HEADER MEMBRANE PROTEIN 13-AUG-20 7CRJ TITLE DARK STATE STRUCTURE OF CHLORIDE ION PUMPING RHODOPSIN (CLR) WITH NTQ TITLE 2 MOTIF 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 CHLORIDE ION PUMPING RHODOPSIN, SFX, XFEL, CLR, NTQ, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.H.YUN,H.LIU,W.T.LEE,M.SCHMIDT REVDAT 3 29-NOV-23 7CRJ 1 REMARK REVDAT 2 14-APR-21 7CRJ 1 JRNL REVDAT 1 16-SEP-20 7CRJ 0 JRNL AUTH J.H.YUN,X.LI,J.YUE,J.H.PARK,Z.JIN,C.LI,H.HU,Y.SHI,S.PANDEY, JRNL AUTH 2 S.CARBAJO,S.BOUTET,M.S.HUNTER,M.LIANG,R.G.SIERRA,T.J.LANE, JRNL AUTH 3 L.ZHOU,U.WEIERSTALL,N.A.ZATSEPIN,M.OHKI,J.R.H.TAME,S.Y.PARK, JRNL AUTH 4 J.C.H.SPENCE,W.ZHANG,M.SCHMIDT,W.LEE,H.LIU JRNL TITL EARLY-STAGE DYNAMICS OF CHLORIDE ION-PUMPING RHODOPSIN JRNL TITL 2 REVEALED BY A FEMTOSECOND X-RAY LASER. JRNL REF PROC.NATL.ACAD.SCI.USA V. 118 2021 JRNL REFN ESSN 1091-6490 JRNL PMID 33753488 JRNL DOI 10.1073/PNAS.2020486118 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 3 NUMBER OF REFLECTIONS : 36965 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950 REMARK 3 FREE R VALUE TEST SET COUNT : 1829 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 20.6400 - 3.8700 1.00 3049 137 0.1860 0.1857 REMARK 3 2 3.8700 - 3.0800 0.99 2989 146 0.1487 0.1621 REMARK 3 3 3.0800 - 2.6900 0.98 2914 141 0.1505 0.1771 REMARK 3 4 2.6900 - 2.4400 0.97 2875 139 0.1465 0.1674 REMARK 3 5 2.4400 - 2.2700 0.96 2859 145 0.1519 0.1874 REMARK 3 6 2.2700 - 2.1300 0.95 2807 153 0.1527 0.1699 REMARK 3 7 2.1300 - 2.0300 0.94 2739 133 0.1590 0.1805 REMARK 3 8 2.0300 - 1.9400 0.92 2695 153 0.1765 0.2453 REMARK 3 9 1.9400 - 1.8700 0.89 2598 146 0.1941 0.2484 REMARK 3 10 1.8700 - 1.8000 0.88 2569 137 0.2133 0.2357 REMARK 3 11 1.8000 - 1.7400 0.86 2517 145 0.2240 0.2313 REMARK 3 12 1.7400 - 1.6900 0.81 2332 141 0.2729 0.2504 REMARK 3 13 1.6900 - 1.6500 0.74 2193 113 0.3139 0.3515 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) : 0.172 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.556 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.13 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.37 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 : 0.018 2236 REMARK 3 ANGLE : 1.516 3013 REMARK 3 CHIRALITY : 0.083 341 REMARK 3 PLANARITY : 0.010 358 REMARK 3 DIHEDRAL : 19.358 799 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 7CRJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-AUG-20. REMARK 100 THE DEPOSITION ID IS D_1300018133. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-OCT-18 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 7 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 : CXI REMARK 200 X-RAY GENERATOR MODEL : SLAC LCLS BEAMLINE CXI REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.30 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : CS-PAD CXI-1 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL 0.8.0 REMARK 200 DATA SCALING SOFTWARE : CRYSTFEL 0.8.0 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40394 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 20.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 200 DATA REDUNDANCY : 424.2 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.5200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.8 REMARK 200 DATA REDUNDANCY IN SHELL : 77.00 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 1.16_3549 REMARK 200 STARTING MODEL: 5G28 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MONOOLEIN (1-OLEOYL-RAC-GLYCEROL), PH REMARK 280 7, BATCH MODE, 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 51.68500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.04500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 51.68500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.04500 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 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 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 O HOH A 503 O HOH A 505 2.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 MET A 24 CG - SD - CE ANGL. DEV. = -10.0 DEGREES 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 GLN A 86 -132.22 -107.06 REMARK 500 ASP A 149 85.70 -153.35 REMARK 500 MET A 214 68.44 -154.99 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 OLA A 304 REMARK 610 OLA A 306 REMARK 610 OLA A 307 REMARK 610 OLA A 309 REMARK 610 OLA A 310 DBREF 7CRJ A 2 265 UNP W8VZW3 W8VZW3_9FLAO 2 265 SEQRES 1 A 264 LYS ASN ILE GLU SER LEU PHE ASP TYR SER ALA GLY GLN SEQRES 2 A 264 PHE GLU PHE ILE ASP HIS LEU LEU THR MET GLY VAL GLY SEQRES 3 A 264 VAL HIS PHE ALA ALA LEU ILE PHE PHE LEU VAL VAL SER SEQRES 4 A 264 GLN PHE VAL ALA PRO LYS TYR ARG ILE ALA THR ALA LEU SEQRES 5 A 264 SER CYS ILE VAL MET VAL SER ALA GLY LEU ILE LEU ASN SEQRES 6 A 264 SER GLN ALA VAL MET TRP THR ASP ALA TYR ALA TYR VAL SEQRES 7 A 264 ASP GLY SER TYR GLN LEU GLN ASP LEU THR PHE SER ASN SEQRES 8 A 264 GLY TYR ARG TYR VAL ASN TRP MET ALA THR ILE PRO CYS SEQRES 9 A 264 LEU LEU LEU GLN LEU LEU ILE VAL LEU ASN LEU LYS GLY SEQRES 10 A 264 LYS GLU LEU PHE SER THR ALA THR TRP LEU ILE LEU ALA SEQRES 11 A 264 ALA TRP GLY MET ILE ILE THR GLY TYR VAL GLY GLN LEU SEQRES 12 A 264 TYR GLU VAL ASP ASP ILE ALA GLN LEU MET ILE TRP GLY SEQRES 13 A 264 ALA VAL SER THR ALA PHE PHE VAL VAL MET ASN TRP ILE SEQRES 14 A 264 VAL GLY THR LYS ILE PHE LYS ASN ARG ALA THR MET LEU SEQRES 15 A 264 GLY GLY THR ASP SER THR ILE THR LYS VAL PHE TRP LEU SEQRES 16 A 264 MET MET PHE ALA TRP THR LEU TYR PRO ILE ALA TYR LEU SEQRES 17 A 264 VAL PRO ALA PHE MET ASN ASN ALA ASP GLY VAL VAL LEU SEQRES 18 A 264 ARG GLN LEU LEU PHE THR ILE ALA ASP ILE SER SER LYS SEQRES 19 A 264 VAL ILE TYR GLY LEU MET ILE THR TYR ILE ALA ILE GLN SEQRES 20 A 264 GLN SER ALA ALA ALA GLY TYR VAL PRO ALA GLN GLN ALA SEQRES 21 A 264 LEU GLY ARG ILE HET CL A 301 1 HET CL A 302 1 HET RET A 303 20 HET OLA A 304 14 HET OLA A 305 20 HET OLA A 306 18 HET OLA A 307 12 HET OLA A 308 20 HET OLA A 309 6 HET OLA A 310 9 HETNAM CL CHLORIDE ION HETNAM RET RETINAL HETNAM OLA OLEIC ACID FORMUL 2 CL 2(CL 1-) FORMUL 4 RET C20 H28 O FORMUL 5 OLA 7(C18 H34 O2) FORMUL 12 HOH *106(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 ALA A 44 ALA A 75 1 32 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 MET A 214 1 30 HELIX 10 AB1 ASN A 216 ALA A 253 1 38 HELIX 11 AB2 TYR A 255 ARG A 264 1 10 SHEET 1 AA1 2 TYR A 76 VAL A 79 0 SHEET 2 AA1 2 SER A 82 LEU A 85 -1 O GLN A 84 N ALA A 77 LINK NZ LYS A 235 C15 RET A 303 1555 1555 1.46 CRYST1 103.370 50.090 69.390 90.00 109.69 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 0.009674 0.000000 0.003462 0.00000 SCALE2 0.000000 0.019964 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015306 0.00000