PDB Short entry for 5HH0 HEADER TRANSFERASE 09-JAN-16 5HH0 TITLE CRYSTAL STRUCTURE OF HUMAN NAA60 IN COMPLEX WITH COA COMPND MOL_ID: 1; COMPND 2 MOLECULE: N-ALPHA-ACETYLTRANSFERASE 60; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-199; COMPND 5 SYNONYM: HISTONE ACETYLTRANSFERASE TYPE B PROTEIN 4,HAT4,N- COMPND 6 ACETYLTRANSFERASE 15,NATF CATALYTIC SUBUNIT; COMPND 7 EC: 2.3.1.48,2.3.1.88; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: NAA60, HAT4, NAT15, UNQ2771/PRO7155; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS N-TERMINAL ACETYLATION, NATS, PROTEIN MODIFICATION, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.Y.CHEN,L.LIU,C.H.YUN REVDAT 2 08-NOV-23 5HH0 1 REMARK REVDAT 1 14-SEP-16 5HH0 0 JRNL AUTH J.Y.CHEN,L.LIU,C.L.CAO,M.J.LI,K.TAN,X.YANG,C.H.YUN JRNL TITL STRUCTURE AND FUNCTION OF HUMAN NAA60 (NATF), A JRNL TITL 2 GOLGI-LOCALIZED BI-FUNCTIONAL ACETYLTRANSFERASE JRNL REF SCI REP V. 6 31425 2016 JRNL REFN ESSN 2045-2322 JRNL PMID 27550639 JRNL DOI 10.1038/SREP31425 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.4_1496 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 28588 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) : 0.181 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1454 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 33.5574 - 3.4470 0.98 2868 153 0.1502 0.1474 REMARK 3 2 3.4470 - 2.7364 1.00 2771 156 0.1787 0.1775 REMARK 3 3 2.7364 - 2.3906 1.00 2744 144 0.1926 0.1818 REMARK 3 4 2.3906 - 2.1721 1.00 2717 146 0.1940 0.2058 REMARK 3 5 2.1721 - 2.0164 1.00 2731 147 0.1994 0.2171 REMARK 3 6 2.0164 - 1.8975 1.00 2710 140 0.2078 0.2097 REMARK 3 7 1.8975 - 1.8025 1.00 2678 157 0.2321 0.2317 REMARK 3 8 1.8025 - 1.7240 1.00 2696 139 0.2418 0.3071 REMARK 3 9 1.7240 - 1.6577 1.00 2677 143 0.2591 0.2829 REMARK 3 10 1.6577 - 1.6005 0.95 2542 129 0.2885 0.3216 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.650 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 : 0.017 1719 REMARK 3 ANGLE : 1.651 2354 REMARK 3 CHIRALITY : 0.237 265 REMARK 3 PLANARITY : 0.008 282 REMARK 3 DIHEDRAL : 20.779 699 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 5HH0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-JAN-16. REMARK 100 THE DEPOSITION ID IS D_1000216960. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-APR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97934 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28597 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 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 (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.02100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 31.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : 0.32500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 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: 5HGZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M L-PROLINE, 0.1 M HEPES PH7.5, REMARK 280 10% W/V PEG 3350, LIQUID DIFFUSION, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 33.55000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.71850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.55000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.71850 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: 4970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 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 73.43700 REMARK 350 BIOMT3 2 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 SER A 0 REMARK 465 MET A 1 REMARK 465 THR A 2 REMARK 465 GLU A 3 REMARK 465 GLU A 4 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 GLU A 5 CG CD OE1 OE2 REMARK 470 PHE A 34 CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 37 CG CD OE1 OE2 REMARK 470 ARG A 44 CD NE CZ NH1 NH2 REMARK 470 LYS A 76 CE NZ 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 GLN A 129 -130.29 56.59 REMARK 500 ASP A 154 4.50 83.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 555 DISTANCE = 6.16 ANGSTROMS REMARK 525 HOH A 556 DISTANCE = 6.66 ANGSTROMS REMARK 525 HOH A 557 DISTANCE = 6.80 ANGSTROMS REMARK 525 HOH A 558 DISTANCE = 6.84 ANGSTROMS 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 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5HH1 RELATED DB: PDB REMARK 900 RELATED ID: 5HGZ RELATED DB: PDB DBREF 5HH0 A 1 199 UNP Q9H7X0 NAA60_HUMAN 1 199 SEQADV 5HH0 SER A 0 UNP Q9H7X0 EXPRESSION TAG SEQADV 5HH0 GLU A 4 UNP Q9H7X0 VAL 4 ENGINEERED MUTATION SEQADV 5HH0 GLU A 5 UNP Q9H7X0 VAL 5 ENGINEERED MUTATION SEQADV 5HH0 ARG A 6 UNP Q9H7X0 PRO 6 ENGINEERED MUTATION SEQRES 1 A 200 SER MET THR GLU GLU GLU ARG SER SER ALA LEU SER GLU SEQRES 2 A 200 VAL SER LEU ARG LEU LEU CYS HIS ASP ASP ILE ASP THR SEQRES 3 A 200 VAL LYS HIS LEU CYS GLY ASP TRP PHE PRO ILE GLU TYR SEQRES 4 A 200 PRO ASP SER TRP TYR ARG ASP ILE THR SER ASN LYS LYS SEQRES 5 A 200 PHE PHE SER LEU ALA ALA THR TYR ARG GLY ALA ILE VAL SEQRES 6 A 200 GLY MET ILE VAL ALA GLU ILE LYS ASN ARG THR LYS ILE SEQRES 7 A 200 HIS LYS GLU ASP GLY ASP ILE LEU ALA SER ASN PHE SER SEQRES 8 A 200 VAL ASP THR GLN VAL ALA TYR ILE LEU SER LEU GLY VAL SEQRES 9 A 200 VAL LYS GLU PHE ARG LYS HIS GLY ILE GLY SER LEU LEU SEQRES 10 A 200 LEU GLU SER LEU LYS ASP HIS ILE SER THR THR ALA GLN SEQRES 11 A 200 ASP HIS CYS LYS ALA ILE TYR LEU HIS VAL LEU THR THR SEQRES 12 A 200 ASN ASN THR ALA ILE ASN PHE TYR GLU ASN ARG ASP PHE SEQRES 13 A 200 LYS GLN HIS HIS TYR LEU PRO TYR TYR TYR SER ILE ARG SEQRES 14 A 200 GLY VAL LEU LYS ASP GLY PHE THR TYR VAL LEU TYR ILE SEQRES 15 A 200 ASN GLY GLY HIS PRO PRO TRP THR ILE LEU ASP TYR ILE SEQRES 16 A 200 GLN HIS LEU GLY SER HET COA A 201 70 HETNAM COA COENZYME A FORMUL 2 COA C21 H36 N7 O16 P3 S FORMUL 3 HOH *258(H2 O) HELIX 1 AA1 SER A 8 SER A 11 5 4 HELIX 2 AA2 CYS A 19 ASP A 21 5 3 HELIX 3 AA3 ASP A 22 PHE A 34 1 13 HELIX 4 AA4 PRO A 39 ASN A 49 1 11 HELIX 5 AA5 THR A 75 ILE A 77 5 3 HELIX 6 AA6 HIS A 78 LEU A 85 5 8 HELIX 7 AA7 LYS A 105 ARG A 108 5 4 HELIX 8 AA8 GLY A 111 GLN A 129 1 19 HELIX 9 AA9 ASN A 143 ASN A 152 1 10 HELIX 10 AB1 THR A 189 SER A 199 1 11 SHEET 1 AA1 7 VAL A 13 LEU A 17 0 SHEET 2 AA1 7 PHE A 52 TYR A 59 -1 O ALA A 56 N ARG A 16 SHEET 3 AA1 7 ALA A 62 ASN A 73 -1 O VAL A 64 N ALA A 57 SHEET 4 AA1 7 GLN A 94 VAL A 103 -1 O SER A 100 N VAL A 68 SHEET 5 AA1 7 CYS A 132 LEU A 140 1 O LYS A 133 N GLN A 94 SHEET 6 AA1 7 GLY A 174 TYR A 180 -1 O LEU A 179 N ILE A 135 SHEET 7 AA1 7 LYS A 156 LEU A 161 -1 N LEU A 161 O GLY A 174 SHEET 1 AA2 2 TYR A 164 SER A 166 0 SHEET 2 AA2 2 GLY A 169 LEU A 171 -1 O LEU A 171 N TYR A 164 SITE 1 AC1 31 TRP A 33 PHE A 34 SER A 100 LEU A 101 SITE 2 AC1 31 GLY A 102 VAL A 103 ARG A 108 LYS A 109 SITE 3 AC1 31 HIS A 110 GLY A 111 GLY A 113 SER A 114 SITE 4 AC1 31 ASN A 143 THR A 145 PHE A 149 ASN A 152 SITE 5 AC1 31 ARG A 153 ILE A 167 HOH A 301 HOH A 323 SITE 6 AC1 31 HOH A 326 HOH A 334 HOH A 342 HOH A 344 SITE 7 AC1 31 HOH A 353 HOH A 358 HOH A 386 HOH A 397 SITE 8 AC1 31 HOH A 435 HOH A 442 HOH A 454 CRYST1 67.100 73.437 43.165 90.00 90.00 90.00 P 21 21 2 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 0.014903 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013617 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023167 0.00000