HEADER TRANSFERASE 08-JUL-20 7CIW TITLE CRYSTAL STRUCTURE OF AGMATINE N-ACETYLTRANSFERASE MUTANT S171A IN TITLE 2 COMPLEX WITH AC-AGM AND COA COMPND MOL_ID: 1; COMPND 2 MOLECULE: AGMATINE N-ACETYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.3.1.5; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: 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: AGMNAT, AANATL8, DMEL\CG15766, CG15766, DMEL_CG15766; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GCN5-RELATED N-ACETYLTRANSFERASE(GNAT), ARYLALKYLAMINE N- KEYWDS 2 ACETYLTRANSFERASE(AANAT), TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.J.CHEN,I.C.HU,C.Y.WU,P.C.LYU REVDAT 2 29-NOV-23 7CIW 1 REMARK REVDAT 1 21-JUL-21 7CIW 0 JRNL AUTH J.J.CHEN,I.C.HU,C.H.LAI,P.C.LYU JRNL TITL CRYSTAL STRUCTURE OF AGMATINE N-ACETYLTRANSFERASE MUTANT JRNL TITL 2 S171A IN COMPLEX WITH AC-AGM AND COA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 23419 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.540 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 25.2070 - 3.8500 0.99 1645 154 0.1773 0.2257 REMARK 3 2 3.8500 - 3.0576 1.00 1568 145 0.1681 0.2117 REMARK 3 3 3.0576 - 2.6716 1.00 1554 146 0.1818 0.2448 REMARK 3 4 2.6716 - 2.4275 1.00 1544 145 0.1982 0.2455 REMARK 3 5 2.4275 - 2.2536 1.00 1536 143 0.1838 0.2262 REMARK 3 6 2.2536 - 2.1208 1.00 1530 142 0.1743 0.2301 REMARK 3 7 2.1208 - 2.0147 1.00 1522 143 0.1710 0.1962 REMARK 3 8 2.0147 - 1.9270 1.00 1532 143 0.1871 0.2440 REMARK 3 9 1.9270 - 1.8528 1.00 1496 139 0.1889 0.2426 REMARK 3 10 1.8528 - 1.7889 1.00 1498 140 0.1860 0.2343 REMARK 3 11 1.7889 - 1.7330 1.00 1528 143 0.2042 0.2846 REMARK 3 12 1.7330 - 1.6835 1.00 1514 142 0.2171 0.2582 REMARK 3 13 1.6835 - 1.6392 0.99 1482 138 0.2440 0.3059 REMARK 3 14 1.6392 - 1.6000 0.97 1470 137 0.2820 0.3196 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.060 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.36 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 7CIW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1300017507. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-OCT-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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) : 1.00000 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 : 23468 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.599 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 (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.1000 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 (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.76100 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: MOLREP REMARK 200 STARTING MODEL: 5K9N REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM HEPES (PH7.0), 2.0M REMARK 280 AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING 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 21.45550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.22950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.61750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.22950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.45550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.61750 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 TOTAL BURIED SURFACE AREA: 1040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 ALA A 6 -128.50 25.90 REMARK 500 ASP A 7 -89.42 -93.19 REMARK 500 GLU A 18 12.87 -174.52 REMARK 500 TYR A 30 -63.47 -106.88 REMARK 500 ASP A 81 -168.25 -127.71 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 COA A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue G0R A 302 DBREF 7CIW A 1 216 UNP Q9W469 Q9W469_DROME 1 216 SEQADV 7CIW ALA A 171 UNP Q9W469 SER 171 ENGINEERED MUTATION SEQRES 1 A 216 MET ALA LYS PRO ILE ALA ASP ASP ILE VAL VAL ARG GLN SEQRES 2 A 216 VAL ASP VAL GLY GLU THR GLU GLN LEU MET THR PHE LEU SEQRES 3 A 216 LEU ALA HIS TYR TYR PRO GLU GLU PRO LEU THR ALA GLY SEQRES 4 A 216 THR HIS PRO PRO GLU PRO GLU ALA ALA ASP LYS GLU PHE SEQRES 5 A 216 LEU LEU SER ASN VAL PRO PHE GLY THR CYS PHE VAL ALA SEQRES 6 A 216 LEU HIS GLU GLY ARG ILE VAL ALA ALA VAL VAL ALA GLY SEQRES 7 A 216 PRO LYS ASP SER HIS GLU PRO GLU HIS MET ALA GLU GLU SEQRES 8 A 216 ALA ARG LYS TYR ALA GLY GLY LYS TRP GLY SER ILE LEU SEQRES 9 A 216 HIS LEU LEU SER ALA VAL GLU THR ALA THR ASP VAL CYS SEQRES 10 A 216 ARG ARG PHE SER VAL PRO SER CYS LEU HIS VAL HIS ALA SEQRES 11 A 216 LEU GLY VAL ASP PRO GLN LEU ARG GLY ARG ASN LEU GLY SEQRES 12 A 216 GLY ARG LEU MET GLU THR VAL ALA GLN ARG GLY ARG ASP SEQRES 13 A 216 LEU GLY HIS GLN LEU VAL SER VAL ASP CYS THR SER VAL SEQRES 14 A 216 TYR ALA ALA ARG LEU VAL GLN ARG LEU GLY TYR GLN LEU SEQRES 15 A 216 ILE ASN THR LEU ARG TYR VAL ASP HIS LEU ASP ALA SER SEQRES 16 A 216 GLY GLN GLN VAL ILE ARG PRO PRO PRO PRO HIS GLU SER SEQRES 17 A 216 VAL GLN THR PHE VAL LEU HIS LEU HET COA A 301 48 HET G0R A 302 12 HETNAM COA COENZYME A HETNAM G0R N-(4-CARBAMIMIDAMIDOBUTYL)ETHANAMIDE FORMUL 2 COA C21 H36 N7 O16 P3 S FORMUL 3 G0R C7 H16 N4 O FORMUL 4 HOH *155(H2 O) HELIX 1 AA1 GLU A 18 TYR A 30 1 13 HELIX 2 AA2 GLU A 34 GLY A 39 1 6 HELIX 3 AA3 GLU A 46 SER A 55 1 10 HELIX 4 AA4 ASN A 56 GLY A 60 5 5 HELIX 5 AA5 HIS A 83 ALA A 96 1 14 HELIX 6 AA6 GLY A 98 ASP A 115 1 18 HELIX 7 AA7 ASP A 115 PHE A 120 1 6 HELIX 8 AA8 PRO A 135 ARG A 138 5 4 HELIX 9 AA9 ASN A 141 LEU A 157 1 17 HELIX 10 AB1 SER A 168 LEU A 178 1 11 HELIX 11 AB2 VAL A 189 HIS A 191 5 3 SHEET 1 AA1 8 ALA A 2 PRO A 4 0 SHEET 2 AA1 8 VAL A 10 GLN A 13 -1 O VAL A 11 N LYS A 3 SHEET 3 AA1 8 CYS A 62 HIS A 67 -1 O LEU A 66 N VAL A 10 SHEET 4 AA1 8 ARG A 70 LYS A 80 -1 O VAL A 72 N ALA A 65 SHEET 5 AA1 8 CYS A 125 VAL A 133 -1 O HIS A 127 N GLY A 78 SHEET 6 AA1 8 LEU A 161 CYS A 166 1 O SER A 163 N VAL A 128 SHEET 7 AA1 8 SER A 208 HIS A 215 -1 O GLN A 210 N CYS A 166 SHEET 8 AA1 8 GLN A 181 ARG A 187 -1 N ILE A 183 O THR A 211 CISPEP 1 HIS A 41 PRO A 42 0 -3.31 CISPEP 2 PRO A 204 PRO A 205 0 10.22 SITE 1 AC1 29 TYR A 30 GLU A 34 PRO A 35 SER A 121 SITE 2 AC1 29 LEU A 131 GLY A 132 VAL A 133 ARG A 138 SITE 3 AC1 29 GLY A 139 ASN A 141 GLY A 143 CYS A 166 SITE 4 AC1 29 THR A 167 SER A 168 TYR A 170 ALA A 171 SITE 5 AC1 29 ARG A 177 GLN A 181 LEU A 182 G0R A 302 SITE 6 AC1 29 HOH A 406 HOH A 415 HOH A 421 HOH A 434 SITE 7 AC1 29 HOH A 445 HOH A 451 HOH A 472 HOH A 503 SITE 8 AC1 29 HOH A 508 SITE 1 AC2 13 TYR A 30 GLU A 34 THR A 37 ASP A 49 SITE 2 AC2 13 TRP A 100 HIS A 129 ALA A 130 LEU A 131 SITE 3 AC2 13 ASP A 165 THR A 167 COA A 301 HOH A 431 SITE 4 AC2 13 HOH A 475 CRYST1 42.911 51.235 78.459 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 0.023304 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019518 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012746 0.00000