HEADER MEMBRANE PROTEIN 01-MAR-22 7U55 TITLE CRYSTAL STRUCTURE OF THERMOPLASMATALES ARCHAEON HELIORHODOPSIN AT PH TITLE 2 4.5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HELIORHODOPSIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOPLASMATALES ARCHAEON SG8-52-1; SOURCE 3 ORGANISM_TAXID: 1803816; SOURCE 4 GENE: AYK20_03510; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MICROBIAL RHODOPSIN, RETINAL PROTEIN, HELIORHODOPSIN, SEVEN KEYWDS 2 TRANSMEMBRANE PROTEIN, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.E.BESAW,P.DE GUZMAN,R.J.D.MILLER,O.P.ERNST REVDAT 2 18-OCT-23 7U55 1 REMARK REVDAT 1 07-SEP-22 7U55 0 JRNL AUTH J.E.BESAW,J.REICHENWALLNER,P.DE GUZMAN,A.TUCS,A.KUO, JRNL AUTH 2 T.MORIZUMI,K.TSUDA,A.SLJOKA,R.J.D.MILLER,O.P.ERNST JRNL TITL LOW PH STRUCTURE OF HELIORHODOPSIN REVEALS CHLORIDE BINDING JRNL TITL 2 SITE AND INTRAMOLECULAR SIGNALING PATHWAY. JRNL REF SCI REP V. 12 13955 2022 JRNL REFN ESSN 2045-2322 JRNL PMID 35977989 JRNL DOI 10.1038/S41598-022-17716-9 REMARK 2 REMARK 2 RESOLUTION. 1.97 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) : 1.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.94 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 3 NUMBER OF REFLECTIONS : 16704 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1671 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 47.9400 - 4.5100 0.88 1286 144 0.2258 0.2603 REMARK 3 2 4.5100 - 3.5800 0.91 1245 138 0.2103 0.2280 REMARK 3 3 3.5800 - 3.1300 0.92 1247 139 0.1937 0.1879 REMARK 3 4 3.1300 - 2.8400 0.94 1252 140 0.1823 0.1971 REMARK 3 5 2.8400 - 2.6400 0.94 1256 140 0.1736 0.1992 REMARK 3 6 2.6400 - 2.4800 0.94 1237 138 0.1665 0.2100 REMARK 3 7 2.4800 - 2.3600 0.95 1260 139 0.1668 0.2087 REMARK 3 8 2.3600 - 2.2600 0.96 1272 141 0.1732 0.1861 REMARK 3 9 2.2600 - 2.1700 0.96 1263 139 0.1812 0.2270 REMARK 3 10 2.1700 - 2.1000 0.97 1274 142 0.1905 0.2161 REMARK 3 11 2.1000 - 2.0300 0.96 1269 141 0.2171 0.2408 REMARK 3 12 2.0300 - 1.9700 0.89 1172 130 0.2457 0.2972 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) : 0.167 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.400 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.85 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.56 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 : 0.009 2135 REMARK 3 ANGLE : 1.133 2917 REMARK 3 CHIRALITY : 0.068 338 REMARK 3 PLANARITY : 0.008 354 REMARK 3 DIHEDRAL : 20.787 756 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 7U55 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1000263511. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-NOV-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 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 : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16754 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.970 REMARK 200 RESOLUTION RANGE LOW (A) : 47.940 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 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: 6IS6 REMARK 200 REMARK 200 REMARK: DIAMOND REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: BICELLE CRYSTALLIZATION WITH 5 MG/ML REMARK 280 PROTEIN IN 8% BICELLE (2.8:1 DMPC:CHAPSO). CRYSTALLIZATION REMARK 280 CONDITION IS 26% POLYETHYLENE GLYCOL 3350, 0.1 M SODIUM REMARK 280 PHOSPHATE MONOBASIC MONOHYDRATE AT PH 4.5, 0.28 M AMMONIUM REMARK 280 SULFATE, 0.18 M 1,6-HEXANEDIOL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 307.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 44.92400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.98700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 44.92400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.98700 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -77.0 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 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 MET A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 HIS A 1 REMARK 465 THR A 2 REMARK 465 GLU A 3 REMARK 465 ASN A 4 REMARK 465 GLU A 5 REMARK 465 GLU A 6 REMARK 465 ILE A 7 REMARK 465 MET A 253 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 VAL A 88 CB - CA - C ANGL. DEV. = -11.8 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 THR A 87 -94.71 -128.12 REMARK 500 THR A 87 -98.77 -128.12 REMARK 500 THR A 125 12.31 89.29 REMARK 500 THR A 125 12.31 89.26 REMARK 500 THR A 249 -15.97 -144.20 REMARK 500 REMARK 500 REMARK: NULL DBREF1 7U55 A 2 253 UNP A0A151EDA9_9ARCH DBREF2 7U55 A A0A151EDA9 2 253 SEQADV 7U55 MET A -5 UNP A0A151EDA INITIATING METHIONINE SEQADV 7U55 HIS A -4 UNP A0A151EDA EXPRESSION TAG SEQADV 7U55 HIS A -3 UNP A0A151EDA EXPRESSION TAG SEQADV 7U55 HIS A -2 UNP A0A151EDA EXPRESSION TAG SEQADV 7U55 HIS A -1 UNP A0A151EDA EXPRESSION TAG SEQADV 7U55 HIS A 0 UNP A0A151EDA EXPRESSION TAG SEQADV 7U55 HIS A 1 UNP A0A151EDA EXPRESSION TAG SEQRES 1 A 259 MET HIS HIS HIS HIS HIS HIS THR GLU ASN GLU GLU ILE SEQRES 2 A 259 ASN PHE ARG LYS PHE ARG ILE PHE ASN GLY ILE MET GLY SEQRES 3 A 259 VAL ILE HIS LEU ILE GLN VAL PHE LEU VAL LEU TYR LEU SEQRES 4 A 259 SER ASN ASN PHE SER LEU PRO ILE THR VAL ASN LYS PRO SEQRES 5 A 259 VAL TYR ASN GLU ILE THR ASN SER ILE SER PRO VAL ALA SEQRES 6 A 259 GLU THR LEU PHE SER ILE GLU ILE GLY PRO LEU VAL ALA SEQRES 7 A 259 MET PHE LEU PHE ILE SER ALA THR ALA HIS ILE LEU ILE SEQRES 8 A 259 ALA THR VAL LEU TYR TYR ARG TYR VAL GLN ASN LEU LYS SEQRES 9 A 259 ASN HIS MET ASN PRO TYR ARG TRP PHE GLU TYR SER ILE SEQRES 10 A 259 SER ALA SER PHE MET ILE VAL ILE ILE ALA MET LEU THR SEQRES 11 A 259 THR ILE TYR ASP LEU GLY THR LEU LEU ALA LEU PHE THR SEQRES 12 A 259 LEU THR ALA VAL MET ASN LEU MET GLY LEU MET MET GLU SEQRES 13 A 259 LEU HIS ASN GLN THR THR GLN ASN THR ASN TRP THR SER SEQRES 14 A 259 TYR ILE ILE GLY CYS ILE ALA GLY PHE VAL PRO TRP ILE SEQRES 15 A 259 VAL ILE PHE ILE PRO LEU ILE SER ALA GLU SER VAL PRO SEQRES 16 A 259 ASP PHE VAL ILE TYR ILE PHE ILE SER ILE ALA ILE PHE SEQRES 17 A 259 PHE ASN CYS PHE ALA ILE ASN MET TYR LEU GLN TYR LYS SEQRES 18 A 259 LYS ILE GLY LYS TRP LYS ASN TYR LEU HIS GLY GLU LYS SEQRES 19 A 259 VAL TYR ILE ILE LEU SER LEU VAL ALA LYS SER ALA LEU SEQRES 20 A 259 ALA TRP GLN VAL PHE ALA GLY THR LEU ARG PRO MET HET RET A 301 20 HET CL A 302 1 HET CL A 303 1 HET D12 A 304 12 HETNAM RET RETINAL HETNAM CL CHLORIDE ION HETNAM D12 DODECANE FORMUL 2 RET C20 H28 O FORMUL 3 CL 2(CL 1-) FORMUL 5 D12 C12 H26 FORMUL 6 HOH *37(H2 O) HELIX 1 AA1 PHE A 9 SER A 34 1 26 HELIX 2 AA2 ILE A 67 THR A 87 1 21 HELIX 3 AA3 LEU A 89 ASN A 99 1 11 HELIX 4 AA4 ASN A 102 THR A 124 1 23 HELIX 5 AA5 ASP A 128 ASN A 153 1 26 HELIX 6 AA6 TRP A 161 ALA A 185 1 25 HELIX 7 AA7 PRO A 189 LYS A 216 1 28 HELIX 8 AA8 ILE A 217 LYS A 221 5 5 HELIX 9 AA9 ASN A 222 LEU A 250 1 29 SHEET 1 AA1 2 SER A 38 ASN A 44 0 SHEET 2 AA1 2 ALA A 59 GLU A 66 -1 O LEU A 62 N ILE A 41 SHEET 1 AA2 2 VAL A 47 ASN A 49 0 SHEET 2 AA2 2 SER A 54 SER A 56 -1 O SER A 54 N ASN A 49 LINK NZ LYS A 238 C15 RET A 301 1555 1555 1.22 CRYST1 89.848 47.974 56.688 90.00 90.00 90.00 P 21 21 2 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 0.011130 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020845 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017640 0.00000