HEADER PROTON TRANSPORT 08-MAY-19 6RNJ TITLE TR-SMX CLOSED STATE STRUCTURE (0-5MS) OF BACTERIORHODOPSIN 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 KEYWDS RETINAL, TIME-RESOLVED CRYSTALLOGRAPHY, SERIAL CRYSTALLOGRAPHY, SMX, KEYWDS 2 PROTON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR T.WEINERT,P.SKOPINTSEV,D.JAMES,D.KEKILLI,F.FURRER,S.BRUENLE,S.MOUS, AUTHOR 2 P.NOGLY,J.STANDFUSS REVDAT 2 24-JAN-24 6RNJ 1 REMARK REVDAT 1 17-JUL-19 6RNJ 0 JRNL AUTH T.WEINERT,P.SKOPINTSEV,D.JAMES,F.DWORKOWSKI,E.PANEPUCCI, JRNL AUTH 2 D.KEKILLI,A.FURRER,S.BRUNLE,S.MOUS,D.OZEROV,P.NOGLY,M.WANG, JRNL AUTH 3 J.STANDFUSS JRNL TITL PROTON UPTAKE MECHANISM IN BACTERIORHODOPSIN CAPTURED BY JRNL TITL 2 SERIAL SYNCHROTRON CRYSTALLOGRAPHY. JRNL REF SCIENCE V. 365 61 2019 JRNL REFN ESSN 1095-9203 JRNL PMID 31273117 JRNL DOI 10.1126/SCIENCE.AAW8634 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.020 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.8 REMARK 3 NUMBER OF REFLECTIONS : 6737 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.253 REMARK 3 R VALUE (WORKING SET) : 0.249 REMARK 3 FREE R VALUE : 0.301 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.220 REMARK 3 FREE R VALUE TEST SET COUNT : 419 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 38.4800 - 3.7500 0.97 2300 141 0.2149 0.2539 REMARK 3 2 3.7500 - 2.9800 0.91 2092 151 0.2903 0.3570 REMARK 3 3 2.9800 - 2.6000 0.84 1926 127 0.3719 0.4750 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) : 0.537 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 44.802 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 62.04 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 83.73 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 : 0.003 1838 REMARK 3 ANGLE : 0.447 2510 REMARK 3 CHIRALITY : 0.035 294 REMARK 3 PLANARITY : 0.003 306 REMARK 3 DIHEDRAL : 9.857 1046 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 6RNJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-MAY-19. REMARK 100 THE DEPOSITION ID IS D_1292101059. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUL-18; 22-JUL-18; 22-JUL-18 REMARK 200 TEMPERATURE (KELVIN) : 298; 298; 298 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y; Y REMARK 200 RADIATION SOURCE : SLS; SLS; SLS REMARK 200 BEAMLINE : X06SA; X06SA; X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0; 1.0; 1.0 REMARK 200 MONOCHROMATOR : SI; NULL; SI REMARK 200 OPTICS : NULL; NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL; PIXEL; PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M; DECTRIS REMARK 200 EIGER X 16M; DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL 0.7 REMARK 200 DATA SCALING SOFTWARE : CRYSTFEL 0.7 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6737 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 38.470 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.1 REMARK 200 DATA REDUNDANCY : 1.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 1.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.00 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; SINGLE WAVELENGTH; SINGLE REMARK 200 WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 5B6Z REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM NA/K PHOSPHATE BUFFER PH 5.6 30 REMARK 280 % PEG 2000, LIPIDIC CUBIC PHASE, TEMPERATURE 294K 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 55.15000 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 55.15000 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 55.15000 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: 6220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.0 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 31.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 53.69358 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -31.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 53.69358 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 LYS A 159 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU A 74 CG CD OE1 OE2 REMARK 480 SER A 158 OG REMARK 480 GLU A 161 CG CD OE1 OE2 REMARK 480 LYS A 172 CG CD CE NZ REMARK 480 ARG A 225 CG CD NE CZ NH1 NH2 REMARK 480 ARG A 227 CG CD NE CZ NH1 NH2 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 HH TYR A 57 OD2 ASP A 212 1.55 REMARK 500 O ALA A 215 O HOH A 453 2.02 REMARK 500 OE2 GLU A 204 O HOH A 458 2.06 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 ARG A 225 32.84 -86.76 REMARK 500 ILE A 229 -149.64 -83.45 REMARK 500 PHE A 230 -166.33 55.37 REMARK 500 REMARK 500 REMARK: NULL 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 501 DBREF 6RNJ A 5 233 UNP P02945 BACR_HALSA 18 246 SEQRES 1 A 229 THR GLY ARG PRO GLU TRP ILE TRP LEU ALA LEU GLY THR SEQRES 2 A 229 ALA LEU MET GLY LEU GLY THR LEU TYR PHE LEU VAL LYS SEQRES 3 A 229 GLY MET GLY VAL SER ASP PRO ASP ALA LYS LYS PHE TYR SEQRES 4 A 229 ALA ILE THR THR LEU VAL PRO ALA ILE ALA PHE THR MET SEQRES 5 A 229 TYR LEU SER MET LEU LEU GLY TYR GLY LEU THR MET VAL SEQRES 6 A 229 PRO PHE GLY GLY GLU GLN ASN PRO ILE TYR TRP ALA ARG SEQRES 7 A 229 TYR ALA ASP TRP LEU PHE THR THR PRO LEU LEU LEU LEU SEQRES 8 A 229 ASP LEU ALA LEU LEU VAL ASP ALA ASP GLN GLY THR ILE SEQRES 9 A 229 LEU ALA LEU VAL GLY ALA ASP GLY ILE MET ILE GLY THR SEQRES 10 A 229 GLY LEU VAL GLY ALA LEU THR LYS VAL TYR SER TYR ARG SEQRES 11 A 229 PHE VAL TRP TRP ALA ILE SER THR ALA ALA MET LEU TYR SEQRES 12 A 229 ILE LEU TYR VAL LEU PHE PHE GLY PHE THR SER LYS ALA SEQRES 13 A 229 GLU SER MET ARG PRO GLU VAL ALA SER THR PHE LYS VAL SEQRES 14 A 229 LEU ARG ASN VAL THR VAL VAL LEU TRP SER ALA TYR PRO SEQRES 15 A 229 VAL VAL TRP LEU ILE GLY SER GLU GLY ALA GLY ILE VAL SEQRES 16 A 229 PRO LEU ASN ILE GLU THR LEU LEU PHE MET VAL LEU ASP SEQRES 17 A 229 VAL SER ALA LYS VAL GLY PHE GLY LEU ILE LEU LEU ARG SEQRES 18 A 229 SER ARG ALA ILE PHE GLY GLU ALA HET RET A 501 47 HETNAM RET RETINAL FORMUL 2 RET C20 H28 O FORMUL 3 HOH *8(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 TYR A 79 ASP A 102 1 24 HELIX 4 AA4 ASP A 104 THR A 128 1 25 HELIX 5 AA5 VAL A 130 PHE A 154 1 25 HELIX 6 AA6 PHE A 154 MET A 163 1 10 HELIX 7 AA7 ARG A 164 GLY A 192 1 29 HELIX 8 AA8 PRO A 200 VAL A 217 1 18 HELIX 9 AA9 VAL A 217 ARG A 225 1 9 SHEET 1 AA1 2 THR A 67 PHE A 71 0 SHEET 2 AA1 2 GLU A 74 ILE A 78 -1 O ILE A 78 N THR A 67 LINK NZ LYS A 216 C15 RET A 501 1555 1555 1.41 SITE 1 AC1 13 TRP A 86 THR A 90 MET A 118 TRP A 138 SITE 2 AC1 13 SER A 141 THR A 142 TRP A 182 TYR A 185 SITE 3 AC1 13 PRO A 186 TRP A 189 ASP A 212 ALA A 215 SITE 4 AC1 13 LYS A 216 CRYST1 62.000 62.000 110.300 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 0.016129 0.009312 0.000000 0.00000 SCALE2 0.000000 0.018624 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009066 0.00000