HEADER MEMBRANE PROTEIN 26-APR-20 6WP8 TITLE PROTON-PUMPING MUTANT OF MASTIGOCLADOPSIS REPENS RHODOPSIN CHLORIDE TITLE 2 PUMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTON-PUMPING RHODOPSIN CHLORIDE PUMP; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MASTIGOCLADOPSIS REPENS; SOURCE 3 ORGANISM_TAXID: 221287; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RETINAL PROTEIN, PROTON PUMP, ION PUMP, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.E.BESAW,O.P.ERNST,W.OU,T.MORIZUMI REVDAT 4 18-OCT-23 6WP8 1 REMARK REVDAT 3 11-NOV-20 6WP8 1 JRNL REVDAT 2 12-AUG-20 6WP8 1 JRNL HETSYN REVDAT 1 29-JUL-20 6WP8 0 JRNL AUTH J.E.BESAW,W.L.OU,T.MORIZUMI,B.T.EGER,J.D.SANCHEZ VASQUEZ, JRNL AUTH 2 J.H.Y.CHU,A.HARRIS,L.S.BROWN,R.J.D.MILLER,O.P.ERNST JRNL TITL THE CRYSTAL STRUCTURES OF A CHLORIDE-PUMPING MICROBIAL JRNL TITL 2 RHODOPSIN AND ITS PROTON-PUMPING MUTANT ILLUMINATE PROTON JRNL TITL 3 TRANSFER DETERMINANTS. JRNL REF J.BIOL.CHEM. V. 295 14793 2020 JRNL REFN ESSN 1083-351X JRNL PMID 32703899 JRNL DOI 10.1074/JBC.RA120.014118 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.6 REMARK 3 NUMBER OF REFLECTIONS : 11093 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.930 REMARK 3 FREE R VALUE TEST SET COUNT : 1101 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 28.9200 - 4.9900 0.87 1244 144 0.2248 0.2463 REMARK 3 2 4.9900 - 3.9700 0.90 1255 134 0.1959 0.2133 REMARK 3 3 3.9700 - 3.4700 0.92 1243 144 0.2067 0.2081 REMARK 3 4 3.4700 - 3.1500 0.92 1254 136 0.2441 0.2817 REMARK 3 5 3.1500 - 2.9200 0.92 1247 139 0.2459 0.2694 REMARK 3 6 2.9200 - 2.7500 0.92 1245 133 0.2655 0.2832 REMARK 3 7 2.7500 - 2.6100 0.93 1247 137 0.2686 0.2984 REMARK 3 8 2.6100 - 2.5000 0.93 1257 134 0.2996 0.3223 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) : 0.292 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.328 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.66 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 : 0.004 1854 REMARK 3 ANGLE : 0.661 2533 REMARK 3 CHIRALITY : 0.039 295 REMARK 3 PLANARITY : 0.004 303 REMARK 3 DIHEDRAL : 11.016 1049 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 6WP8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-APR-20. REMARK 100 THE DEPOSITION ID IS D_1000246676. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-NOV-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.0-4.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.033 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11125 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 28.920 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.000 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: 6NWF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.6 M SODIUM PHOSPHATE MONOBASIC REMARK 280 MONOHYDRATE, PH 4.0, 180 MM 1,6 HEXANEDIOL, 3.5% TRIETHYLENE REMARK 280 GLYCOL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 307.15K 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: 6920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 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 103.74100 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 179.68468 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -103.74100 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 179.68468 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 223 REMARK 465 PRO A 224 REMARK 465 ALA A 225 REMARK 465 ARG A 226 REMARK 465 GLU A 227 REMARK 465 THR A 228 REMARK 465 HIS A 229 REMARK 465 LEU A 230 REMARK 465 SER A 231 REMARK 465 TYR A 232 REMARK 465 LEU A 233 REMARK 465 GLU A 234 REMARK 465 HIS A 235 REMARK 465 HIS A 236 REMARK 465 HIS A 237 REMARK 465 HIS A 238 REMARK 465 HIS A 239 REMARK 465 HIS A 240 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 LYS A 28 -80.94 -61.23 REMARK 500 ASN A 29 -158.90 -113.80 REMARK 500 GLN A 142 -75.06 -117.70 REMARK 500 ARG A 154 32.74 -97.91 REMARK 500 SER A 155 42.07 -149.67 REMARK 500 ALA A 221 43.28 -83.95 REMARK 500 REMARK 500 REMARK: NULL DBREF 6WP8 A 1 240 PDB 6WP8 6WP8 1 240 SEQRES 1 A 240 MET THR GLN ALA TRP LEU TRP ILE GLY VAL ILE SER MET SEQRES 2 A 240 ALA LEU GLY SER VAL PHE PHE GLY PHE GLY ALA HIS ASN SEQRES 3 A 240 ALA LYS ASN GLU ARG TRP GLN ILE LEU TYR THR LEU ASN SEQRES 4 A 240 PHE PHE ILE CYS LEU ILE ALA ALA GLY LEU TYR LEU ALA SEQRES 5 A 240 MET ALA LEU GLY LEU GLY VAL ASN VAL ILE ASN GLY ARG SEQRES 6 A 240 PRO THR TYR TRP VAL ARG PHE VAL ASP TRP PHE CYS SER SEQRES 7 A 240 THR PRO LEU LEU LEU LEU ASP LEU THR PHE LEU GLY ARG SEQRES 8 A 240 THR SER LEU PRO LEU THR GLY SER LEU LEU GLY ALA ASN SEQRES 9 A 240 ALA TYR MET LEU VAL THR GLY PHE VAL ALA THR VAL THR SEQRES 10 A 240 PRO LYS PRO MET SER TYR ILE TRP TYR ILE VAL SER CYS SEQRES 11 A 240 ALA ALA TYR LEU ALA ILE VAL TYR LEU LEU ALA GLN PRO SEQRES 12 A 240 TYR ARG ILE ALA ALA GLU ARG LYS HIS PRO ARG SER LYS SEQRES 13 A 240 GLN ALA PHE ARG THR LEU VAL THR VAL HIS LEU VAL LEU SEQRES 14 A 240 TRP THR LEU TYR PRO ILE VAL TRP ILE LEU SER PRO GLU SEQRES 15 A 240 GLY PHE SER THR PHE THR GLN GLY SER GLU THR MET PHE SEQRES 16 A 240 TYR THR LEU LEU ASP ILE ALA SER LYS VAL GLY PHE GLY SEQRES 17 A 240 PHE LEU SER LEU ASN THR LEU HIS THR LEU GLU GLN ALA SEQRES 18 A 240 THR GLU PRO ALA ARG GLU THR HIS LEU SER TYR LEU GLU SEQRES 19 A 240 HIS HIS HIS HIS HIS HIS HET RET A 301 20 HET BOG A 302 20 HETNAM RET RETINAL HETNAM BOG OCTYL BETA-D-GLUCOPYRANOSIDE HETSYN BOG BETA-OCTYLGLUCOSIDE; OCTYL BETA-D-GLUCOSIDE; OCTYL D- HETSYN 2 BOG GLUCOSIDE; OCTYL GLUCOSIDE FORMUL 2 RET C20 H28 O FORMUL 3 BOG C14 H28 O6 FORMUL 4 HOH *15(H2 O) HELIX 1 AA1 MET A 1 ASN A 26 1 26 HELIX 2 AA2 ASN A 29 LEU A 55 1 27 HELIX 3 AA3 VAL A 70 ARG A 91 1 22 HELIX 4 AA4 SER A 93 THR A 117 1 25 HELIX 5 AA5 PRO A 120 GLN A 142 1 23 HELIX 6 AA6 GLN A 142 HIS A 152 1 11 HELIX 7 AA7 SER A 155 SER A 180 1 26 HELIX 8 AA8 THR A 188 ALA A 221 1 34 SHEET 1 AA1 2 ASN A 60 ILE A 62 0 SHEET 2 AA1 2 ARG A 65 THR A 67 -1 O THR A 67 N ASN A 60 LINK NZ LYS A 204 C15 RET A 301 1555 1555 1.31 CISPEP 1 LYS A 119 PRO A 120 0 1.18 CRYST1 103.741 103.741 55.213 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 0.009639 0.005565 0.000000 0.00000 SCALE2 0.000000 0.011131 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018112 0.00000