HEADER TRANSFERASE 22-JUN-16 5GI6 TITLE CRYSTAL STRUCTURE OF DROSOPHILA MELANOGASTER DOPAMINE N- TITLE 2 ACETYLTRANSFERASE BOUND TO COA AND PHENYLETHYLAMINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DOPAMINE N-ACETYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 56-265; COMPND 5 SYNONYM: ARYLALKYLAMINE N-ACETYLTRANSFERASE,AANAT1; COMPND 6 EC: 2.3.1.87; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 GENE: DAT, NAT1, CG3318; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 83333; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: K-12 KEYWDS DOPAMINE N-ACETYLTRANSFERASE(DAT), GCN5-RELATED N- KEYWDS 2 ACETYLTRANSFERASE(GNAT), ARYLALKYLAMINE N-ACETYLTRANSFERASE(AANAT), KEYWDS 3 ORDER BI-BI SEQUENTIAL MECHANISM, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.C.YANG,H.C.CHENG,P.C.LYU REVDAT 2 20-MAR-24 5GI6 1 REMARK REVDAT 1 05-JUL-17 5GI6 0 JRNL AUTH Y.C.YANG,H.C.CHENG,P.C.LYU JRNL TITL CRYSTAL STRUCTURE OF DROSOPHILA MELANOGASTER DOPAMINE JRNL TITL 2 N-ACETYLTRANSFERASE BOUND TO COA AND PHENYLETHYLAMINE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 24777 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 1231 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 25.2908 - 3.4296 0.99 2845 148 0.1709 0.1835 REMARK 3 2 3.4296 - 2.7232 1.00 2744 144 0.1911 0.2215 REMARK 3 3 2.7232 - 2.3793 0.99 2684 143 0.2016 0.2329 REMARK 3 4 2.3793 - 2.1619 0.99 2668 137 0.1904 0.2359 REMARK 3 5 2.1619 - 2.0070 0.97 2598 132 0.1820 0.1833 REMARK 3 6 2.0070 - 1.8887 0.94 2529 134 0.1893 0.2238 REMARK 3 7 1.8887 - 1.7941 0.94 2500 136 0.1984 0.2577 REMARK 3 8 1.7941 - 1.7161 0.94 2502 126 0.2136 0.2375 REMARK 3 9 1.7161 - 1.6500 0.93 2476 131 0.2260 0.2955 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.700 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.24 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.11 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 : 0.007 1723 REMARK 3 ANGLE : 1.212 2328 REMARK 3 CHIRALITY : 0.079 244 REMARK 3 PLANARITY : 0.006 296 REMARK 3 DIHEDRAL : 16.230 663 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): 1.7848 -19.1016 -8.9811 REMARK 3 T TENSOR REMARK 3 T11: 0.1802 T22: 0.1469 REMARK 3 T33: 0.2262 T12: 0.0033 REMARK 3 T13: -0.0092 T23: 0.0584 REMARK 3 L TENSOR REMARK 3 L11: 3.2609 L22: 1.3708 REMARK 3 L33: 1.4842 L12: 1.0239 REMARK 3 L13: -0.2952 L23: -0.1851 REMARK 3 S TENSOR REMARK 3 S11: 0.0337 S12: -0.1623 S13: -0.5503 REMARK 3 S21: -0.0248 S22: -0.0997 S23: -0.2022 REMARK 3 S31: 0.0877 S32: -0.0274 S33: -0.0480 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 5GI6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1300000817. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUL-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5-7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL13B1 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26434 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : 0.61400 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 2.5.2, PHENIX 1.8.1_1168 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0M NAH2PO4/1.6M K2HPO4, 0.1M REMARK 280 IMIDAZOLE, 0.2M NACL, PH 7.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277.0K 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 23.84400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.74000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.26800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.74000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.84400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.26800 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 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 GLY A 16 REMARK 465 PRO A 17 REMARK 465 LEU A 18 REMARK 465 ASP A 99 REMARK 465 ASP A 100 REMARK 465 VAL A 101 REMARK 465 PRO A 102 REMARK 465 GLU A 103 REMARK 465 LYS A 104 REMARK 465 ALA A 105 REMARK 465 ALA A 106 REMARK 465 ASP A 107 REMARK 465 SER A 108 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 O HOH A 521 O HOH A 529 2.10 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 PHE A 42 -91.47 -109.12 REMARK 500 CYS A 73 35.46 -147.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEA A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue COA A 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5GI5 RELATED DB: PDB REMARK 900 5GI5 CONTAINS THE SAME PROTEIN BUT DIFFERENT LIGANDS. DBREF 5GI6 A 21 230 UNP Q94521 DNAT_DROME 56 265 SEQADV 5GI6 GLY A 16 UNP Q94521 EXPRESSION TAG SEQADV 5GI6 PRO A 17 UNP Q94521 EXPRESSION TAG SEQADV 5GI6 LEU A 18 UNP Q94521 EXPRESSION TAG SEQADV 5GI6 GLY A 19 UNP Q94521 EXPRESSION TAG SEQADV 5GI6 SER A 20 UNP Q94521 EXPRESSION TAG SEQRES 1 A 215 GLY PRO LEU GLY SER PRO TYR THR ILE GLU LEU ILE GLN SEQRES 2 A 215 PRO GLU ASP GLY GLU ALA VAL ILE ALA MET LEU LYS THR SEQRES 3 A 215 PHE PHE PHE LYS ASP GLU PRO LEU ASN THR PHE LEU ASP SEQRES 4 A 215 LEU GLY GLU CYS LYS GLU LEU GLU LYS TYR SER LEU LYS SEQRES 5 A 215 PRO LEU PRO ASP ASN CYS SER TYR LYS ALA VAL ASN LYS SEQRES 6 A 215 LYS GLY GLU ILE ILE GLY VAL PHE LEU ASN GLY LEU MET SEQRES 7 A 215 ARG ARG PRO SER PRO ASP ASP VAL PRO GLU LYS ALA ALA SEQRES 8 A 215 ASP SER CYS GLU HIS PRO LYS PHE LYS LYS ILE LEU SER SEQRES 9 A 215 LEU MET ASP HIS VAL GLU GLU GLN PHE ASN ILE PHE ASP SEQRES 10 A 215 VAL TYR PRO ASP GLU GLU LEU ILE LEU ASP GLY LYS ILE SEQRES 11 A 215 LEU SER VAL ASP THR ASN TYR ARG GLY LEU GLY ILE ALA SEQRES 12 A 215 GLY ARG LEU THR GLU ARG ALA TYR GLU TYR MET ARG GLU SEQRES 13 A 215 ASN GLY ILE ASN VAL TYR HIS VAL LEU CYS SER SER HIS SEQRES 14 A 215 TYR SER ALA ARG VAL MET GLU LYS LEU GLY PHE HIS GLU SEQRES 15 A 215 VAL PHE ARG MET GLN PHE ALA ASP TYR LYS PRO GLN GLY SEQRES 16 A 215 GLU VAL VAL PHE LYS PRO ALA ALA PRO HIS VAL GLY ILE SEQRES 17 A 215 GLN VAL MET ALA LYS GLU VAL HET PEA A 301 9 HET COA A 302 48 HETNAM PEA 2-PHENYLETHYLAMINE HETNAM COA COENZYME A FORMUL 2 PEA C8 H12 N 1+ FORMUL 3 COA C21 H36 N7 O16 P3 S FORMUL 4 HOH *145(H2 O) HELIX 1 AA1 GLN A 28 GLU A 30 5 3 HELIX 2 AA2 ASP A 31 PHE A 42 1 12 HELIX 3 AA3 PHE A 42 GLU A 47 1 6 HELIX 4 AA4 GLU A 47 ASP A 54 1 8 HELIX 5 AA5 CYS A 58 LYS A 67 1 10 HELIX 6 AA6 PRO A 68 ASN A 72 5 5 HELIX 7 AA7 HIS A 111 PHE A 128 1 18 HELIX 8 AA8 ASN A 129 TYR A 134 1 6 HELIX 9 AA9 THR A 150 ARG A 153 5 4 HELIX 10 AB1 GLY A 156 GLY A 173 1 18 HELIX 11 AB2 SER A 183 LEU A 193 1 11 HELIX 12 AB3 ALA A 204 TYR A 206 5 3 HELIX 13 AB4 LYS A 207 GLU A 211 5 5 SHEET 1 AA1 7 TYR A 22 LEU A 26 0 SHEET 2 AA1 7 TYR A 75 ASN A 79 -1 O LYS A 76 N GLU A 25 SHEET 3 AA1 7 ILE A 84 ARG A 94 -1 O ILE A 85 N ALA A 77 SHEET 4 AA1 7 LEU A 139 VAL A 148 -1 O ILE A 145 N LEU A 89 SHEET 5 AA1 7 VAL A 176 CYS A 181 1 O HIS A 178 N LEU A 141 SHEET 6 AA1 7 GLY A 222 GLU A 229 -1 O MET A 226 N VAL A 179 SHEET 7 AA1 7 HIS A 196 GLN A 202 -1 N PHE A 199 O VAL A 225 CISPEP 1 ALA A 218 PRO A 219 0 7.20 SITE 1 AC1 6 GLU A 47 ASN A 50 LYS A 144 LEU A 180 SITE 2 AC1 6 SER A 182 HOH A 454 SITE 1 AC2 36 ASP A 46 GLU A 47 PRO A 48 LEU A 146 SITE 2 AC2 36 VAL A 148 ARG A 153 GLY A 154 LEU A 155 SITE 3 AC2 36 GLY A 156 ILE A 157 ALA A 158 CYS A 181 SITE 4 AC2 36 SER A 182 SER A 183 TYR A 185 SER A 186 SITE 5 AC2 36 ARG A 188 VAL A 189 LYS A 192 GLU A 197 SITE 6 AC2 36 VAL A 198 HOH A 407 HOH A 408 HOH A 413 SITE 7 AC2 36 HOH A 417 HOH A 423 HOH A 443 HOH A 446 SITE 8 AC2 36 HOH A 450 HOH A 451 HOH A 458 HOH A 466 SITE 9 AC2 36 HOH A 474 HOH A 498 HOH A 504 HOH A 522 CRYST1 47.688 48.536 89.480 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 0.020970 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020603 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011176 0.00000