HEADER TRANSFERASE/PEPTIDE 05-DEC-14 4X5K TITLE HUMAN NAA50 COMPLEX WITH COENZYME A AND AN ACETYLATED PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: N-ALPHA-ACETYLTRANSFERASE 50; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: N-ACETYLTRANSFERASE 13,N-ACETYLTRANSFERASE 5,HNAT5,N- COMPND 5 ACETYLTRANSFERASE SAN HOMOLOG,HSAN,NATE CATALYTIC SUBUNIT; COMPND 6 EC: 2.3.1.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: ACE-MMAS; COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 CELL_LINE: A549; SOURCE 6 GENE: NAA50, MAK3, NAT13, NAT5; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630; SOURCE 16 OTHER_DETAILS: SYNTHETIC PEPTIDE KEYWDS N-ACETYL TRANSFERASE, GCN-5. COTRANSLATION MODIFICATION, TRANSFERASE- KEYWDS 2 PEPTIDE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.REDDI,A.ADDLAGATTA REVDAT 4 23-OCT-24 4X5K 1 REMARK REVDAT 3 08-NOV-23 4X5K 1 REMARK REVDAT 2 04-OCT-17 4X5K 1 REMARK REVDAT 1 16-DEC-15 4X5K 0 JRNL AUTH R.REDDI,A.ADDLAGATTA JRNL TITL HUMAN NAA50 WITH COENZYMEA AND A PEPTIDE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8_1069 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) : 2.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.52 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 5836 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.610 REMARK 3 FREE R VALUE TEST SET COUNT : 269 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 28.5256 - 3.1421 0.99 2866 144 0.1844 0.2337 REMARK 3 2 3.1421 - 2.4944 0.97 2701 125 0.2701 0.3471 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) : 0.380 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.540 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 : 0.010 1328 REMARK 3 ANGLE : 1.357 1799 REMARK 3 CHIRALITY : 0.092 197 REMARK 3 PLANARITY : 0.005 225 REMARK 3 DIHEDRAL : 18.278 496 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 4X5K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-DEC-14. REMARK 100 THE DEPOSITION ID IS D_1000205109. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5836 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.390 REMARK 200 RESOLUTION RANGE LOW (A) : 30.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.2 REMARK 200 DATA REDUNDANCY : 2.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.2700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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 <I/SIGMA(I)> 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: MOLREP REMARK 200 STARTING MODEL: 2OB0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM FORMATE, 20% PEG 3350, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 22.31300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.79300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.59650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.79300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.31300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.59650 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: 2390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 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 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 LYS A 2 REMARK 465 VAL A 156 REMARK 465 PRO A 157 REMARK 465 SER A 158 REMARK 465 GLY A 159 REMARK 465 GLN A 160 REMARK 465 ASN A 161 REMARK 465 ALA A 162 REMARK 465 ASP A 163 REMARK 465 VAL A 164 REMARK 465 GLN A 165 REMARK 465 LYS A 166 REMARK 465 THR A 167 REMARK 465 ASP A 168 REMARK 465 ASN A 169 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 34 NZ REMARK 470 LYS A 37 CD CE NZ REMARK 470 LYS A 102 CD CE NZ REMARK 470 LYS A 140 CG CD CE NZ REMARK 470 ARG A 141 CD NE CZ NH1 NH2 REMARK 470 LYS A 155 CG CD CE NZ REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 COA A 201 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 201 DBREF 4X5K A 1 169 UNP Q9GZZ1 NAA50_HUMAN 1 169 DBREF 4X5K B 1 5 PDB 4X5K 4X5K 1 5 SEQRES 1 A 169 MET LYS GLY SER ARG ILE GLU LEU GLY ASP VAL THR PRO SEQRES 2 A 169 HIS ASN ILE LYS GLN LEU LYS ARG LEU ASN GLN VAL ILE SEQRES 3 A 169 PHE PRO VAL SER TYR ASN ASP LYS PHE TYR LYS ASP VAL SEQRES 4 A 169 LEU GLU VAL GLY GLU LEU ALA LYS LEU ALA TYR PHE ASN SEQRES 5 A 169 ASP ILE ALA VAL GLY ALA VAL CYS CYS ARG VAL ASP HIS SEQRES 6 A 169 SER GLN ASN GLN LYS ARG LEU TYR ILE MET THR LEU GLY SEQRES 7 A 169 CYS LEU ALA PRO TYR ARG ARG LEU GLY ILE GLY THR LYS SEQRES 8 A 169 MET LEU ASN HIS VAL LEU ASN ILE CYS GLU LYS ASP GLY SEQRES 9 A 169 THR PHE ASP ASN ILE TYR LEU HIS VAL GLN ILE SER ASN SEQRES 10 A 169 GLU SER ALA ILE ASP PHE TYR ARG LYS PHE GLY PHE GLU SEQRES 11 A 169 ILE ILE GLU THR LYS LYS ASN TYR TYR LYS ARG ILE GLU SEQRES 12 A 169 PRO ALA ASP ALA HIS VAL LEU GLN LYS ASN LEU LYS VAL SEQRES 13 A 169 PRO SER GLY GLN ASN ALA ASP VAL GLN LYS THR ASP ASN SEQRES 1 B 5 ACE MET MET ALA SER HET ACE B 1 3 HET COA A 201 48 HETNAM ACE ACETYL GROUP HETNAM COA COENZYME A FORMUL 2 ACE C2 H4 O FORMUL 3 COA C21 H36 N7 O16 P3 S FORMUL 4 HOH *17(H2 O) HELIX 1 AA1 ASN A 15 PHE A 27 1 13 HELIX 2 AA2 ASN A 32 VAL A 39 1 8 HELIX 3 AA3 LEU A 40 GLU A 44 5 5 HELIX 4 AA4 ALA A 81 ARG A 84 5 4 HELIX 5 AA5 GLY A 87 GLU A 101 1 15 HELIX 6 AA6 ASN A 117 PHE A 127 1 11 SHEET 1 AA1 7 ILE A 6 ASP A 10 0 SHEET 2 AA1 7 ALA A 46 PHE A 51 -1 O TYR A 50 N GLU A 7 SHEET 3 AA1 7 ALA A 55 SER A 66 -1 O GLY A 57 N ALA A 49 SHEET 4 AA1 7 GLN A 69 CYS A 79 -1 O TYR A 73 N ARG A 62 SHEET 5 AA1 7 ASN A 108 GLN A 114 1 O TYR A 110 N LEU A 72 SHEET 6 AA1 7 ALA A 147 ASN A 153 -1 O LYS A 152 N ILE A 109 SHEET 7 AA1 7 GLU A 130 ILE A 131 -1 N GLU A 130 O GLN A 151 LINK C ACE B 1 N MET B 2 1555 1555 1.46 CISPEP 1 GLU A 143 PRO A 144 0 -1.02 SITE 1 AC1 22 ILE A 26 PHE A 27 LEU A 77 GLY A 78 SITE 2 AC1 22 CYS A 79 ARG A 84 ARG A 85 LEU A 86 SITE 3 AC1 22 GLY A 87 ILE A 88 GLY A 89 THR A 90 SITE 4 AC1 22 VAL A 113 ASN A 117 SER A 119 ALA A 120 SITE 5 AC1 22 ASP A 122 PHE A 123 TYR A 124 LYS A 126 SITE 6 AC1 22 HOH A 304 ACE B 1 CRYST1 44.626 53.193 67.586 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 0.022408 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018799 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014796 0.00000