HEADER TRANSFERASE 21-JUL-17 5WJD TITLE CRYSTAL STRUCTURE OF NAA80 BOUND TO ACETYL-COA COMPND MOL_ID: 1; COMPND 2 MOLECULE: CG8481, ISOFORM B; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FI06462P; COMPND 5 EC: 2.3.1.-; COMPND 6 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: DMEL\CG8481, CG8481-RB, CG8481, DMEL_CG8481; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ACETYLTRANSFERASE, ACETYL-COA, GNAT FOLD, ACETYLATION, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.GORIS,R.S.MAGIN,R.MARMORSTEIN,T.ARNESEN REVDAT 4 04-OCT-23 5WJD 1 REMARK REVDAT 3 02-MAY-18 5WJD 1 JRNL REVDAT 2 11-APR-18 5WJD 1 JRNL REVDAT 1 28-MAR-18 5WJD 0 JRNL AUTH M.GORIS,R.S.MAGIN,H.FOYN,L.M.MYKLEBUST,S.VARLAND,R.REE, JRNL AUTH 2 A.DRAZIC,P.BHAMBRA,S.I.STOVE,M.BAUMANN,B.E.HAUG, JRNL AUTH 3 R.MARMORSTEIN,T.ARNESEN JRNL TITL STRUCTURAL DETERMINANTS AND CELLULAR ENVIRONMENT DEFINE JRNL TITL 2 PROCESSED ACTIN AS THE SOLE SUBSTRATE OF THE N-TERMINAL JRNL TITL 3 ACETYLTRANSFERASE NAA80. JRNL REF PROC. NATL. ACAD. SCI. V. 115 4405 2018 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 29581307 JRNL DOI 10.1073/PNAS.1719251115 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 11681 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) : 0.184 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.050 REMARK 3 FREE R VALUE TEST SET COUNT : 1174 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 44.6954 - 4.0003 1.00 1411 163 0.1830 0.2049 REMARK 3 2 4.0003 - 3.1755 1.00 1343 149 0.1588 0.1859 REMARK 3 3 3.1755 - 2.7741 1.00 1324 144 0.1869 0.2221 REMARK 3 4 2.7741 - 2.5205 1.00 1309 149 0.1959 0.2499 REMARK 3 5 2.5205 - 2.3399 0.99 1298 142 0.1910 0.2424 REMARK 3 6 2.3399 - 2.2019 1.00 1291 143 0.1925 0.2377 REMARK 3 7 2.2019 - 2.0916 0.99 1272 142 0.1993 0.2665 REMARK 3 8 2.0916 - 2.0006 0.97 1259 142 0.2119 0.2853 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) : 22.030 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.54 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 : 0.003 1313 REMARK 3 ANGLE : 0.744 1785 REMARK 3 CHIRALITY : 0.045 197 REMARK 3 PLANARITY : 0.003 219 REMARK 3 DIHEDRAL : 9.966 780 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 5WJD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JUL-17. REMARK 100 THE DEPOSITION ID IS D_1000229133. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAR-17 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 : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.03319 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11715 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 12.30 REMARK 200 R MERGE (I) : 0.17700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 10.00 REMARK 200 R MERGE FOR SHELL (I) : 0.75600 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: PHENIX REMARK 200 STARTING MODEL: 2CNM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24% POLYETHYLENE GLYCOL (PEG) 3350, REMARK 280 0.1 M BIS TRIS PROPANE (PH 7.6, PH ADJUSTED WITH CITRIC ACID) REMARK 280 AND 10 MM NABR, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293.15K 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 20.84250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.87900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.32150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.87900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.84250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.32150 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 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 10 REMARK 465 SER A 11 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 26 CD CE NZ REMARK 470 GLU A 63 CG CD OE1 OE2 REMARK 470 LYS A 81 CG CD CE NZ REMARK 470 LYS A 82 CD CE NZ REMARK 470 LYS A 119 CE NZ REMARK 470 GLU A 133 CG CD OE1 OE2 REMARK 470 ARG A 134 CD NE CZ NH1 NH2 REMARK 470 GLU A 138 CD OE1 OE2 REMARK 470 LYS A 160 CG CD CE NZ REMARK 470 LYS A 162 CE NZ 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 LYS A 161 O HOH A 301 2.07 REMARK 500 O6 CIT A 202 O HOH A 302 2.13 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 SER A 53 -106.23 -123.65 REMARK 500 ARG A 149 36.75 -77.84 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 ACO A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CIT A 202 DBREF 5WJD A 10 168 UNP Q59DX8 Q59DX8_DROME 20 178 SEQRES 1 A 159 GLY SER PRO PHE ASN VAL VAL PRO ILE HIS ASN TYR PRO SEQRES 2 A 159 GLU LEU MET LYS ASP THR CYS ALA LEU ILE ASN ALA GLU SEQRES 3 A 159 TRP PRO ARG SER GLU THR ALA ARG MET ARG SER LEU GLU SEQRES 4 A 159 ALA SER CYS ASP SER LEU PRO CYS SER LEU VAL LEU THR SEQRES 5 A 159 THR GLU GLY MET CYS ARG VAL ILE ALA HIS LEU LYS LEU SEQRES 6 A 159 SER PRO ILE ASN SER LYS LYS LYS ALA CYS PHE VAL GLU SEQRES 7 A 159 SER VAL VAL VAL ASP LYS ARG HIS ARG GLY GLN GLY PHE SEQRES 8 A 159 GLY LYS LEU ILE MET LYS PHE ALA GLU ASP TYR CYS ARG SEQRES 9 A 159 VAL VAL LEU ASP LEU LYS THR ILE TYR LEU SER THR ILE SEQRES 10 A 159 ASP GLN ASP GLY PHE TYR GLU ARG ILE GLY TYR GLU TYR SEQRES 11 A 159 CYS ALA PRO ILE THR MET TYR GLY PRO ARG HIS CYS GLU SEQRES 12 A 159 LEU PRO SER LEU GLN ASN ALA LYS LYS LYS TYR MET LYS SEQRES 13 A 159 LYS VAL LEU HET ACO A 201 51 HET CIT A 202 13 HETNAM ACO ACETYL COENZYME *A HETNAM CIT CITRIC ACID FORMUL 2 ACO C23 H38 N7 O17 P3 S FORMUL 3 CIT C6 H8 O7 FORMUL 4 HOH *129(H2 O) HELIX 1 AA1 HIS A 19 GLU A 23 5 5 HELIX 2 AA2 LEU A 24 TRP A 36 1 13 HELIX 3 AA3 SER A 39 ALA A 49 1 11 HELIX 4 AA4 LYS A 93 ARG A 96 5 4 HELIX 5 AA5 GLY A 99 VAL A 115 1 17 HELIX 6 AA6 GLN A 128 ILE A 135 1 8 HELIX 7 AA7 LEU A 153 GLN A 157 5 5 SHEET 1 AA1 7 PHE A 13 PRO A 17 0 SHEET 2 AA1 7 CYS A 56 THR A 62 -1 O THR A 61 N ASN A 14 SHEET 3 AA1 7 VAL A 68 ILE A 77 -1 O LEU A 74 N CYS A 56 SHEET 4 AA1 7 LYS A 80 VAL A 91 -1 O PHE A 85 N SER A 75 SHEET 5 AA1 7 THR A 120 THR A 125 1 O TYR A 122 N CYS A 84 SHEET 6 AA1 7 LYS A 162 VAL A 167 -1 O LYS A 162 N THR A 125 SHEET 7 AA1 7 GLU A 138 TYR A 139 -1 N GLU A 138 O LYS A 165 LINK OE1 GLN A 128 N6A ACO A 201 1555 1555 1.30 CISPEP 1 LEU A 54 PRO A 55 0 -1.40 SITE 1 AC1 22 GLU A 35 SER A 88 VAL A 89 VAL A 90 SITE 2 AC1 22 VAL A 91 ARG A 96 GLY A 97 GLN A 98 SITE 3 AC1 22 GLY A 99 GLY A 101 LYS A 102 SER A 124 SITE 4 AC1 22 THR A 125 GLN A 128 GLY A 130 PHE A 131 SITE 5 AC1 22 TYR A 132 ARG A 134 HOH A 307 HOH A 339 SITE 6 AC1 22 HOH A 369 HOH A 387 SITE 1 AC2 8 ARG A 38 ARG A 43 ARG A 45 LYS A 106 SITE 2 AC2 8 HOH A 302 HOH A 308 HOH A 309 HOH A 310 CRYST1 41.685 62.643 63.758 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 0.023989 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015963 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015684 0.00000