HEADER TRANSFERASE/TRANSFERASE SUBSTRATE 16-AUG-14 4R3L TITLE CRYSTAL STRUCTURE OF ARD1 N-TERMINAL ACETYLTRANSFERASE FROM SULFOLOBUS TITLE 2 SOLFATARICUS BOUND TO SUBSTRATE PEPTIDE FRAGMENT AND COA COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED N-ACETYLTRANSFERASE SSO0209; COMPND 3 CHAIN: A; COMPND 4 EC: 2.3.1.-; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: N-TERMINAL 6-MER PEPTIDE FROM ALBA; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS SOLFATARICUS P2; SOURCE 3 ORGANISM_TAXID: 273057; SOURCE 4 STRAIN: P2; SOURCE 5 GENE: SSO0209; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-28A; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SULFOLOBUS SOLFATARICUS; SOURCE 14 ORGANISM_TAXID: 2287; SOURCE 15 OTHER_DETAILS: THE PEPTIDE SEQUENCE DERIVED FROM ALBA PROTEIN IN SOURCE 16 SULFOLOBUS SOLFATARICUS KEYWDS PROTEIN-SUBSTRATE COMPLEX, GNAT DOMAIN, N-ACETYLTRANSFERASE, KEYWDS 2 TRANSFERASE-TRANSFERASE SUBSTRATE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.Y.CHANG,C.H.HSU REVDAT 2 08-NOV-23 4R3L 1 REMARK SEQADV REVDAT 1 18-MAR-15 4R3L 0 JRNL AUTH Y.Y.CHANG,C.H.HSU JRNL TITL STRUCTURAL BASIS FOR SUBSTRATE-SPECIFIC ACETYLATION OF N JRNL TITL 2 ALPHA-ACETYLTRANSFERASE ARD1 FROM SULFOLOBUS SOLFATARICUS JRNL REF SCI REP V. 5 8673 2015 JRNL REFN ESSN 2045-2322 JRNL PMID 25728374 JRNL DOI 10.1038/SREP08673 REMARK 2 REMARK 2 RESOLUTION. 1.84 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 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) : 1.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 15532 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1554 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 23.8771 - 4.0846 0.99 0 152 0.1848 0.2323 REMARK 3 2 4.0846 - 3.2447 1.00 0 143 0.1763 0.2438 REMARK 3 3 3.2447 - 2.8353 1.00 0 143 0.2005 0.2533 REMARK 3 4 2.8353 - 2.5764 1.00 0 141 0.1962 0.2534 REMARK 3 5 2.5764 - 2.3919 1.00 0 141 0.2012 0.2556 REMARK 3 6 2.3919 - 2.2510 1.00 0 140 0.1929 0.2679 REMARK 3 7 2.2510 - 2.1383 1.00 0 139 0.1899 0.2373 REMARK 3 8 2.1383 - 2.0453 1.00 0 138 0.1893 0.2365 REMARK 3 9 2.0453 - 1.9666 1.00 0 140 0.1873 0.2352 REMARK 3 10 1.9666 - 1.8988 1.00 0 139 0.2065 0.2503 REMARK 3 11 1.8988 - 1.8394 1.00 0 138 0.2405 0.2844 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL 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 : 0.007 NULL REMARK 3 ANGLE : 1.090 NULL REMARK 3 CHIRALITY : 0.043 NULL REMARK 3 PLANARITY : 0.005 NULL REMARK 3 DIHEDRAL : 16.956 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 4R3L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-SEP-14. REMARK 100 THE DEPOSITION ID IS D_1000086855. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUL-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL15A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15532 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.839 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : 0.04400 REMARK 200 FOR THE DATA SET : NULL 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 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: BALBES REMARK 200 STARTING MODEL: 2X7B REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12.5% PEG 4000, 0.1M SODIUM ACETATE REMARK 280 TRIHYDRATE PH 4.2, 0.1M AMMONIUM SULFATE, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 283K 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 17.59250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.05450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.00200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.05450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.59250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.00200 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: 1760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 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 GLU A 2 REMARK 465 LEU A 3 REMARK 465 ALA A 4 REMARK 465 GLU A 5 REMARK 465 LYS A 6 REMARK 465 ASP A 7 REMARK 465 LYS A 8 REMARK 465 GLY A 9 REMARK 465 ARG A 10 REMARK 465 HIS A 168 REMARK 465 HIS A 169 REMARK 465 HIS A 170 REMARK 465 HIS A 171 REMARK 465 HIS A 172 REMARK 465 HIS A 173 REMARK 465 GLY B 3 REMARK 465 THR B 4 REMARK 465 PRO B 5 REMARK 465 THR B 6 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 OH TYR A 154 N SER B 1 2.16 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 ASP A 59 65.22 37.17 REMARK 500 PRO A 81 107.85 -53.70 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 COA A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN B OF N-TERMINAL 6-MER REMARK 800 PEPTIDE FROM ALBA REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4R3K RELATED DB: PDB DBREF 4R3L A 1 167 UNP Q980R9 Y209_SULSO 1 167 DBREF 4R3L B 1 6 PDB 4R3L 4R3L 1 6 SEQADV 4R3L HIS A 168 UNP Q980R9 EXPRESSION TAG SEQADV 4R3L HIS A 169 UNP Q980R9 EXPRESSION TAG SEQADV 4R3L HIS A 170 UNP Q980R9 EXPRESSION TAG SEQADV 4R3L HIS A 171 UNP Q980R9 EXPRESSION TAG SEQADV 4R3L HIS A 172 UNP Q980R9 EXPRESSION TAG SEQADV 4R3L HIS A 173 UNP Q980R9 EXPRESSION TAG SEQRES 1 A 173 MET GLU LEU ALA GLU LYS ASP LYS GLY ARG ASP PHE THR SEQRES 2 A 173 LEU ARG ASN ALA ARG MET ASP ASP ILE ASP GLN ILE ILE SEQRES 3 A 173 LYS ILE ASN ARG LEU THR LEU PRO GLU ASN TYR PRO TYR SEQRES 4 A 173 TYR PHE PHE VAL GLU HIS LEU LYS GLU TYR GLY LEU ALA SEQRES 5 A 173 PHE PHE VAL ALA ILE VAL ASP ASN SER VAL VAL GLY TYR SEQRES 6 A 173 ILE MET PRO ARG ILE GLU TRP GLY PHE SER ASN ILE LYS SEQRES 7 A 173 GLN LEU PRO SER LEU VAL ARG LYS GLY HIS VAL VAL SER SEQRES 8 A 173 ILE ALA VAL LEU GLU GLU TYR ARG ARG LYS GLY ILE ALA SEQRES 9 A 173 THR THR LEU LEU GLU ALA SER MET LYS SER MET LYS ASN SEQRES 10 A 173 ASP TYR ASN ALA GLU GLU ILE TYR LEU GLU VAL ARG VAL SEQRES 11 A 173 SER ASN TYR PRO ALA ILE ALA LEU TYR GLU LYS LEU ASN SEQRES 12 A 173 PHE LYS LYS VAL LYS VAL LEU LYS GLY TYR TYR ALA ASP SEQRES 13 A 173 GLY GLU ASP ALA TYR LEU MET ALA ARG PRO LEU HIS HIS SEQRES 14 A 173 HIS HIS HIS HIS SEQRES 1 B 6 SER SER GLY THR PRO THR HET COA A 400 48 HETNAM COA COENZYME A FORMUL 3 COA C21 H36 N7 O16 P3 S FORMUL 4 HOH *85(H2 O) HELIX 1 1 ARG A 18 ASP A 20 5 3 HELIX 2 2 ASP A 21 LEU A 33 1 13 HELIX 3 3 PRO A 38 GLY A 50 1 13 HELIX 4 4 GLU A 96 ARG A 99 5 4 HELIX 5 5 GLY A 102 ASN A 120 1 19 HELIX 6 6 ASN A 132 LEU A 142 1 11 SHEET 1 A 7 THR A 13 ASN A 16 0 SHEET 2 A 7 PHE A 54 VAL A 58 -1 O VAL A 55 N ARG A 15 SHEET 3 A 7 SER A 61 PHE A 74 -1 O VAL A 63 N ALA A 56 SHEET 4 A 7 LEU A 83 VAL A 94 -1 O VAL A 84 N GLY A 73 SHEET 5 A 7 GLU A 123 ARG A 129 1 O GLU A 123 N GLY A 87 SHEET 6 A 7 ALA A 160 PRO A 166 -1 O TYR A 161 N VAL A 128 SHEET 7 A 7 LYS A 145 LEU A 150 -1 N LYS A 148 O LEU A 162 SITE 1 AC1 27 THR A 32 LEU A 33 LYS A 47 ILE A 92 SITE 2 AC1 27 ALA A 93 VAL A 94 ARG A 99 ARG A 100 SITE 3 AC1 27 LYS A 101 GLY A 102 ILE A 103 ALA A 104 SITE 4 AC1 27 THR A 105 ASN A 132 TYR A 133 PRO A 134 SITE 5 AC1 27 ALA A 137 LEU A 138 TYR A 139 LYS A 141 SITE 6 AC1 27 HOH A 502 HOH A 526 HOH A 528 HOH A 540 SITE 7 AC1 27 HOH A 568 HOH A 584 SER B 1 SITE 1 AC2 12 GLU A 35 TYR A 37 HIS A 88 VAL A 89 SITE 2 AC2 12 VAL A 90 GLU A 127 VAL A 128 TYR A 153 SITE 3 AC2 12 TYR A 154 COA A 400 HOH A 520 HOH A 585 CRYST1 35.185 58.004 84.109 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 0.028421 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017240 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011889 0.00000