEU VAL ALA THR LEU SER ALA GLY SER GLY SEQRES 11 A 250 VAL LEU SER ALA GLY ALA GLU ARG LEU VAL TRP TRP GLY SEQRES 12 A 250 ILE SER THR ALA PHE LEU LEU VAL LEU LEU TYR PHE LEU SEQRES 13 A 250 PHE SER SER LEU SER GLY ARG VAL ALA ASP LEU PRO SER SEQRES 14 A 250 ASP THR ARG SER THR PHE LYS THR LEU ARG ASN LEU VAL SEQRES 15 A 250 THR VAL VAL TRP LEU VAL TYR PRO VAL TRP TRP LEU VAL SEQRES 16 A 250 GLY THR GLU GLY ILE GLY LEU VAL GLY ILE GLY ILE GLU SEQRES 17 A 250 THR ALA GLY PHE MET VAL ILE ASP LEU VAL ALA LYS VAL SEQRES 18 A 250 GLY PHE GLY ILE ILE LEU LEU ARG SER HIS GLY VAL LEU SEQRES 19 A 250 ASP GLY ALA ALA GLU THR THR GLY ALA GLY ALA THR ALA SEQRES 20 A 250 THR ALA ASP HET RET A 301 20 HET 22B A 302 37 HETNAM RET RETINAL HETNAM 22B BACTERIORUBERIN FORMUL 2 RET C20 H28 O FORMUL 3 22B C50 H76 O4 FORMUL 4 HOH *26(H2 O) HELIX 1 1 GLU A 7 TRP A 30 1 24 HELIX 2 2 ASP A 34 LEU A 60 1 27 HELIX 3 3 TRP A 78 GLY A 100 1 23 HELIX 4 4 ASP A 102 SER A 126 1 25 HELIX 5 5 SER A 133 SER A 159 1 27 HELIX 6 6 LEU A 160 ASP A 166 1 7 HELIX 7 7 PRO A 168 GLY A 196 1 29 HELIX 8 8 GLY A 204 LEU A 228 1 25 HELIX 9 9 SER A 230 GLY A 236 1 7 HELIX 10 10 ALA A 237 GLU A 239 5 3 SHEET 1 A 2 LEU A 64 ILE A 69 0 SHEET 2 A 2 GLU A 72 TYR A 77 -1 O ARG A 74 N VAL A 67 LINK NZ LYS A 220 C15 RET A 301 1555 1555 1.35 SITE 1 AC1 14 TYR A 81 TRP A 84 THR A 87 THR A 88 SITE 2 AC1 14 LEU A 91 MET A 116 TRP A 142 SER A 145 SITE 3 AC1 14 THR A 146 TRP A 186 TYR A 189 PRO A 190 SITE 4 AC1 14 TRP A 193 LYS A 220 SITE 1 AC2 9 GLY A 29 TRP A 30 TYR A 41 PHE A 52 SITE 2 AC2 9 ASN A 104 THR A 105 LEU A 112 PHE A 148 SITE 3 AC2 9 SER A 159 CRYST1 106.010 106.010 55.440 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 0.009433 0.005446 0.000000 0.00000 SCALE2 0.000000 0.010892 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018038 0.00000