HEADER MEMBRANE PROTEIN 28-MAR-22 7ZCM TITLE DARK STATE STRUCTURE OF SENSORY RHODOPSIN II IN COMPLEX WITH HTRII TITLE 2 SOLVED BY ROOM TEMPERATURE SERIAL SYNCHROTRON CRYSTALLOGRAPHY COMPND MOL_ID: 1; COMPND 2 MOLECULE: SENSORY RHODOPSIN-2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SENSORY RHODOPSIN II,SR-II; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: SENSORY RHODOPSIN II TRANSDUCER; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: HTR-II,METHYL-ACCEPTING PHOTOTAXIS PROTEIN II,MPP-II; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NATRONOMONAS PHARAONIS; SOURCE 3 ORGANISM_TAXID: 2257; SOURCE 4 GENE: SOP2, SOPII; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: NATRONOMONAS PHARAONIS; SOURCE 9 ORGANISM_TAXID: 2257; SOURCE 10 GENE: HTR2, HTRII; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SRII, HTRII, SERIAL SYNCHROTRON CRYSTALLOGRAPHY, SENSORY RHODOPSIN, KEYWDS 2 SENSORY RHODOPSIN II, HALOBACTERIAL TRANSDUCER II, SSX, SIGNALLING KEYWDS 3 PROTEIN, TCL, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.ORTOLANI,R.BOSMAN,L.OSTOJIC REVDAT 1 29-NOV-23 7ZCM 0 JRNL AUTH G.ORTOLANI,R.BOSMAN,L.OSTOJIC,G.BRANDEN,R.NEUTZE JRNL TITL SERIAL SYNCHROTRON CRYSTALLOGRAPHY STRUCTURE OF THE SENSORY JRNL TITL 2 RHODOPSIN II TRANSDUCER COMPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.65 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 10065 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.302 REMARK 3 R VALUE (WORKING SET) : 0.297 REMARK 3 FREE R VALUE : 0.350 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1006 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 27.6500 - 5.4400 1.00 1387 153 0.2681 0.3536 REMARK 3 2 5.4400 - 4.3200 0.99 1298 144 0.2070 0.2400 REMARK 3 3 4.3200 - 3.7800 1.00 1284 143 0.2381 0.3436 REMARK 3 4 3.7800 - 3.4300 1.00 1286 143 0.3195 0.3423 REMARK 3 5 3.4300 - 3.1900 1.00 1272 142 0.3546 0.3713 REMARK 3 6 3.1900 - 3.0000 1.00 1262 140 0.3700 0.4021 REMARK 3 7 3.0000 - 2.8500 1.00 1270 141 0.3940 0.4492 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) : 0.510 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 37.680 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.93 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7ZCM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1292121670. 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) : 298 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000342 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 : CARELESS REMARK 200 DATA SCALING SOFTWARE : CARELESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10066 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.850 REMARK 200 RESOLUTION RANGE LOW (A) : 27.650 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 1.050 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.7300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 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: 1H2S REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 400 38%, CALCIUM CHLORIDE 0.15 M, REMARK 280 GLYCINE 0.1 M, PH 7.5, LIPIDIC CUBIC PHASE, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 2 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,-Z REMARK 290 4555 -X+1/2,-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 SMTRY1 3 1.000000 0.000000 0.000000 26.43500 REMARK 290 SMTRY2 3 0.000000 -1.000000 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 26.43500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 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: 2760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 222 REMARK 465 HIS A 223 REMARK 465 GLY A 224 REMARK 465 GLU A 225 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 VAL A 2 -50.18 -149.01 REMARK 500 ALA A 29 -177.30 -68.60 REMARK 500 SER A 31 -76.93 -57.27 REMARK 500 TRP A 60 96.28 -64.88 REMARK 500 ALA A 64 97.43 44.49 REMARK 500 GLU A 65 -17.11 68.21 REMARK 500 ASP A 94 -118.69 -64.83 REMARK 500 SER A 95 -46.18 -152.80 REMARK 500 GLN A 151 48.24 -88.38 REMARK 500 ALA A 186 72.49 -52.09 REMARK 500 ALA B 18 -159.67 -114.46 REMARK 500 MET B 22 92.00 63.87 REMARK 500 REMARK 500 REMARK: NULL DBREF 7ZCM A 1 225 UNP P42196 BACS2_NATPH 1 225 DBREF 7ZCM B 19 82 UNP P42259 HTR2_NATPH 19 82 SEQADV 7ZCM ILE B 17 UNP P42259 EXPRESSION TAG SEQADV 7ZCM ALA B 18 UNP P42259 EXPRESSION TAG SEQRES 1 A 225 MET VAL GLY LEU THR THR LEU PHE TRP LEU GLY ALA ILE SEQRES 2 A 225 GLY MET LEU VAL GLY THR LEU ALA PHE ALA TRP ALA GLY SEQRES 3 A 225 ARG ASP ALA GLY SER GLY GLU ARG ARG TYR TYR VAL THR SEQRES 4 A 225 LEU VAL GLY ILE SER GLY ILE ALA ALA VAL ALA TYR VAL SEQRES 5 A 225 VAL MET ALA LEU GLY VAL GLY TRP VAL PRO VAL ALA GLU SEQRES 6 A 225 ARG THR VAL PHE ALA PRO ARG TYR ILE ASP TRP ILE LEU SEQRES 7 A 225 THR THR PRO LEU ILE VAL TYR PHE LEU GLY LEU LEU ALA SEQRES 8 A 225 GLY LEU ASP SER ARG GLU PHE GLY ILE VAL ILE THR LEU SEQRES 9 A 225 ASN THR VAL VAL MET LEU ALA GLY PHE ALA GLY ALA MET SEQRES 10 A 225 VAL PRO GLY ILE GLU ARG TYR ALA LEU PHE GLY MET GLY SEQRES 11 A 225 ALA VAL ALA PHE LEU GLY LEU VAL TYR TYR LEU VAL GLY SEQRES 12 A 225 PRO MET THR GLU SER ALA SER GLN ARG SER SER GLY ILE SEQRES 13 A 225 LYS SER LEU TYR VAL ARG LEU ARG ASN LEU THR VAL ILE SEQRES 14 A 225 LEU TRP ALA ILE TYR PRO PHE ILE TRP LEU LEU GLY PRO SEQRES 15 A 225 PRO GLY VAL ALA LEU LEU THR PRO THR VAL ASP VAL ALA SEQRES 16 A 225 LEU ILE VAL TYR LEU ASP LEU VAL THR LYS VAL GLY PHE SEQRES 17 A 225 GLY PHE ILE ALA LEU ASP ALA ALA ALA THR LEU ARG ALA SEQRES 18 A 225 GLU HIS GLY GLU SEQRES 1 B 66 ILE ALA THR GLY LYS MET GLY ALA VAL PHE ILE PHE VAL SEQRES 2 B 66 GLY ALA LEU THR VAL LEU PHE GLY ALA ILE ALA TYR GLY SEQRES 3 B 66 GLU VAL THR ALA ALA ALA ALA THR GLY ASP ALA ALA ALA SEQRES 4 B 66 VAL GLN GLU ALA ALA VAL SER ALA ILE LEU GLY LEU ILE SEQRES 5 B 66 ILE LEU LEU GLY ILE ASN LEU GLY LEU VAL ALA ALA THR SEQRES 6 B 66 LEU HET RET A 301 20 HETNAM RET RETINAL FORMUL 3 RET C20 H28 O FORMUL 4 HOH *12(H2 O) HELIX 1 AA1 GLY A 3 ALA A 25 1 23 HELIX 2 AA2 GLY A 32 GLY A 57 1 26 HELIX 3 AA3 ALA A 70 GLY A 92 1 23 HELIX 4 AA4 SER A 95 VAL A 118 1 24 HELIX 5 AA5 ILE A 121 GLY A 143 1 23 HELIX 6 AA6 GLY A 143 GLN A 151 1 9 HELIX 7 AA7 SER A 153 ALA A 172 1 20 HELIX 8 AA8 ILE A 173 LEU A 180 1 8 HELIX 9 AA9 THR A 189 ARG A 220 1 32 HELIX 10 AB1 ALA B 24 THR B 50 1 27 HELIX 11 AB2 ASP B 52 LEU B 82 1 31 SHEET 1 AA1 2 TRP A 60 VAL A 63 0 SHEET 2 AA1 2 ARG A 66 PHE A 69 -1 O VAL A 68 N VAL A 61 LINK NZ LYS A 205 C15 RET A 301 1555 1555 1.43 CRYST1 52.870 67.650 114.420 90.00 90.00 90.00 P 21 2 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 0.018914 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014782 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008740 0.00000