HEADER NEUROTRANSMITTER-BINDING PROTEIN 21-NOV-19 6V1R TITLE CRYSTAL STRUCTURE OF IACHSNFR FLUORESCENT ACETYLCHOLINE SENSOR TITLE 2 PRECURSOR BINDING PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: IACHSNFR FLUORESCENT ACETYLCHOLINE SENSOR V9 PRECURSOR COMPND 3 BINDING PROTEIN; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOANAEROBACTER SP. X513; SOURCE 3 ORGANISM_TAXID: 573062; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS NEUROTRANSMITTER-BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.FAN,P.M.BORDEN,L.L.LOOGER,H.A.LESTER,D.C.REES REVDAT 2 11-OCT-23 6V1R 1 REMARK REVDAT 1 25-NOV-20 6V1R 0 JRNL AUTH P.M.BORDEN,A.V.SHIVANGE,C.FAN,D.C.REES,H.A.LESTER,L.L.LOOGER JRNL TITL A GENETICALLY ENCODED FLUORESCENT SENSOR FOR IN VIVO JRNL TITL 2 ACETYLCHOLINE DETECTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.64 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 36533 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1828 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 38.1100 - 3.8700 0.99 2860 151 0.1474 0.1945 REMARK 3 2 3.8700 - 3.0700 1.00 2755 146 0.1674 0.1963 REMARK 3 3 3.0700 - 2.6800 0.99 2704 142 0.1827 0.2496 REMARK 3 4 2.6800 - 2.4400 1.00 2687 141 0.1790 0.2013 REMARK 3 5 2.4400 - 2.2600 0.99 2712 143 0.1845 0.2215 REMARK 3 6 2.2600 - 2.1300 0.99 2630 139 0.1965 0.2385 REMARK 3 7 2.1300 - 2.0200 1.00 2669 140 0.1878 0.2260 REMARK 3 8 2.0200 - 1.9300 1.00 2669 140 0.2071 0.2294 REMARK 3 9 1.9300 - 1.8600 0.99 2670 140 0.2569 0.3196 REMARK 3 10 1.8600 - 1.8000 0.99 2613 137 0.2214 0.2499 REMARK 3 11 1.8000 - 1.7400 0.99 2656 141 0.2248 0.2773 REMARK 3 12 1.7400 - 1.6900 0.99 2652 140 0.2382 0.2763 REMARK 3 13 1.6900 - 1.6400 0.92 2428 128 0.2848 0.3314 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) : 0.166 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.379 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.94 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 : 0.006 2366 REMARK 3 ANGLE : 0.863 3209 REMARK 3 CHIRALITY : 0.053 358 REMARK 3 PLANARITY : 0.005 409 REMARK 3 DIHEDRAL : 9.678 336 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 1.2579 5.5209 30.1156 REMARK 3 T TENSOR REMARK 3 T11: 0.1875 T22: 0.1847 REMARK 3 T33: 0.1674 T12: 0.0147 REMARK 3 T13: -0.0185 T23: -0.0115 REMARK 3 L TENSOR REMARK 3 L11: 1.9486 L22: 1.6663 REMARK 3 L33: 0.8567 L12: 0.3759 REMARK 3 L13: -0.7106 L23: -0.2144 REMARK 3 S TENSOR REMARK 3 S11: -0.0629 S12: 0.0108 S13: 0.0157 REMARK 3 S21: -0.0363 S22: 0.0519 S23: -0.0815 REMARK 3 S31: 0.0416 S32: -0.0338 S33: 0.0026 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 6V1R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1000245469. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUL-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36549 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.640 REMARK 200 RESOLUTION RANGE LOW (A) : 38.110 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.06946 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.1800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : 1.25700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.170 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: 6EFR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 8,000 0.1 M CHES, PH 9.5 10 MM REMARK 280 SPERMIDINE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 23.38000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.29600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.89050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.29600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.38000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.89050 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 GLY A -6 REMARK 465 ALA A -5 REMARK 465 GLN A -4 REMARK 465 PRO A -3 REMARK 465 ALA A -2 REMARK 465 ARG A -1 REMARK 465 SER A 0 REMARK 465 ASP A 279 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACH A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NHE A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SPD A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 304 DBREF 6V1R A -13 279 PDB 6V1R 6V1R -13 279 SEQRES 1 A 293 MET HIS HIS HIS HIS HIS HIS GLY ALA GLN PRO ALA ARG SEQRES 2 A 293 SER ALA ASN ASP THR VAL VAL VAL GLY SER ILE ILE PHE SEQRES 3 A 293 THR GLU GLY ILE ILE VAL ALA ASN MET VAL ALA GLU MET SEQRES 4 A 293 ILE GLU ALA HIS THR ASP LEU LYS VAL VAL ARG LYS LEU SEQRES 5 A 293 ASN LEU GLY GLY VAL ASN VAL ASN PHE GLU ALA ILE LYS SEQRES 6 A 293 ARG GLY GLY ALA ASN ASN GLY ILE ASP ILE TYR VAL GLU SEQRES 7 A 293 TYR THR GLY HIS GLY LEU VAL ASP ILE LEU GLY PHE PRO SEQRES 8 A 293 ALA THR THR ASP PRO GLU GLY ALA TYR GLU THR VAL LYS SEQRES 9 A 293 LYS GLU TYR LYS ARG LYS TRP ASN ILE VAL TRP LEU LYS SEQRES 10 A 293 PRO LEU GLY PHE ASN ASN THR TYR THR LEU THR VAL LYS SEQRES 11 A 293 ASP GLU LEU ALA LYS GLN TYR ASN LEU LYS THR PHE SER SEQRES 12 A 293 ASP LEU ALA LYS ILE SER ASP LYS LEU ILE LEU GLY ALA SEQRES 13 A 293 THR MET PHE PHE LEU GLU GLY PRO ASP GLY TYR PRO GLY SEQRES 14 A 293 LEU GLN LYS LEU TYR ASN PHE LYS PHE LYS HIS THR LYS SEQRES 15 A 293 SER MET ASP MET GLY ILE ARG TYR THR ALA ILE ASP ASN SEQRES 16 A 293 ASN GLU VAL GLN VAL ILE ASP ALA TRP ALA THR ASP GLY SEQRES 17 A 293 LEU LEU VAL SER HIS LYS LEU LYS ILE LEU GLU ASP ASP SEQRES 18 A 293 LYS ALA PHE PHE PRO PRO TYR TYR ALA ALA PRO ILE ILE SEQRES 19 A 293 ARG GLN ASP VAL LEU ASP LYS HIS PRO GLU LEU LYS ASP SEQRES 20 A 293 VAL LEU ASN LYS LEU ALA ASN GLN ILE SER LEU GLU GLU SEQRES 21 A 293 MET GLN LYS LEU ASN TYR LYS VAL ASP GLY GLU GLY GLN SEQRES 22 A 293 ASP PRO ALA LYS VAL ALA LYS GLU PHE LEU LYS GLU LYS SEQRES 23 A 293 GLY LEU ILE LEU GLN VAL ASP HET ACH A 301 10 HET NHE A 302 13 HET SPD A 303 10 HET PEG A 304 7 HETNAM ACH ACETYLCHOLINE HETNAM NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID HETNAM SPD SPERMIDINE HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN NHE N-CYCLOHEXYLTAURINE; CHES HETSYN SPD N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE; PA(34) FORMUL 2 ACH C7 H16 N O2 1+ FORMUL 3 NHE C8 H17 N O3 S FORMUL 4 SPD C7 H19 N3 FORMUL 5 PEG C4 H10 O3 FORMUL 6 HOH *206(H2 O) HELIX 1 AA1 PHE A 12 THR A 30 1 19 HELIX 2 AA2 ASN A 44 GLY A 53 1 10 HELIX 3 AA3 GLY A 54 ASN A 57 5 4 HELIX 4 AA4 THR A 66 GLY A 75 1 10 HELIX 5 AA5 ASP A 81 ASN A 98 1 18 HELIX 6 AA6 ASP A 117 ASN A 124 1 8 HELIX 7 AA7 THR A 127 SER A 135 1 9 HELIX 8 AA8 ASP A 136 LEU A 138 5 3 HELIX 9 AA9 THR A 143 GLY A 149 1 7 HELIX 10 AB1 GLY A 152 ASN A 161 1 10 HELIX 11 AB2 ASP A 171 ASN A 181 1 11 HELIX 12 AB3 LEU A 195 HIS A 199 5 5 HELIX 13 AB4 GLN A 222 HIS A 228 1 7 HELIX 14 AB5 GLU A 230 ASN A 236 1 7 HELIX 15 AB6 LYS A 237 ALA A 239 5 3 HELIX 16 AB7 SER A 243 GLY A 256 1 14 HELIX 17 AB8 ASP A 260 LYS A 272 1 13 SHEET 1 AA1 2 THR A 4 ILE A 10 0 SHEET 2 AA1 2 LYS A 33 ASN A 39 1 O ASN A 39 N SER A 9 SHEET 1 AA2 3 ILE A 61 TYR A 65 0 SHEET 2 AA2 3 ALA A 216 ARG A 221 -1 O ILE A 219 N TYR A 62 SHEET 3 AA2 3 ILE A 99 TRP A 101 -1 N VAL A 100 O ILE A 220 SHEET 1 AA3 5 THR A 167 SER A 169 0 SHEET 2 AA3 5 LEU A 140 ALA A 142 1 N ALA A 142 O LYS A 168 SHEET 3 AA3 5 VAL A 186 ILE A 187 1 O VAL A 186 N GLY A 141 SHEET 4 AA3 5 THR A 114 LYS A 116 -1 N THR A 114 O ILE A 187 SHEET 5 AA3 5 LEU A 201 ILE A 203 -1 O LYS A 202 N VAL A 115 SITE 1 AC1 8 PHE A 12 TYR A 65 ASN A 109 TYR A 111 SITE 2 AC1 8 TRP A 190 TYR A 214 SPD A 303 HOH A 401 SITE 1 AC2 8 THR A 13 ILE A 16 GLU A 92 ARG A 95 SITE 2 AC2 8 GLY A 173 ASP A 255 HOH A 411 HOH A 416 SITE 1 AC3 11 VAL A 43 GLU A 64 TYR A 65 HIS A 68 SITE 2 AC3 11 TYR A 111 PHE A 145 GLY A 149 ASP A 151 SITE 3 AC3 11 ACH A 301 HOH A 401 HOH A 439 SITE 1 AC4 5 ASN A 181 GLU A 183 LYS A 249 TYR A 252 SITE 2 AC4 5 HOH A 463 CRYST1 46.760 65.781 96.592 90.00 90.00 90.00 P 21 21 21 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 0.021386 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015202 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010353 0.00000