HEADER MEMBRANE PROTEIN 25-JAN-24 8RSS TITLE CRYSTAL STRUCTURE OF MARINE ACTINOBACTERIA CLADE RHODOPSIN (MAR) IN TITLE 2 THE O* STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: MICROBIAL RHODOPSIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MARINE ACTINOBACTERIA CLADE; SOURCE 3 ORGANISM_TAXID: 62676; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MAC, MACR, MAR, PROTEORHODOPSIN, PR, XANTHORODOPSIN, XR, MEMBRANE KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.BUKHDRUKER,K.KOVALEV,R.ASTASHKIN,V.GORDELIY REVDAT 1 02-APR-25 8RSS 0 JRNL AUTH V.SHEVCHENKO,I.GUSHCHIN,V.POLOVINKIN,K.KOVALEV JRNL TITL PROTEORHODOPSIN INSIGHTS INTO MOLECULAR MECHANISM OF JRNL TITL 2 VECTORIAL PROTON TRANSPORT JRNL REF SCI ADV 2025 JRNL REFN ESSN 2375-2548 REMARK 2 REMARK 2 RESOLUTION. 1.41 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.41 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 60.2 REMARK 3 NUMBER OF REFLECTIONS : 27486 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1347 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 40.1700 - 3.0500 0.94 4222 221 0.1642 0.1962 REMARK 3 2 3.0500 - 2.4200 0.97 4218 212 0.1530 0.1869 REMARK 3 3 2.4200 - 2.1100 0.97 4241 220 0.1457 0.1834 REMARK 3 4 2.1100 - 1.9200 0.80 3493 171 0.1576 0.1962 REMARK 3 5 1.9200 - 1.7800 0.68 2932 150 0.1695 0.2243 REMARK 3 6 1.7800 - 1.6800 0.60 2566 125 0.1718 0.2258 REMARK 3 7 1.6800 - 1.5900 0.51 2195 123 0.1702 0.2342 REMARK 3 8 1.5900 - 1.5200 0.34 1483 88 0.1833 0.2432 REMARK 3 9 1.5200 - 1.4700 0.15 639 35 0.1643 0.2362 REMARK 3 10 1.4600 - 1.4100 0.03 150 2 0.1934 0.1791 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.414 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.12 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.08 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 2116 REMARK 3 ANGLE : 0.579 2852 REMARK 3 CHIRALITY : 0.056 301 REMARK 3 PLANARITY : 0.004 352 REMARK 3 DIHEDRAL : 13.572 812 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 8RSS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1292135963. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JAN-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8856 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 20220110 REMARK 200 DATA SCALING SOFTWARE : STARANISO 2.3.94 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27492 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.410 REMARK 200 RESOLUTION RANGE LOW (A) : 40.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.8 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 4.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 40.17 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 19.70 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.4 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.6 M AMMONIUM PHOSPHATE BUFFER, PH REMARK 280 8.4, LIPIDIC CUBIC PHASE, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 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 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 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: 5030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 19.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 692 LIES ON A SPECIAL POSITION. 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 VAL A 219 REMARK 465 SER A 220 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 GLU A 2 CG CD OE1 OE2 REMARK 470 GLU A 3 CD OE1 OE2 REMARK 470 ARG A 7 NH1 NH2 REMARK 470 MET A 10 CE REMARK 470 ARG A 36 NH1 NH2 REMARK 470 GLU A 148 CG CD OE1 OE2 REMARK 470 LYS A 218 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 GLU A 148 103.24 -55.33 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 502 REMARK 610 LFA A 504 REMARK 610 LFA A 505 REMARK 610 LFA A 506 REMARK 610 LFA A 507 REMARK 610 LFA A 508 REMARK 610 LFA A 509 REMARK 610 LFA A 510 REMARK 610 LFA A 511 REMARK 610 LFA A 512 REMARK 610 LFA A 513 REMARK 610 LFA A 514 DBREF 8RSS A 1 220 PDB 8RSS 8RSS 1 220 SEQRES 1 A 220 MET GLU GLU LEU THR TYR ARG LEU PHE MET VAL ALA THR SEQRES 2 A 220 VAL GLY MET LEU ALA GLY THR VAL PHE LEU LEU ALA SER SEQRES 3 A 220 SER ARG GLU VAL LYS PRO GLU HIS ARG ARG GLY VAL TYR SEQRES 4 A 220 ILE SER ALA LEU VAL CYS GLY ILE ALA TRP TYR HIS TYR SEQRES 5 A 220 GLN LYS MET GLY ALA SER TRP GLU SER GLY SER TYR ASP SEQRES 6 A 220 THR GLY LEU ARG TYR VAL ASP TRP VAL LEU THR VAL PRO SEQRES 7 A 220 LEU MET PHE VAL GLU VAL LEU ALA VAL THR ARG LYS GLY SEQRES 8 A 220 ALA ALA TYR ASN GLU ALA VAL ARG ASN TRP GLY ILE ALA SEQRES 9 A 220 ALA THR VAL MET ILE GLY ALA GLY TYR TYR GLY GLU THR SEQRES 10 A 220 SER ALA ALA GLY SER ASN GLU TYR TRP THR GLY PHE VAL SEQRES 11 A 220 ILE ALA MET ALA THR TYR VAL TRP LEU MET ARG ASN LEU SEQRES 12 A 220 GLN ALA GLU GLY GLU GLY LEU LYS GLY ASP GLN ALA VAL SEQRES 13 A 220 ALA PHE GLU ASN ILE LYS ASN LEU ILE LEU VAL GLY TRP SEQRES 14 A 220 ILE ILE TYR PRO LEU GLY TYR ILE ALA PRO VAL VAL GLY SEQRES 15 A 220 ASP PHE ASP ALA ILE ARG GLU VAL LEU TYR THR ILE ALA SEQRES 16 A 220 ASP ILE ILE ASN LYS VAL GLY LEU GLY VAL LEU VAL LEU SEQRES 17 A 220 GLN MET ALA ARG VAL GLN SER GLY GLU LYS VAL SER HET OLA A 501 20 HET OLA A 502 16 HET OLA A 503 20 HET LFA A 504 8 HET LFA A 505 9 HET LFA A 506 11 HET LFA A 507 8 HET LFA A 508 6 HET LFA A 509 3 HET LFA A 510 7 HET LFA A 511 9 HET LFA A 512 13 HET LFA A 513 4 HET LFA A 514 3 HET RET A 515 20 HETNAM OLA OLEIC ACID HETNAM LFA EICOSANE HETNAM RET RETINAL HETSYN LFA LIPID FRAGMENT FORMUL 2 OLA 3(C18 H34 O2) FORMUL 5 LFA 11(C20 H42) FORMUL 16 RET C20 H28 O FORMUL 17 HOH *147(H2 O) HELIX 1 AA1 MET A 1 SER A 27 1 27 HELIX 2 AA2 ARG A 28 VAL A 30 5 3 HELIX 3 AA3 LYS A 31 HIS A 34 5 4 HELIX 4 AA4 ARG A 35 GLY A 62 1 28 HELIX 5 AA5 THR A 66 ARG A 89 1 24 HELIX 6 AA6 LYS A 90 THR A 117 1 28 HELIX 7 AA7 SER A 122 GLU A 146 1 25 HELIX 8 AA8 LYS A 151 TRP A 169 1 19 HELIX 9 AA9 ILE A 170 GLY A 182 1 13 HELIX 10 AB1 PHE A 184 SER A 215 1 32 LINK NZ LYS A 200 C15 RET A 515 1555 1555 1.45 CRYST1 50.608 40.174 60.307 90.00 101.22 90.00 P 1 2 1 2 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 0.019760 0.000000 0.003920 0.00000 SCALE2 0.000000 0.024892 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016905 0.00000