HEADER FLUORESCENT PROTEIN 17-SEP-21 7S7Y TITLE CRYSTAL STRUCTURE OF ICYTSNFR CYTISINE SENSOR PRECURSOR BINDING TITLE 2 PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: INICSNFR 4.0 FLUORESCENT NICOTINE SENSOR PRECURSOR BINDING COMPND 3 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 NICOTINE, GFP, PERIPLASMIC BINDING PROTEIN, NICOTINE-BINDING PROTEIN, KEYWDS 2 FLUORESCENT SENSOR, PHARMACOKINETIC SENSOR, CHOLINE-BINDING PROTEIN, KEYWDS 3 FLUORESCENT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.FAN,N.L.NICHOLS,L.LUEBBERT,L.L.LOOGER,H.A.LESTER,D.C.REES REVDAT 4 18-OCT-23 7S7Y 1 REMARK REVDAT 3 27-APR-22 7S7Y 1 JRNL REVDAT 2 03-NOV-21 7S7Y 1 HEADER TITLE KEYWDS REVDAT 1 13-OCT-21 7S7Y 0 JRNL AUTH C.FAN JRNL TITL STRUCTURE, FUNCTION, AND APPLICATION OF BACTERIAL ABC JRNL TITL 2 TRANSPORTERS JRNL REF PH.D.THESIS,CALIFORNIA 2020 JRNL REF 2 INSTITUTE OF TECHNOLOGY JRNL DOI 10.7907/5T65-0047 REMARK 2 REMARK 2 RESOLUTION. 1.30 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 69273 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.890 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 34.0300 - 3.1300 0.98 4959 148 0.1557 0.1632 REMARK 3 2 3.1300 - 2.4900 0.98 4837 143 0.1882 0.2115 REMARK 3 3 2.4900 - 2.1700 0.99 4876 145 0.1815 0.2150 REMARK 3 4 2.1700 - 1.9700 0.99 4897 145 0.1766 0.2130 REMARK 3 5 1.9700 - 1.8300 0.97 4780 142 0.1890 0.2074 REMARK 3 6 1.8300 - 1.7200 0.99 4835 144 0.1727 0.2091 REMARK 3 7 1.7200 - 1.6400 0.99 4898 146 0.1639 0.2230 REMARK 3 8 1.6400 - 1.5700 0.98 4810 143 0.1669 0.1951 REMARK 3 9 1.5700 - 1.5100 0.96 4749 141 0.1913 0.2161 REMARK 3 10 1.5100 - 1.4500 0.98 4778 142 0.2191 0.2555 REMARK 3 11 1.4500 - 1.4100 0.98 4831 144 0.2419 0.2730 REMARK 3 12 1.4100 - 1.3700 0.98 4794 143 0.2746 0.3134 REMARK 3 13 1.3700 - 1.3300 0.97 4721 140 0.3188 0.3504 REMARK 3 14 1.3300 - 1.3000 0.93 4508 134 0.3860 0.4414 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.159 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.827 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.21 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.86 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 : 0.005 2307 REMARK 3 ANGLE : 0.760 3129 REMARK 3 CHIRALITY : 0.077 350 REMARK 3 PLANARITY : 0.005 399 REMARK 3 DIHEDRAL : 13.111 867 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 7S7Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-SEP-21. REMARK 100 THE DEPOSITION ID IS D_1000247609. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUL-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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 : 69428 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 34.030 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.05284 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.2200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 1.38100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.030 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: 7S7T REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 8,000 3% MPD 0.1 M IMIDAZOLE, REMARK 280 PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 30.55000 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 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 ALA A 1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE1 GLU A 267 O HOH A 401 2.15 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 79 86.43 -69.28 REMARK 500 LYS A 126 -33.79 -130.12 REMARK 500 MET A 172 -140.48 50.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 648 DISTANCE = 6.11 ANGSTROMS REMARK 525 HOH A 649 DISTANCE = 6.31 ANGSTROMS DBREF 7S7Y A -13 279 PDB 7S7Y 7S7Y -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 TYR 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 TRP 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 IMD A 301 5 HETNAM IMD IMIDAZOLE FORMUL 2 IMD C3 H5 N2 1+ FORMUL 3 HOH *249(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 ASP A 72 1 7 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 THR A 143 GLU A 148 1 6 HELIX 9 AA9 GLY A 152 ASN A 161 1 10 HELIX 10 AB1 GLY A 173 ASN A 181 1 9 HELIX 11 AB2 GLN A 222 HIS A 228 1 7 HELIX 12 AB3 GLU A 230 LYS A 237 1 8 HELIX 13 AB4 SER A 243 GLY A 256 1 14 HELIX 14 AB5 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 LEU A 40 1 O LYS A 37 N VAL A 7 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 HIS A 166 SER A 169 0 SHEET 2 AA3 5 ILE A 139 ALA A 142 1 N LEU A 140 O LYS A 168 SHEET 3 AA3 5 VAL A 186 TRP A 190 1 O VAL A 186 N GLY A 141 SHEET 4 AA3 5 TYR A 111 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 CRYST1 41.688 61.100 58.546 90.00 100.64 90.00 P 1 21 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 0.023988 0.000000 0.004507 0.00000 SCALE2 0.000000 0.016367 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017379 0.00000