HEADER TRANSFERASE 21-JUL-17 5WJE TITLE CRYSTAL STRUCTURE OF NAA80 BOUND TO A BISUBSTRATE ANALOGUE 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; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: ACTIN N-TERMINUS PEPTIDE; COMPND 9 CHAIN: B; COMPND 10 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; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 11 ORGANISM_TAXID: 7227 KEYWDS ACETYLTRANSFERASE, ACETYL-COA, GNAT FOLD, ACETYLATION, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.GORIS,R.S.MAGIN,R.MARMORSTEIN,T.ARNESEN REVDAT 5 04-OCT-23 5WJE 1 REMARK REVDAT 4 26-FEB-20 5WJE 1 COMPND SOURCE REMARK DBREF REVDAT 4 2 1 SEQRES LINK SITE ATOM REVDAT 3 02-MAY-18 5WJE 1 JRNL REVDAT 2 11-APR-18 5WJE 1 JRNL REVDAT 1 28-MAR-18 5WJE 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. 1.77 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 : LS_WUNIT_K1 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 16670 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1667 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 34.3010 - 4.0398 1.00 1364 153 0.1384 0.1806 REMARK 3 2 4.0398 - 3.2072 1.00 1293 142 0.1360 0.1950 REMARK 3 3 3.2072 - 2.8020 1.00 1264 137 0.1786 0.2499 REMARK 3 4 2.8020 - 2.5459 1.00 1258 147 0.1901 0.2326 REMARK 3 5 2.5459 - 2.3635 1.00 1249 134 0.2031 0.2205 REMARK 3 6 2.3635 - 2.2242 1.00 1237 143 0.2049 0.2103 REMARK 3 7 2.2242 - 2.1128 1.00 1237 142 0.2030 0.2263 REMARK 3 8 2.1128 - 2.0209 1.00 1245 127 0.2079 0.2245 REMARK 3 9 2.0209 - 1.9431 1.00 1234 139 0.2260 0.2522 REMARK 3 10 1.9431 - 1.8760 1.00 1238 143 0.2456 0.2692 REMARK 3 11 1.8760 - 1.8174 1.00 1229 134 0.2476 0.2803 REMARK 3 12 1.8174 - 1.7650 0.94 1155 126 0.2551 0.2681 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.330 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.86 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.33 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 : 0.002 1364 REMARK 3 ANGLE : 0.641 1851 REMARK 3 CHIRALITY : 0.042 204 REMARK 3 PLANARITY : 0.003 228 REMARK 3 DIHEDRAL : 10.626 1142 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 5WJE 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_1000229134. 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 : 16748 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.765 REMARK 200 RESOLUTION RANGE LOW (A) : 34.294 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 10.50 REMARK 200 R MERGE (I) : 0.13000 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) : 1.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.86900 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: 5WJD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 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 18.56800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.29450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.18500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.29450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.56800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.18500 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: 2190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 1.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 81 CG CD CE NZ REMARK 470 LYS A 102 CG CD CE NZ REMARK 470 LYS A 106 CD CE NZ REMARK 470 GLU A 133 CG CD OE1 OE2 REMARK 470 GLU A 138 OE1 OE2 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 ILE B 4 O - C - N ANGL. DEV. = -13.2 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 SER A 53 -111.29 -111.74 REMARK 500 MET A 65 59.49 29.17 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 CMC B 101 DBREF 5WJE A 10 168 UNP Q59DX8 Q59DX8_DROME 20 178 DBREF 5WJE B 1 5 PDB 5WJE 5WJE 1 5 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 SEQRES 1 B 5 ASP ASP ASP ILE NH2 HET NH2 B 5 1 HET CMC B 101 51 HETNAM NH2 AMINO GROUP HETNAM CMC CARBOXYMETHYL COENZYME *A FORMUL 2 NH2 H2 N FORMUL 3 CMC C23 H38 N7 O18 P3 S FORMUL 4 HOH *162(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 156 LYS A 161 1 6 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 ALA A 70 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 N ASP B 1 C2 CMC B 101 1555 1555 1.43 LINK C ILE B 4 N NH2 B 5 1555 1555 1.43 CISPEP 1 LEU A 54 PRO A 55 0 0.89 SITE 1 AC1 25 GLU A 35 SER A 88 VAL A 89 VAL A 90 SITE 2 AC1 25 VAL A 91 ARG A 96 GLY A 97 GLN A 98 SITE 3 AC1 25 GLY A 99 GLY A 101 LYS A 102 SER A 124 SITE 4 AC1 25 THR A 125 GLN A 128 GLY A 130 PHE A 131 SITE 5 AC1 25 TYR A 132 ARG A 134 HOH A 203 HOH A 212 SITE 6 AC1 25 HOH A 227 ASP B 1 HOH B 202 HOH B 206 SITE 7 AC1 25 HOH B 210 CRYST1 37.136 64.370 68.589 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 0.026928 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015535 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014580 0.00000