HEADER TRANSFERASE 08-JUL-20 7CIX TITLE CRYSTAL STRUCTURE OF AGMATINE N-ACETYLTRANSFERASE MUTANT S171A IN TITLE 2 COMPLEX WITH 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 7CIX 1 REMARK REVDAT 1 21-JUL-21 7CIX 0 JRNL AUTH J.J.CHEN,I.C.HU,C.Y.WU,P.C.LYU JRNL TITL CRYSTAL STRUCTURE OF AGMATINE N-ACETYLTRANSFERASE MUTANT JRNL TITL 2 S171A IN COMPLEX WITH COA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.75 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 19408 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1941 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 25.8990 - 4.2078 1.00 1354 151 0.1662 0.1804 REMARK 3 2 4.2078 - 3.3422 1.00 1293 143 0.1552 0.1903 REMARK 3 3 3.3422 - 2.9203 1.00 1251 139 0.1817 0.2099 REMARK 3 4 2.9203 - 2.6536 1.00 1267 141 0.1918 0.2290 REMARK 3 5 2.6536 - 2.4636 1.00 1233 136 0.1936 0.2274 REMARK 3 6 2.4636 - 2.3184 0.99 1234 138 0.1884 0.2406 REMARK 3 7 2.3184 - 2.2024 1.00 1235 138 0.1816 0.2182 REMARK 3 8 2.2024 - 2.1066 1.00 1242 137 0.1832 0.2415 REMARK 3 9 2.1066 - 2.0255 1.00 1244 138 0.1830 0.2274 REMARK 3 10 2.0255 - 1.9556 1.00 1236 138 0.2000 0.2298 REMARK 3 11 1.9556 - 1.8945 1.00 1214 135 0.1993 0.2645 REMARK 3 12 1.8945 - 1.8404 1.00 1219 136 0.1982 0.3120 REMARK 3 13 1.8404 - 1.7919 1.00 1242 138 0.2149 0.2934 REMARK 3 14 1.7919 - 1.7482 0.99 1203 133 0.2247 0.2972 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.570 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.42 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 7CIX 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_1300017690. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-NOV-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) : 1.0000 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 : 19454 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.748 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : 0.52900 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 2.8.3 REMARK 200 STARTING MODEL: 5K9N REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM HEPES (PH7.0), 2.1M 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 22.09950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.71700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.79250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.71700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.09950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.79250 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: 1080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 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: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 7 CB - CG - OD2 ANGL. DEV. = -6.2 DEGREES 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 TYR A 30 -63.44 -105.52 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 DBREF 7CIX A 1 216 UNP Q9W469 Q9W469_DROME 1 216 SEQADV 7CIX 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 HETNAM COA COENZYME A FORMUL 2 COA C21 H36 N7 O16 P3 S FORMUL 3 HOH *167(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 TYR A 95 1 13 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 ILE A 9 GLN A 13 -1 O VAL A 11 N LYS A 3 SHEET 3 AA1 8 PHE A 63 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 129 N VAL A 76 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 GLN A 181 O VAL A 213 CISPEP 1 HIS A 41 PRO A 42 0 -8.02 CISPEP 2 PRO A 204 PRO A 205 0 6.33 SITE 1 AC1 21 TYR A 30 GLU A 34 LEU A 131 GLY A 132 SITE 2 AC1 21 VAL A 133 ARG A 138 GLY A 139 GLY A 143 SITE 3 AC1 21 ASP A 165 SER A 168 TYR A 170 ALA A 171 SITE 4 AC1 21 HOH A 401 HOH A 421 HOH A 423 HOH A 435 SITE 5 AC1 21 HOH A 453 HOH A 464 HOH A 469 HOH A 479 SITE 6 AC1 21 HOH A 520 CRYST1 44.199 51.585 81.434 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 0.022625 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019385 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012280 0.00000