HEADER MEMBRANE PROTEIN 18-SEP-21 7VGT TITLE TIME-RESOLVED SERIAL FEMTOSECOND CRYSTALLOGRAPHY STRUCTURE OF LIGHT- TITLE 2 DRIVEN CHLORIDE ION-PUMPING RHODOPSIN, NM-R3: RESTING STATE STRUCTURE TITLE 3 WITH BROMIDE ION COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHLORIDE PUMPING RHODOPSIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NONLABENS MARINUS S1-08; SOURCE 3 ORGANISM_TAXID: 1454201; SOURCE 4 GENE: CLR, NMS_1267; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SACLA SERIAL FEMTOSECOND CRYSTALLOGRAPHY CELL-FREE SYNTHESIS KEYWDS 2 BACTERIAL TYPE RHODOPSIN CHLORIDE ION PUMP RHODOPSIN, MEMBRANE KEYWDS 3 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.HOSAKA,E.NANGO,T.NAKANE,F.LUO,T.KIMURA-SOMEYA,M.SHIROUZU REVDAT 4 29-NOV-23 7VGT 1 REMARK REVDAT 3 06-SEP-23 7VGT 1 REMARK REVDAT 2 09-MAR-22 7VGT 1 JRNL REVDAT 1 16-FEB-22 7VGT 0 JRNL AUTH T.HOSAKA,T.NOMURA,M.KUBO,T.NAKANE,L.FANGJIA,S.I.SEKINE, JRNL AUTH 2 T.ITO,K.MURAYAMA,K.IHARA,H.EHARA,K.KASHIWAGI,K.KATSURA, JRNL AUTH 3 R.AKASAKA,T.HISANO,T.TANAKA,R.TANAKA,T.ARIMA,A.YAMASHITA, JRNL AUTH 4 M.SUGAHARA,H.NAITOW,Y.MATSUURA,S.YOSHIZAWA,K.TONO,S.OWADA, JRNL AUTH 5 O.NUREKI,T.KIMURA-SOMEYA,S.IWATA,E.NANGO,M.SHIROUZU JRNL TITL CONFORMATIONAL ALTERATIONS IN UNIDIRECTIONAL ION TRANSPORT JRNL TITL 2 OF A LIGHT-DRIVEN CHLORIDE PUMP REVEALED USING X-RAY FREE JRNL TITL 3 ELECTRON LASERS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 119 2022 JRNL REFN ESSN 1091-6490 JRNL PMID 35197289 JRNL DOI 10.1073/PNAS.2117433119 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 18203 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 899 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 29.3590 - 3.8140 1.00 2962 151 0.1883 0.2194 REMARK 3 2 3.8140 - 3.0283 1.00 2889 143 0.1668 0.1853 REMARK 3 3 3.0283 - 2.6457 1.00 2900 141 0.1685 0.2001 REMARK 3 4 2.6457 - 2.4040 1.00 2859 161 0.1647 0.2039 REMARK 3 5 2.4040 - 2.2317 1.00 2828 163 0.1698 0.2110 REMARK 3 6 2.2317 - 2.1002 0.99 2866 140 0.1852 0.2368 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.510 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.79 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 7VGT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-SEP-21. REMARK 100 THE DEPOSITION ID IS D_1300024657. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-FEB-19 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : FREE ELECTRON LASER REMARK 200 BEAMLINE : BL3 REMARK 200 X-RAY GENERATOR MODEL : SACLA BEAMLINE BL3 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.7714 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MPCCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL 0.63 REMARK 200 DATA SCALING SOFTWARE : CRYSTFEL 0.63 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18261 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 42.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 213.0 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.3500 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) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: PHENIX REMARK 200 STARTING MODEL: 5B2N REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 38% PEG400, 300 MM K PHOSPHATE, AND REMARK 280 100 MM HEPES (PH7.0), LIPIDIC CUBIC PHASE, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 52.15000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.55000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 52.15000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.55000 REMARK 290 SMTRY3 4 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 13.0 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 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 GLY A 266 REMARK 465 MET A 267 REMARK 465 ASP A 268 REMARK 465 SER A 269 REMARK 465 LYS A 270 REMARK 465 ALA A 271 REMARK 465 ALA A 272 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 LYS A 117 CG CD CE NZ 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 GLN A 86 -151.35 -107.33 REMARK 500 REMARK 500 REMARK: NULL DBREF 7VGT A 1 272 UNP W8VZW3 W8VZW3_9FLAO 1 272 SEQADV 7VGT GLY A -6 UNP W8VZW3 EXPRESSION TAG SEQADV 7VGT SER A -5 UNP W8VZW3 EXPRESSION TAG SEQADV 7VGT SER A -4 UNP W8VZW3 EXPRESSION TAG SEQADV 7VGT GLY A -3 UNP W8VZW3 EXPRESSION TAG SEQADV 7VGT SER A -2 UNP W8VZW3 EXPRESSION TAG SEQADV 7VGT SER A -1 UNP W8VZW3 EXPRESSION TAG SEQADV 7VGT GLY A 0 UNP W8VZW3 EXPRESSION TAG SEQRES 1 A 279 GLY SER SER GLY SER SER GLY MET LYS ASN ILE GLU SER SEQRES 2 A 279 LEU PHE ASP TYR SER ALA GLY GLN PHE GLU PHE ILE ASP SEQRES 3 A 279 HIS LEU LEU THR MET GLY VAL GLY VAL HIS PHE ALA ALA SEQRES 4 A 279 LEU ILE PHE PHE LEU VAL VAL SER GLN PHE VAL ALA PRO SEQRES 5 A 279 LYS TYR ARG ILE ALA THR ALA LEU SER CYS ILE VAL MET SEQRES 6 A 279 VAL SER ALA GLY LEU ILE LEU ASN SER GLN ALA VAL MET SEQRES 7 A 279 TRP THR ASP ALA TYR ALA TYR VAL ASP GLY SER TYR GLN SEQRES 8 A 279 LEU GLN ASP LEU THR PHE SER ASN GLY TYR ARG TYR VAL SEQRES 9 A 279 ASN TRP MET ALA THR ILE PRO CYS LEU LEU LEU GLN LEU SEQRES 10 A 279 LEU ILE VAL LEU ASN LEU LYS GLY LYS GLU LEU PHE SER SEQRES 11 A 279 THR ALA THR TRP LEU ILE LEU ALA ALA TRP GLY MET ILE SEQRES 12 A 279 ILE THR GLY TYR VAL GLY GLN LEU TYR GLU VAL ASP ASP SEQRES 13 A 279 ILE ALA GLN LEU MET ILE TRP GLY ALA VAL SER THR ALA SEQRES 14 A 279 PHE PHE VAL VAL MET ASN TRP ILE VAL GLY THR LYS ILE SEQRES 15 A 279 PHE LYS ASN ARG ALA THR MET LEU GLY GLY THR ASP SER SEQRES 16 A 279 THR ILE THR LYS VAL PHE TRP LEU MET MET PHE ALA TRP SEQRES 17 A 279 THR LEU TYR PRO ILE ALA TYR LEU VAL PRO ALA PHE MET SEQRES 18 A 279 ASN ASN ALA ASP GLY VAL VAL LEU ARG GLN LEU LEU PHE SEQRES 19 A 279 THR ILE ALA ASP ILE SER SER LYS VAL ILE TYR GLY LEU SEQRES 20 A 279 MET ILE THR TYR ILE ALA ILE GLN GLN SER ALA ALA ALA SEQRES 21 A 279 GLY TYR VAL PRO ALA GLN GLN ALA LEU GLY ARG ILE GLY SEQRES 22 A 279 MET ASP SER LYS ALA ALA HET RET A 301 20 HET HEX A 302 6 HET HEX A 303 6 HET HEX A 304 6 HET HEX A 305 6 HET D10 A 306 10 HET D10 A 307 10 HET D10 A 308 10 HET BR A 309 1 HET BR A 310 1 HET BR A 311 1 HETNAM RET RETINAL HETNAM HEX HEXANE HETNAM D10 DECANE HETNAM BR BROMIDE ION FORMUL 2 RET C20 H28 O FORMUL 3 HEX 4(C6 H14) FORMUL 7 D10 3(C10 H22) FORMUL 10 BR 3(BR 1-) FORMUL 13 HOH *53(H2 O) HELIX 1 AA1 ASN A 3 PHE A 8 5 6 HELIX 2 AA2 SER A 11 SER A 40 1 30 HELIX 3 AA3 GLN A 41 VAL A 43 5 3 HELIX 4 AA4 TYR A 47 ALA A 75 1 29 HELIX 5 AA5 ASN A 92 LEU A 114 1 23 HELIX 6 AA6 LYS A 117 LEU A 144 1 28 HELIX 7 AA7 ASP A 149 ARG A 179 1 31 HELIX 8 AA8 ALA A 180 MET A 182 5 3 HELIX 9 AA9 GLY A 185 LEU A 209 1 25 HELIX 10 AB1 LEU A 209 MET A 214 1 6 HELIX 11 AB2 ASN A 216 ALA A 253 1 38 HELIX 12 AB3 TYR A 255 ILE A 265 1 11 SHEET 1 AA1 2 TYR A 76 VAL A 79 0 SHEET 2 AA1 2 SER A 82 LEU A 85 -1 O SER A 82 N VAL A 79 LINK NZ LYS A 235 C15 RET A 301 1555 1555 1.31 CRYST1 104.300 51.100 78.400 90.00 131.50 90.00 C 1 2 1 4 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 0.009588 0.000000 0.008483 0.00000 SCALE2 0.000000 0.019569 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017031 0.00000