HEADER PLANT PROTEIN 15-JUN-21 7OVU TITLE CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA NAT9 IN COMPLEX WITH ACCOA COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACYL-COA N-ACYLTRANSFERASES (NAT) SUPERFAMILY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: EXPRESSED PROTEIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: AT2G04845; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693 KEYWDS GNAT N-ACETYLTRANSFERASE ACCOA PLANT PROTEIN NAT9, PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.LAYER,F.A.WEYER,J.KOPP,I.SINNING REVDAT 2 31-JAN-24 7OVU 1 REMARK REVDAT 1 21-DEC-22 7OVU 0 JRNL AUTH D.LAYER,F.A.WEYER,J.KOPP,I.SINNING JRNL TITL CRYSTAL STRUCTURE OF THE ARABIDOPSIS THALIANA JRNL TITL 2 N-ACETYLTRANSFERASE 9 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 39.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 33757 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.150 REMARK 3 R VALUE (WORKING SET) : 0.149 REMARK 3 FREE R VALUE : 0.181 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 1673 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 39.1900 - 3.3200 1.00 2755 149 0.1473 0.1757 REMARK 3 2 3.3200 - 2.6300 1.00 2696 140 0.1524 0.1553 REMARK 3 3 2.6300 - 2.3000 1.00 2652 155 0.1423 0.1778 REMARK 3 4 2.3000 - 2.0900 1.00 2692 140 0.1266 0.1673 REMARK 3 5 2.0900 - 1.9400 1.00 2679 139 0.1315 0.1854 REMARK 3 6 1.9400 - 1.8300 1.00 2665 142 0.1328 0.1721 REMARK 3 7 1.8300 - 1.7400 1.00 2664 147 0.1407 0.2066 REMARK 3 8 1.7400 - 1.6600 1.00 2672 126 0.1585 0.2079 REMARK 3 9 1.6600 - 1.6000 1.00 2676 123 0.1805 0.2235 REMARK 3 10 1.6000 - 1.5400 1.00 2638 137 0.1973 0.2544 REMARK 3 11 1.5400 - 1.4900 1.00 2670 140 0.2130 0.2658 REMARK 3 12 1.4900 - 1.4500 0.97 2625 135 0.2377 0.3011 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.75 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 7OVU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1292115031. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-DEC-16 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 : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976251 REMARK 200 MONOCHROMATOR : NULL 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 : 33777 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 39.190 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 13.10 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.9000 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 : 1.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER, MRBUMP REMARK 200 STARTING MODEL: 3EO4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: ATNAT9 WAS CONCENTRATED TO 15 MG/ML REMARK 280 AND INCUBATED WITH A THREEFOLD MOLAR EXCESS OF ACCOA FOR 18 H ON REMARK 280 ICE. CRYSTALLIZATION DROPS CONTAINED 200 NL PROTEIN SOLUTION AND REMARK 280 200 NL PRECIPITANT SOLUTION (0.1 M HEPES (PH 7) AND 20 % PEG6000) REMARK 280 AND CRYSTALS APPEARED AFTER SEVEN DAYS. THE CRYSTALS WERE CRYO- REMARK 280 PROTECTED WITH 20 % GLYCEROL AND FLASH-FROZEN IN LIQUID REMARK 280 NITROGEN., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K 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 33.60100 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.44750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 33.60100 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.44750 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 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 475 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 529 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 553 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 MET A 1 REMARK 465 VAL A 2 REMARK 465 THR A 3 REMARK 465 ARG A 4 REMARK 465 MET A 5 REMARK 465 ALA A 6 REMARK 465 SER A 203 REMARK 465 SER A 204 REMARK 465 ASN A 205 REMARK 465 ASN A 206 REMARK 465 PRO A 207 REMARK 465 SER A 208 REMARK 465 ASP A 209 REMARK 465 SER A 210 REMARK 465 LEU A 211 REMARK 465 LEU A 212 REMARK 465 SER A 213 REMARK 465 GLY A 214 REMARK 465 GLU A 215 REMARK 465 ALA A 216 REMARK 465 THR A 217 REMARK 465 ALA A 218 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 408 O HOH A 525 1.96 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 91 -31.69 -132.40 REMARK 500 REMARK 500 REMARK: NULL DBREF 7OVU A 1 218 UNP Q8S8E7 Q8S8E7_ARATH 1 218 SEQRES 1 A 218 MET VAL THR ARG MET ALA THR LYS VAL SER LEU GLU GLY SEQRES 2 A 218 LYS ARG VAL VAL LEU VAL PRO TYR MET ALA GLU HIS VAL SEQRES 3 A 218 PRO LYS TYR HIS GLN TRP MET GLN ASP SER ALA LEU LEU SEQRES 4 A 218 GLU ALA THR GLY SER GLU PRO LEU SER LEU GLU GLN GLU SEQRES 5 A 218 TYR GLU MET GLN LEU SER TRP THR GLN ASP PRO ASN LYS SEQRES 6 A 218 ARG THR PHE ILE VAL LEU ASP LYS ASP PHE VAL LYS GLY SEQRES 7 A 218 ASP LEU ALA HIS GLY GLN PRO HIS VAL GLU ALA MET THR SEQRES 8 A 218 GLY ASP VAL ASN ILE TYR MET ASN ASP VAL ASP ASP PRO SEQRES 9 A 218 LYS VAL ALA GLU VAL GLU ILE MET ILE ALA GLU PRO ARG SEQRES 10 A 218 SER ARG GLY LYS GLY LEU GLY LYS GLU SER VAL LEU ILE SEQRES 11 A 218 MET MET ALA TYR GLY VAL LYS ASN LEU GLU ILE HIS LYS SEQRES 12 A 218 PHE THR ALA LYS ILE GLY GLU SER ASN THR ALA SER LEU SEQRES 13 A 218 SER LEU PHE ARG LYS LEU GLY PHE GLU GLU SER SER TYR SEQRES 14 A 218 SER GLY ILE PHE LYS GLU VAL THR LEU GLU TYR PRO VAL SEQRES 15 A 218 THR ASN LEU ARG ARG GLU GLU LEU LEU LYS LEU LEU ASP SEQRES 16 A 218 GLU VAL ILE ARG HIS THR HIS SER SER ASN ASN PRO SER SEQRES 17 A 218 ASP SER LEU LEU SER GLY GLU ALA THR ALA HET ACO A 301 51 HETNAM ACO ACETYL COENZYME *A FORMUL 2 ACO C23 H38 N7 O17 P3 S FORMUL 3 HOH *153(H2 O) HELIX 1 AA1 MET A 22 GLU A 24 5 3 HELIX 2 AA2 HIS A 25 MET A 33 1 9 HELIX 3 AA3 ASP A 35 THR A 42 1 8 HELIX 4 AA4 SER A 48 ASP A 62 1 15 HELIX 5 AA5 ASP A 74 VAL A 76 5 3 HELIX 6 AA6 HIS A 86 GLU A 88 5 3 HELIX 7 AA7 GLU A 115 ARG A 119 5 5 HELIX 8 AA8 GLY A 122 GLU A 140 1 19 HELIX 9 AA9 ASN A 152 LEU A 162 1 11 HELIX 10 AB1 THR A 183 GLU A 196 1 14 SHEET 1 AA1 9 GLU A 165 SER A 170 0 SHEET 2 AA1 9 GLU A 175 PRO A 181 -1 O THR A 177 N SER A 168 SHEET 3 AA1 9 LYS A 143 GLY A 149 -1 N ILE A 148 O VAL A 176 SHEET 4 AA1 9 VAL A 106 ILE A 113 1 N VAL A 109 O THR A 145 SHEET 5 AA1 9 MET A 90 TYR A 97 -1 N TYR A 97 O GLU A 108 SHEET 6 AA1 9 LYS A 65 ASP A 72 -1 N VAL A 70 O THR A 91 SHEET 7 AA1 9 VAL A 16 VAL A 19 -1 N VAL A 17 O LEU A 71 SHEET 8 AA1 9 VAL A 9 GLU A 12 -1 N LEU A 11 O LEU A 18 SHEET 9 AA1 9 ILE A 198 THR A 201 -1 O ILE A 198 N GLU A 12 CRYST1 67.202 48.895 60.123 90.00 102.75 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 0.014881 0.000000 0.003366 0.00000 SCALE2 0.000000 0.020452 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017053 0.00000