HEADER MEMBRANE PROTEIN 14-JAN-10 2KSY TITLE SOLUTION NMR STRUCTURE OF SENSORY RHODOPSIN II COMPND MOL_ID: 1; COMPND 2 MOLECULE: SENSORY RHODOPSIN II; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NATRONOMONAS PHARAONIS; SOURCE 3 ORGANISM_TAXID: 2257; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR: PET28 KEYWDS MEMBRANE PROTEINS, NMR SPECTROSCOPY, RECEPTORS, STRUCTURE KEYWDS 2 ELUCIDATION, TRANSMEMBRANE, MEMBRANE PROTEIN EXPDTA SOLUTION NMR NUMMDL 30 AUTHOR A.GAUTIER,H.R.MOTT,M.J.BOSTOCK,J.P.KIRKPATRICK,D.NIETLISPACH REVDAT 3 10-JUN-15 2KSY 1 ATOM FORMUL HET HETATM REVDAT 3 2 1 HETNAM REMARK VERSN REVDAT 2 16-JUN-10 2KSY 1 JRNL REVDAT 1 02-JUN-10 2KSY 0 JRNL AUTH A.GAUTIER,H.R.MOTT,M.J.BOSTOCK,J.P.KIRKPATRICK,D.NIETLISPACH JRNL TITL STRUCTURE DETERMINATION OF THE SEVEN-HELIX TRANSMEMBRANE JRNL TITL 2 RECEPTOR SENSORY RHODOPSIN II BY SOLUTION NMR SPECTROSCOPY. JRNL REF NAT.STRUCT.MOL.BIOL. V. 17 768 2010 JRNL REFN ISSN 1545-9993 JRNL PMID 20512150 JRNL DOI 10.1038/NSMB.1807 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KSY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-FEB-10. REMARK 100 THE RCSB ID CODE IS RCSB101534. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 323 REMARK 210 PH : 6 REMARK 210 IONIC STRENGTH : 20 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-100% 15N] SENSORY REMARK 210 RHODOPSIN II-1, 50 MM SODIUM REMARK 210 CHLORIDE-2, 50 MM SODIUM REMARK 210 PHOSPHATE-3, 0.05 % SODIUM AZIDE- REMARK 210 4, 90% H2O/10% D2O; 0.5 MM [U- REMARK 210 100% 13C; U-100% 15N] SENSORY REMARK 210 RHODOPSIN II-5, 50 MM SODIUM REMARK 210 CHLORIDE-6, 50 MM SODIUM REMARK 210 PHOSPHATE-7, 0.05 % SODIUM AZIDE- REMARK 210 8, 90% H2O/10% D2O; 0.5 MM [U- REMARK 210 13C; U-15N; U-2H] SENSORY REMARK 210 RHODOPSIN II-9, 50 MM SODIUM REMARK 210 CHLORIDE-10, 50 MM SODIUM REMARK 210 PHOSPHATE-11, 0.05 % SODIUM AZIDE REMARK 210 -12, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCA; 3D HN(CO)CA; 3D HNCO; 3D REMARK 210 HN(CA)CO; 3D HN(CA)CB; 3D REMARK 210 HN(COCA)CB; 3D 1H-15N NOESY; 3D REMARK 210 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ARIA, CNS, CCPNMR_ANALYSIS, REMARK 210 AZARA, TALOS REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING, MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 30 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 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 1 ALA A 64 -89.55 57.67 REMARK 500 1 PRO A 183 -9.95 -55.30 REMARK 500 1 ALA A 186 85.36 56.18 REMARK 500 1 LEU A 188 -154.99 -90.13 REMARK 500 1 HIS A 223 5.69 -150.05 REMARK 500 1 GLU A 225 147.07 65.19 REMARK 500 1 THR A 234 89.32 58.37 REMARK 500 1 ALA A 238 -31.95 -140.83 REMARK 500 1 LEU A 240 -36.01 -151.22 REMARK 500 1 GLU A 241 112.94 63.98 REMARK 500 1 HIS A 245 -40.90 -136.37 REMARK 500 2 ARG A 27 77.49 59.88 REMARK 500 2 ASP A 28 86.76 50.97 REMARK 500 2 SER A 31 -55.22 -156.63 REMARK 500 2 ALA A 64 -86.86 59.90 REMARK 500 2 PHE A 113 -73.53 -53.27 REMARK 500 2 ALA A 186 85.40 55.17 REMARK 500 2 HIS A 223 -176.24 62.17 REMARK 500 2 GLU A 225 101.41 59.93 REMARK 500 2 LEU A 240 4.14 -155.26 REMARK 500 2 HIS A 243 109.04 62.01 REMARK 500 2 HIS A 245 102.04 61.39 REMARK 500 3 ALA A 64 -87.79 58.04 REMARK 500 3 ALA A 186 85.90 57.56 REMARK 500 3 LEU A 188 -158.39 -95.87 REMARK 500 3 HIS A 223 164.76 64.83 REMARK 500 3 THR A 232 -32.40 -132.78 REMARK 500 3 VAL A 237 120.76 64.10 REMARK 500 3 HIS A 243 111.83 -169.29 REMARK 500 4 ALA A 29 -66.26 -160.92 REMARK 500 4 ALA A 64 -86.42 59.51 REMARK 500 4 PHE A 113 -75.09 -57.67 REMARK 500 4 ALA A 186 86.70 -56.94 REMARK 500 4 LEU A 188 -147.97 -97.80 REMARK 500 4 HIS A 223 131.34 64.82 REMARK 500 4 SER A 226 -30.02 -143.16 REMARK 500 4 ALA A 238 99.58 59.38 REMARK 500 4 ASP A 239 -3.55 -143.04 REMARK 500 4 HIS A 245 -62.24 -92.64 REMARK 500 5 SER A 31 90.57 55.91 REMARK 500 5 TRP A 60 92.94 -66.88 REMARK 500 5 ALA A 64 -88.93 58.09 REMARK 500 5 ALA A 186 85.41 57.65 REMARK 500 5 THR A 232 -65.46 -139.12 REMARK 500 5 ASP A 233 -78.35 -88.79 REMARK 500 5 ALA A 236 109.81 63.16 REMARK 500 5 VAL A 237 176.94 52.23 REMARK 500 5 ASP A 239 98.10 59.89 REMARK 500 5 HIS A 245 106.00 60.05 REMARK 500 6 VAL A 2 103.77 62.47 REMARK 500 REMARK 500 THIS ENTRY HAS 305 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 LIGAND LYR IS LYSINE_RETINAL 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 301 DBREF 2KSY A 1 239 UNP Q3IMZ8 Q3IMZ8_NATPD 1 239 SEQADV 2KSY LEU A 240 UNP Q3IMZ8 EXPRESSION TAG SEQADV 2KSY GLU A 241 UNP Q3IMZ8 EXPRESSION TAG SEQADV 2KSY HIS A 242 UNP Q3IMZ8 EXPRESSION TAG SEQADV 2KSY HIS A 243 UNP Q3IMZ8 EXPRESSION TAG SEQADV 2KSY HIS A 244 UNP Q3IMZ8 EXPRESSION TAG SEQADV 2KSY HIS A 245 UNP Q3IMZ8 EXPRESSION TAG SEQADV 2KSY HIS A 246 UNP Q3IMZ8 EXPRESSION TAG SEQADV 2KSY HIS A 247 UNP Q3IMZ8 EXPRESSION TAG SEQRES 1 A 247 MET VAL GLY LEU THR THR LEU PHE TRP LEU GLY ALA ILE SEQRES 2 A 247 GLY MET LEU VAL GLY THR LEU ALA PHE ALA TRP ALA GLY SEQRES 3 A 247 ARG ASP ALA GLY SER GLY GLU ARG ARG TYR TYR VAL THR SEQRES 4 A 247 LEU VAL GLY ILE SER GLY ILE ALA ALA VAL ALA TYR ALA SEQRES 5 A 247 VAL MET ALA LEU GLY VAL GLY TRP VAL PRO VAL ALA GLU SEQRES 6 A 247 ARG THR VAL PHE VAL PRO ARG TYR ILE ASP TRP ILE LEU SEQRES 7 A 247 THR THR PRO LEU ILE VAL TYR PHE LEU GLY LEU LEU ALA SEQRES 8 A 247 GLY LEU ASP SER ARG GLU PHE GLY ILE VAL ILE THR LEU SEQRES 9 A 247 ASN THR VAL VAL MET LEU ALA GLY PHE ALA GLY ALA MET SEQRES 10 A 247 VAL PRO GLY ILE GLU ARG TYR ALA LEU PHE GLY MET GLY SEQRES 11 A 247 ALA VAL ALA PHE ILE GLY LEU VAL TYR TYR LEU VAL GLY SEQRES 12 A 247 PRO MET THR GLU SER ALA SER GLN ARG SER SER GLY ILE SEQRES 13 A 247 LYS SER LEU TYR VAL ARG LEU ARG ASN LEU THR VAL VAL SEQRES 14 A 247 LEU TRP ALA ILE TYR PRO PHE ILE TRP LEU LEU GLY PRO SEQRES 15 A 247 PRO GLY VAL ALA LEU LEU THR PRO THR VAL ASP VAL ALA SEQRES 16 A 247 LEU ILE VAL TYR LEU ASP LEU VAL THR LYS VAL GLY PHE SEQRES 17 A 247 GLY PHE ILE ALA LEU ASP ALA ALA ALA THR LEU ARG ALA SEQRES 18 A 247 GLU HIS GLY GLU SER LEU ALA GLY VAL ASP THR ASP THR SEQRES 19 A 247 PRO ALA VAL ALA ASP LEU GLU HIS HIS HIS HIS HIS HIS HET RET A 301 48 HETNAM RET RETINAL FORMUL 2 RET C20 H28 O HELIX 1 1 LEU A 4 ASP A 28 1 25 HELIX 2 2 GLU A 33 ALA A 55 1 23 HELIX 3 3 VAL A 70 GLY A 92 1 23 HELIX 4 4 ASP A 94 MET A 117 1 24 HELIX 5 5 GLU A 122 VAL A 142 1 21 HELIX 6 6 PRO A 144 SER A 150 1 7 HELIX 7 7 SER A 153 ALA A 172 1 20 HELIX 8 8 ILE A 173 GLY A 181 1 9 HELIX 9 9 THR A 189 GLU A 222 1 34 SHEET 1 A 2 TRP A 60 VAL A 63 0 SHEET 2 A 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 1.26 SITE 1 AC1 15 TRP A 76 THR A 79 THR A 80 ILE A 83 SITE 2 AC1 15 VAL A 108 MET A 109 GLY A 112 PHE A 127 SITE 3 AC1 15 GLY A 130 PHE A 134 TRP A 171 TYR A 174 SITE 4 AC1 15 ASP A 201 THR A 204 LYS A 205 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1