HEADER TRANSFERASE 21-DEC-23 8XJB TITLE CRYSTAL STRUCTURE OF ATNATA2 BOUND TO SPERMINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GCN5-RELATED N-ACETYLTRANSFERASE 8; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROBABLE ACETYLTRANSFERASE NATA1-LIKE; COMPND 5 EC: 2.3.1.48; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: THALE CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: GNAT8; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS POLYAMINE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.T.AROLD,U.F.S.HAMEED REVDAT 1 25-DEC-24 8XJB 0 JRNL AUTH S.T.AROLD,U.F.S.HAMEED JRNL TITL CRYSTAL STRUCTURE OF ATNATA2 BOUND TO SPERMINE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1-4487-000) 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 33619 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.154 REMARK 3 R VALUE (WORKING SET) : 0.151 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.950 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 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 34.9290 - 3.4880 1.00 2344 147 0.1567 0.1478 REMARK 3 2 3.4880 - 2.7689 1.00 2299 145 0.1467 0.1708 REMARK 3 3 2.7689 - 2.4190 1.00 2262 144 0.1438 0.2089 REMARK 3 4 2.4190 - 2.1978 1.00 2278 144 0.1303 0.2051 REMARK 3 5 2.1978 - 2.0403 1.00 2281 144 0.1237 0.1891 REMARK 3 6 2.0403 - 1.9200 1.00 2260 143 0.1238 0.1858 REMARK 3 7 1.9200 - 1.8239 1.00 2307 146 0.1280 0.2118 REMARK 3 8 1.8239 - 1.7445 1.00 2274 144 0.1361 0.2316 REMARK 3 9 1.7445 - 1.6773 1.00 2220 140 0.1690 0.2212 REMARK 3 10 1.6773 - 1.6195 1.00 2282 145 0.2167 0.3096 REMARK 3 11 1.6195 - 1.5688 1.00 2265 143 0.2266 0.3271 REMARK 3 12 1.5688 - 1.5240 1.00 2253 143 0.2450 0.3096 REMARK 3 13 1.5240 - 1.4839 1.00 2234 141 0.2679 0.2920 REMARK 3 14 1.4839 - 1.4500 0.90 2061 130 0.3538 0.4198 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.440 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 1743 REMARK 3 ANGLE : 0.833 2364 REMARK 3 CHIRALITY : 0.077 257 REMARK 3 PLANARITY : 0.006 302 REMARK 3 DIHEDRAL : 5.396 631 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 8XJB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-DEC-23. REMARK 100 THE DEPOSITION ID IS D_1300043653. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-DEC-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33619 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.448 REMARK 200 RESOLUTION RANGE LOW (A) : 34.930 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.9100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 0.1 M TRIS PH REMARK 280 8.5, AND 25% W/V POLYETHYLENE GLYCOL 3,350, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 36.86500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.44500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 36.86500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 27.44500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -51.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 702 LIES ON A SPECIAL POSITION. 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 25 REMARK 465 PRO A 26 REMARK 465 LEU A 27 REMARK 465 GLY A 28 REMARK 465 LEU A 115 REMARK 465 ASP A 116 REMARK 465 LEU A 117 REMARK 465 PRO A 118 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 NZ LYS A 205 O HOH A 601 2.08 REMARK 500 NE2 GLN A 213 O HOH A 602 2.09 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 79 -13.87 73.15 REMARK 500 SER A 81 -137.00 -145.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8XBN RELATED DB: PDB REMARK 900 RELATED ID: 8XJ9 RELATED DB: PDB DBREF 8XJB A 30 236 UNP Q9ZV06 GNAT8_ARATH 30 236 SEQADV 8XJB GLY A 25 UNP Q9ZV06 EXPRESSION TAG SEQADV 8XJB PRO A 26 UNP Q9ZV06 EXPRESSION TAG SEQADV 8XJB LEU A 27 UNP Q9ZV06 EXPRESSION TAG SEQADV 8XJB GLY A 28 UNP Q9ZV06 EXPRESSION TAG SEQADV 8XJB SER A 29 UNP Q9ZV06 EXPRESSION TAG SEQRES 1 A 212 GLY PRO LEU GLY SER MET PHE SER ARG ILE ARG LEU ALA SEQRES 2 A 212 THR PRO SER ASP VAL PRO PHE ILE HIS LYS LEU ILE HIS SEQRES 3 A 212 GLN MET ALA VAL PHE GLU ARG LEU THR HIS LEU PHE SER SEQRES 4 A 212 ALA THR GLU SER GLY LEU ALA SER THR LEU PHE THR SER SEQRES 5 A 212 ARG PRO PHE GLN SER PHE THR VAL PHE LEU LEU GLU VAL SEQRES 6 A 212 SER ARG SER PRO PHE PRO ALA THR ILE THR SER SER PRO SEQRES 7 A 212 SER PRO ASP PHE THR PRO PHE PHE LYS THR HIS ASN LEU SEQRES 8 A 212 ASP LEU PRO ILE ASP ASP PRO GLU SER TYR ASN PHE SER SEQRES 9 A 212 PRO ASP MET LEU ASN ASP VAL VAL VAL ALA GLY PHE VAL SEQRES 10 A 212 LEU PHE PHE PRO ASN TYR SER SER PHE LEU SER LYS PRO SEQRES 11 A 212 GLY PHE TYR ILE GLU ASP ILE PHE VAL ARG GLU PRO TYR SEQRES 12 A 212 ARG ARG LYS GLY PHE GLY SER MET LEU LEU THR ALA VAL SEQRES 13 A 212 ALA LYS GLN ALA VAL LYS MET GLY TYR GLY ARG VAL GLU SEQRES 14 A 212 TRP VAL VAL LEU ASP TRP ASN VAL ASN ALA ILE LYS PHE SEQRES 15 A 212 TYR GLU GLN MET GLY ALA GLN ILE LEU GLN GLU TRP ARG SEQRES 16 A 212 VAL CYS ARG LEU THR GLY ASP ALA LEU GLU ALA PHE ASP SEQRES 17 A 212 GLN VAL ASN ILE HET SPM A 500 14 HETNAM SPM SPERMINE FORMUL 2 SPM C10 H26 N4 FORMUL 3 HOH *139(H2 O) HELIX 1 AA1 THR A 38 SER A 40 5 3 HELIX 2 AA2 ASP A 41 ARG A 57 1 17 HELIX 3 AA3 LEU A 58 PHE A 62 5 5 HELIX 4 AA4 THR A 65 LEU A 73 1 9 HELIX 5 AA5 GLU A 123 PHE A 127 5 5 HELIX 6 AA6 GLU A 165 ARG A 168 5 4 HELIX 7 AA7 GLY A 171 GLY A 188 1 18 HELIX 8 AA8 ASN A 200 MET A 210 1 11 HELIX 9 AA9 THR A 224 ALA A 230 1 7 HELIX 10 AB1 PHE A 231 VAL A 234 5 4 SHEET 1 AA1 6 PHE A 109 HIS A 113 0 SHEET 2 AA1 6 MET A 30 LEU A 36 -1 N MET A 30 O HIS A 113 SHEET 3 AA1 6 THR A 83 SER A 90 -1 O SER A 90 N PHE A 31 SHEET 4 AA1 6 VAL A 135 SER A 148 -1 O ALA A 138 N LEU A 87 SHEET 5 AA1 6 LYS A 153 VAL A 163 -1 O TYR A 157 N PHE A 144 SHEET 6 AA1 6 VAL A 192 GLU A 193 1 O GLU A 193 N ILE A 158 CRYST1 73.730 54.890 51.910 90.00 113.64 90.00 C 1 2 1 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 0.013563 0.000000 0.005937 0.00000 SCALE2 0.000000 0.018218 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021029 0.00000