HEADER MEMBRANE PROTEIN 19-OCT-22 8H79 TITLE THE CRYSTAL STRUCTURE OF CYANORHODOPSIN-II (CYR-II) P7104R FROM TITLE 2 NODOSILINEA NODULOSA PCC 7104 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYANORHODOPSIN-II (CYR-II) P7104R; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: SEQUENCE HAS BEEN DEPOSITED TO GENBANK WITH ACCESSION COMPND 6 NUMBER WP_017301364.1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NODOSILINEA NODULOSA PCC 7104; SOURCE 3 ORGANISM_TAXID: 118166; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RETINAL CELL-FREE SYNTHESIS BACTERIAL TYPE RHODOPSIN CYANOBACTERIA, KEYWDS 2 MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.HOSAKA,T.KIMURA-SOMEYA,M.SHIROUZU REVDAT 1 25-OCT-23 8H79 0 JRNL AUTH M.HASEGAWA,T.HOSAKA,K.KOJIMA,Y.NISHIMURA,M.KURIHARA, JRNL AUTH 2 Y.NAKAJIMA,Y.ISHIZUKA-KATSURA,T.KIMURA-SOMEYA,M.SHIROUZU, JRNL AUTH 3 Y.SUDO,S.YOSHIZAWA JRNL TITL CYANORHODOPSIN-II: DIVERSE PROTON-PUMPING RHODOPSINS IN THE JRNL TITL 2 CYANOBACTERIAL LINEAGE ILLUMINATED BY LARGE-SCALE JRNL TITL 3 METAGENOMIC JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.07 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 17186 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1718 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 49.6000 - 4.7400 1.00 1407 152 0.2432 0.2791 REMARK 3 2 4.7400 - 3.7600 0.99 1310 146 0.2085 0.2472 REMARK 3 3 3.7600 - 3.2900 1.00 1295 140 0.1904 0.2134 REMARK 3 4 3.2900 - 2.9900 1.00 1297 145 0.2094 0.2372 REMARK 3 5 2.9900 - 2.7700 1.00 1276 147 0.1627 0.2212 REMARK 3 6 2.7700 - 2.6100 1.00 1274 144 0.1786 0.2331 REMARK 3 7 2.6100 - 2.4800 1.00 1284 142 0.1686 0.2308 REMARK 3 8 2.4800 - 2.3700 1.00 1269 140 0.1737 0.2524 REMARK 3 9 2.3700 - 2.2800 1.00 1255 144 0.1946 0.2666 REMARK 3 10 2.2800 - 2.2000 1.00 1259 138 0.1982 0.2593 REMARK 3 11 2.2000 - 2.1300 1.00 1283 142 0.2068 0.2740 REMARK 3 12 2.1300 - 2.0700 1.00 1259 138 0.2378 0.2797 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.660 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.86 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.55 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8H79 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-OCT-22. REMARK 100 THE DEPOSITION ID IS D_1300032968. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUL-20 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL32XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17190 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.070 REMARK 200 RESOLUTION RANGE LOW (A) : 49.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 12.40 REMARK 200 R MERGE (I) : 0.22700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.2500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.39 REMARK 200 R MERGE FOR SHELL (I) : 1.64500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1C3W REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM HEPES, 46% PEG 400, 400MM REMARK 280 LITHIUM SULFATE, PH 6.8, LIPIDIC CUBIC PHASE, TEMPERATURE 293K 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 300 REMARK: THERE IS NO CLEAR EVIDENCE THAT THE ASSEMBLY SHOULD BE A REMARK 300 MONOMER OR TRIMER. 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: 15940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -162.0 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 31.57500 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 54.68950 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -31.57500 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 54.68950 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 GLY A -6 REMARK 465 SER A -5 REMARK 465 SER A -4 REMARK 465 GLY A -3 REMARK 465 SER A -2 REMARK 465 SER A -1 REMARK 465 GLY A 0 REMARK 465 SER A 237 REMARK 465 VAL A 238 REMARK 465 PRO A 239 REMARK 465 ASN A 240 REMARK 465 SER A 241 REMARK 465 GLY A 242 REMARK 465 SER A 243 REMARK 465 GLY A 244 REMARK 465 VAL A 245 REMARK 465 GLY A 246 REMARK 465 ASN A 247 REMARK 465 TYR A 248 REMARK 465 ARG A 249 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 VAL A 216 -61.21 -99.77 REMARK 500 REMARK 500 REMARK: NULL DBREF 8H79 A -6 249 PDB 8H79 8H79 -6 249 SEQRES 1 A 256 GLY SER SER GLY SER SER GLY MET ASN LEU LEU SER GLN SEQRES 2 A 256 VAL SER PHE TRP VAL GLY CYS GLY ILE LEU ALA PHE GLY SEQRES 3 A 256 SER ILE VAL PHE GLY LEU GLY ALA TRP ASN ALA LYS ARG SEQRES 4 A 256 GLN SER TRP GLU GLU PHE TYR ILE VAL HIS PHE THR VAL SEQRES 5 A 256 THR THR VAL ALA ALA CYS ALA TYR LEU ALA MET ALA MET SEQRES 6 A 256 GLY GLN GLY GLU ILE THR LEU GLN ASN THR ASP LEU ALA SEQRES 7 A 256 ALA GLU GLY VAL ARG HIS ILE TYR TRP ALA ARG TYR CYS SEQRES 8 A 256 ASP TRP ILE VAL THR THR PRO LEU ILE LEU PHE SER ILE SEQRES 9 A 256 CYS ARG LEU SER LYS VAL ARG GLY THR MET ILE ALA GLY SEQRES 10 A 256 ILE ILE MET SER ASP VAL LEU MET ILE ILE THR GLY ALA SEQRES 11 A 256 ILE ALA ALA PHE SER PHE ALA PRO GLU ARG TYR VAL TRP SEQRES 12 A 256 TYR ILE VAL SER CYS MET PHE GLU VAL ALA ILE PHE VAL SEQRES 13 A 256 ILE LEU LEU GLY ALA VAL ARG THR SER ALA MET ARG GLN SEQRES 14 A 256 HIS TYR ASP VAL LYS ASN LEU PHE ASN LEU VAL PHE THR SEQRES 15 A 256 VAL PHE SER ILE TYR PHE TRP ALA TYR PRO ILE VAL TRP SEQRES 16 A 256 ILE LEU GLY GLN LYS GLY VAL GLY LEU TYR GLY THR GLY SEQRES 17 A 256 VAL GLU SER LEU LEU ILE MET LEU LEU ASP ILE THR ALA SEQRES 18 A 256 LYS VAL PHE TYR GLY PHE LEU LEU LEU ARG ASP ARG GLU SEQRES 19 A 256 THR LEU GLN ARG MET GLY GLN LEU SER SER VAL PRO ASN SEQRES 20 A 256 SER GLY SER GLY VAL GLY ASN TYR ARG HET RET A 301 20 HET PG4 A 302 13 HET HEX A 303 6 HET HEX A 304 6 HET HEX A 305 6 HET OCT A 306 8 HET OCT A 307 8 HET OCT A 308 8 HET C14 A 309 14 HET C14 A 310 14 HET R16 A 311 16 HET SO4 A 312 5 HET CL A 313 1 HETNAM RET RETINAL HETNAM PG4 TETRAETHYLENE GLYCOL HETNAM HEX HEXANE HETNAM OCT N-OCTANE HETNAM C14 TETRADECANE HETNAM R16 HEXADECANE HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION FORMUL 2 RET C20 H28 O FORMUL 3 PG4 C8 H18 O5 FORMUL 4 HEX 3(C6 H14) FORMUL 7 OCT 3(C8 H18) FORMUL 10 C14 2(C14 H30) FORMUL 12 R16 C16 H34 FORMUL 13 SO4 O4 S 2- FORMUL 14 CL CL 1- FORMUL 15 HOH *46(H2 O) HELIX 1 AA1 ASN A 2 ALA A 30 1 29 HELIX 2 AA2 ARG A 32 MET A 58 1 27 HELIX 3 AA3 TRP A 80 LYS A 102 1 23 HELIX 4 AA4 ARG A 104 SER A 128 1 25 HELIX 5 AA5 PRO A 131 LEU A 152 1 22 HELIX 6 AA6 GLY A 153 GLN A 162 1 10 HELIX 7 AA7 VAL A 166 GLY A 191 1 26 HELIX 8 AA8 GLY A 199 VAL A 216 1 18 HELIX 9 AA9 VAL A 216 GLY A 233 1 18 SHEET 1 AA1 2 ILE A 63 GLN A 66 0 SHEET 2 AA1 2 VAL A 75 ILE A 78 -1 O ILE A 78 N ILE A 63 LINK NZ LYS A 215 C15 RET A 301 1555 1555 1.43 CISPEP 1 ALA A 130 PRO A 131 0 -0.41 CRYST1 63.150 63.150 117.760 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 0.015835 0.009143 0.000000 0.00000 SCALE2 0.000000 0.018285 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008492 0.00000