HEADER MEMBRANE PROTEIN 07-MAY-19 6RMK TITLE BACTERIORHODOPSIN, DARK STATE, CELL 2, REFINED USING THE SAME PROTOCOL TITLE 2 AS SUB-PS TIME DELAYS COMPND MOL_ID: 1; COMPND 2 MOLECULE: BACTERIORHODOPSIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BR,BACTERIOOPSIN,BO SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HALOBACTERIUM SALINARUM NRC-1; SOURCE 3 ORGANISM_TAXID: 64091; SOURCE 4 VARIANT: ATCC 700922 / JCM 11081 / NRC-1 KEYWDS MEMBRANE PROTEIN, PROTON PUMP, TIME-RESOLVED CRYSTALLOGRAPHY, FREE- KEYWDS 2 ELECTRON LASER EXPDTA X-RAY DIFFRACTION AUTHOR G.NASS KOVACS,J.-P.COLLETIER,M.L.GRUENBEIN,T.STENSITZKI,A.BATYUK, AUTHOR 2 S.CARBAJO,R.B.DOAK,D.EHRENBERG,L.FOUCAR,R.GASPER,A.GOREL,M.HILPERT, AUTHOR 3 M.KLOOS,J.KOGLIN,J.REINSTEIN,C.M.ROOME,R.SCHLESINGER,M.SEABERG, AUTHOR 4 R.L.SHOEMAN,M.STRICKER,S.BOUTET,S.HAACKE,J.HEBERLE,T.DOMRATCHEVA, AUTHOR 5 T.R.M.BARENDS,I.SCHLICHTING REVDAT 3 24-JAN-24 6RMK 1 REMARK REVDAT 2 31-JUL-19 6RMK 1 JRNL REVDAT 1 05-JUN-19 6RMK 0 JRNL AUTH G.NASS KOVACS,J.P.COLLETIER,M.L.GRUNBEIN,Y.YANG, JRNL AUTH 2 T.STENSITZKI,A.BATYUK,S.CARBAJO,R.B.DOAK,D.EHRENBERG, JRNL AUTH 3 L.FOUCAR,R.GASPER,A.GOREL,M.HILPERT,M.KLOOS,J.E.KOGLIN, JRNL AUTH 4 J.REINSTEIN,C.M.ROOME,R.SCHLESINGER,M.SEABERG,R.L.SHOEMAN, JRNL AUTH 5 M.STRICKER,S.BOUTET,S.HAACKE,J.HEBERLE,K.HEYNE, JRNL AUTH 6 T.DOMRATCHEVA,T.R.M.BARENDS,I.SCHLICHTING JRNL TITL THREE-DIMENSIONAL VIEW OF ULTRAFAST DYNAMICS IN PHOTOEXCITED JRNL TITL 2 BACTERIORHODOPSIN. JRNL REF NAT COMMUN V. 10 3177 2019 JRNL REFN ESSN 2041-1723 JRNL PMID 31320619 JRNL DOI 10.1038/S41467-019-10758-0 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (DEV_2645: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.44 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 22360 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.244 REMARK 3 R VALUE (WORKING SET) : 0.244 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1137 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 20.4427 - 3.5944 1.00 2682 154 0.2394 0.2491 REMARK 3 2 3.5944 - 2.8554 1.00 2665 142 0.2024 0.2088 REMARK 3 3 2.8554 - 2.4952 1.00 2645 130 0.2199 0.2273 REMARK 3 4 2.4952 - 2.2674 1.00 2674 134 0.2499 0.2508 REMARK 3 5 2.2674 - 2.1051 1.00 2640 141 0.2623 0.2472 REMARK 3 6 2.1051 - 1.9811 1.00 2620 143 0.2923 0.2974 REMARK 3 7 1.9811 - 1.8819 1.00 2637 144 0.3474 0.3468 REMARK 3 8 1.8819 - 1.8000 1.00 2660 149 0.3984 0.4349 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.330 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.006 1855 REMARK 3 ANGLE : 0.933 2533 REMARK 3 CHIRALITY : 0.048 298 REMARK 3 PLANARITY : 0.010 304 REMARK 3 DIHEDRAL : 15.581 1051 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 6RMK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-MAY-19. REMARK 100 THE DEPOSITION ID IS D_1292102209. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-AUG-17 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : NULL 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) : 1.26 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : CS-PAD CXI-2 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL REMARK 200 DATA SCALING SOFTWARE : CRYSTFEL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22403 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 20.444 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 476.0 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 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: PHASER REMARK 200 STARTING MODEL: 5B6V REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 32% (W/V) PEG 2000, 0.1 M K2HPO4 REMARK 280 /NAH2PO4, IN HAMILTON SYRINGES, PH 5.6, LIPIDIC CUBIC PHASE,, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 55.25000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 55.25000 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 55.25000 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: 6420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -52.0 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 -62.10000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -31.05000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 -53.78018 REMARK 350 BIOMT3 3 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 OG1 THR A 157 NH1 ARG A 175 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 435 DISTANCE = 9.20 ANGSTROMS REMARK 525 HOH A 436 DISTANCE = 9.53 ANGSTROMS 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 300 DBREF 6RMK A 4 234 UNP P02945 BACR_HALSA 17 247 SEQRES 1 A 231 ILE THR GLY ARG PRO GLU TRP ILE TRP LEU ALA LEU GLY SEQRES 2 A 231 THR ALA LEU MET GLY LEU GLY THR LEU TYR PHE LEU VAL SEQRES 3 A 231 LYS GLY MET GLY VAL SER ASP PRO ASP ALA LYS LYS PHE SEQRES 4 A 231 TYR ALA ILE THR THR LEU VAL PRO ALA ILE ALA PHE THR SEQRES 5 A 231 MET TYR LEU SER MET LEU LEU GLY TYR GLY LEU THR MET SEQRES 6 A 231 VAL PRO PHE GLY GLY GLU GLN ASN PRO ILE TYR TRP ALA SEQRES 7 A 231 ARG TYR ALA ASP TRP LEU PHE THR THR PRO LEU LEU LEU SEQRES 8 A 231 LEU ASP LEU ALA LEU LEU VAL ASP ALA ASP GLN GLY THR SEQRES 9 A 231 ILE LEU ALA LEU VAL GLY ALA ASP GLY ILE MET ILE GLY SEQRES 10 A 231 THR GLY LEU VAL GLY ALA LEU THR LYS VAL TYR SER TYR SEQRES 11 A 231 ARG PHE VAL TRP TRP ALA ILE SER THR ALA ALA MET LEU SEQRES 12 A 231 TYR ILE LEU TYR VAL LEU PHE PHE GLY PHE THR SER LYS SEQRES 13 A 231 ALA GLU SER MET ARG PRO GLU VAL ALA SER THR PHE LYS SEQRES 14 A 231 VAL LEU ARG ASN VAL THR VAL VAL LEU TRP SER ALA TYR SEQRES 15 A 231 PRO VAL VAL TRP LEU ILE GLY SER GLU GLY ALA GLY ILE SEQRES 16 A 231 VAL PRO LEU ASN ILE GLU THR LEU LEU PHE MET VAL LEU SEQRES 17 A 231 ASP VAL SER ALA LYS VAL GLY PHE GLY LEU ILE LEU LEU SEQRES 18 A 231 ARG SER ARG ALA ILE PHE GLY GLU ALA GLU HET RET A 300 20 HETNAM RET RETINAL FORMUL 2 RET C20 H28 O FORMUL 3 HOH *36(H2 O) HELIX 1 AA1 GLU A 9 GLY A 31 1 23 HELIX 2 AA2 ASP A 36 LEU A 62 1 27 HELIX 3 AA3 TRP A 80 VAL A 101 1 22 HELIX 4 AA4 ASP A 104 THR A 128 1 25 HELIX 5 AA5 VAL A 130 GLY A 155 1 26 HELIX 6 AA6 PHE A 156 GLU A 161 1 6 HELIX 7 AA7 ARG A 164 GLY A 192 1 29 HELIX 8 AA8 PRO A 200 ARG A 225 1 26 HELIX 9 AA9 SER A 226 PHE A 230 5 5 SHEET 1 AA1 2 LEU A 66 PHE A 71 0 SHEET 2 AA1 2 GLU A 74 TYR A 79 -1 O ILE A 78 N THR A 67 LINK NZ LYS A 216 C15 RET A 300 1555 1555 1.30 SITE 1 AC1 9 TRP A 86 THR A 90 TRP A 138 SER A 141 SITE 2 AC1 9 TRP A 182 TYR A 185 TRP A 189 ASP A 212 SITE 3 AC1 9 LYS A 216 CRYST1 62.100 62.100 110.500 90.00 90.00 120.00 P 63 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 0.016103 0.009297 0.000000 0.00000 SCALE2 0.000000 0.018594 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009050 0.00000