HEADER TRANSFERASE 07-AUG-14 4U9Y TITLE STRUCTURE OF THE ALPHA-TUBULIN ACETYLTRANSFERASE ALPHA-TAT1/MEC-17 IN TITLE 2 COMPLEX WITH COA COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-TUBULIN N-ACETYLTRANSFERASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-194; COMPND 5 SYNONYM: TAT,ACETYLTRANSFERASE MEC-17 HOMOLOG; COMPND 6 EC: 2.3.1.108; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ATAT1, C6ORF134, MEC17, NBLA00487; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PRSFDUET-1 KEYWDS GNAT SUPERFAMILY FOLD, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.YUZAWA,H.SUMIMOTO REVDAT 3 08-NOV-23 4U9Y 1 REMARK REVDAT 2 29-JAN-20 4U9Y 1 REMARK REVDAT 1 12-AUG-15 4U9Y 0 JRNL AUTH S.YUZAWA,S.KAMAKURA,H.SUMIMOTO JRNL TITL STRUCTURE OF THE ALPHA-TUBULIN ACETYLTRANSFERASE JRNL TITL 2 ALPHA-TAT1/MEC-17 IN COMPLEX WITH COA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX PHENIX.REFINE: 1.9_1692 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 10421 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.830 REMARK 3 FREE R VALUE TEST SET COUNT : 503 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 40.4325 - 3.4930 0.98 2576 133 0.1765 0.1875 REMARK 3 2 3.4930 - 2.7727 1.00 2481 122 0.2014 0.2523 REMARK 3 3 2.7727 - 2.4222 1.00 2451 131 0.2191 0.2547 REMARK 3 4 2.4222 - 2.2008 1.00 2410 117 0.2111 0.2993 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.420 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.42 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.11 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 : 0.004 1603 REMARK 3 ANGLE : 0.944 2174 REMARK 3 CHIRALITY : 0.037 238 REMARK 3 PLANARITY : 0.003 278 REMARK 3 DIHEDRAL : 19.330 606 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 4U9Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-AUG-14. REMARK 100 THE DEPOSITION ID IS D_1000203039. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.900 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000, HKL REMARK 200 DATA SCALING SOFTWARE : HKL-2000, HKL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10461 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 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 (%) : 99.3 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.13300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.44700 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: PHASER 2.5.0 REMARK 200 STARTING MODEL: 3VWD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES, 20% PEG 3350, 0.2M NABR, REMARK 280 PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 21.42450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 60.96900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.42450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 60.96900 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 300 REMARK: BIOLOGICAL UNIT IS THE SAME AS ASYM. 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 TOTAL BURIED SURFACE AREA: 1300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 326 LIES ON A SPECIAL POSITION. 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 -3 REMARK 465 PRO A -2 REMARK 465 SER A 83 REMARK 465 SER A 84 REMARK 465 ALA A 85 REMARK 465 ARG A 86 REMARK 465 PRO A 87 REMARK 465 HIS A 194 REMARK 465 GLU A 195 REMARK 465 PHE A 196 REMARK 465 GLY A 197 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 ARG A 28 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 111 CD OE1 OE2 REMARK 470 HIS A 192 CG ND1 CD2 CE1 NE2 REMARK 470 GLN A 193 CG CD OE1 NE2 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 PRO A 4 43.91 -77.82 REMARK 500 ASP A 19 -156.22 -124.31 REMARK 500 ARG A 27 -166.37 -112.80 REMARK 500 ARG A 74 58.05 -112.40 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BR A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VWD RELATED DB: PDB REMARK 900 RELATED ID: 3VWE RELATED DB: PDB REMARK 900 RELATED ID: 4U9Z RELATED DB: PDB DBREF 4U9Y A 1 194 UNP Q5SQI0 ATAT_HUMAN 1 194 SEQADV 4U9Y GLY A -3 UNP Q5SQI0 EXPRESSION TAG SEQADV 4U9Y PRO A -2 UNP Q5SQI0 EXPRESSION TAG SEQADV 4U9Y GLY A -1 UNP Q5SQI0 EXPRESSION TAG SEQADV 4U9Y SER A 0 UNP Q5SQI0 EXPRESSION TAG SEQADV 4U9Y GLU A 195 UNP Q5SQI0 EXPRESSION TAG SEQADV 4U9Y PHE A 196 UNP Q5SQI0 EXPRESSION TAG SEQADV 4U9Y GLY A 197 UNP Q5SQI0 EXPRESSION TAG SEQRES 1 A 201 GLY PRO GLY SER MET GLU PHE PRO PHE ASP VAL ASP ALA SEQRES 2 A 201 LEU PHE PRO GLU ARG ILE THR VAL LEU ASP GLN HIS LEU SEQRES 3 A 201 ARG PRO PRO ALA ARG ARG PRO GLY THR THR THR PRO ALA SEQRES 4 A 201 ARG VAL ASP LEU GLN GLN GLN ILE MET THR ILE ILE ASP SEQRES 5 A 201 GLU LEU GLY LYS ALA SER ALA LYS ALA GLN ASN LEU SER SEQRES 6 A 201 ALA PRO ILE THR SER ALA SER ARG MET GLN SER ASN ARG SEQRES 7 A 201 HIS VAL VAL TYR ILE LEU LYS ASP SER SER ALA ARG PRO SEQRES 8 A 201 ALA GLY LYS GLY ALA ILE ILE GLY PHE ILE LYS VAL GLY SEQRES 9 A 201 TYR LYS LYS LEU PHE VAL LEU ASP ASP ARG GLU ALA HIS SEQRES 10 A 201 ASN GLU VAL GLU PRO LEU CYS ILE LEU ASP PHE TYR ILE SEQRES 11 A 201 HIS GLU SER VAL GLN ARG HIS GLY HIS GLY ARG GLU LEU SEQRES 12 A 201 PHE GLN TYR MET LEU GLN LYS GLU ARG VAL GLU PRO HIS SEQRES 13 A 201 GLN LEU ALA ILE ASP ARG PRO SER GLN LYS LEU LEU LYS SEQRES 14 A 201 PHE LEU ASN LYS HIS TYR ASN LEU GLU THR THR VAL PRO SEQRES 15 A 201 GLN VAL ASN ASN PHE VAL ILE PHE GLU GLY PHE PHE ALA SEQRES 16 A 201 HIS GLN HIS GLU PHE GLY HET COA A 201 48 HET BR A 202 1 HETNAM COA COENZYME A HETNAM BR BROMIDE ION FORMUL 2 COA C21 H36 N7 O16 P3 S FORMUL 3 BR BR 1- FORMUL 4 HOH *106(H2 O) HELIX 1 AA1 ASP A 6 PHE A 11 1 6 HELIX 2 AA2 ALA A 35 GLN A 58 1 24 HELIX 3 AA3 SER A 66 SER A 72 1 7 HELIX 4 AA4 GLU A 128 GLN A 131 5 4 HELIX 5 AA5 GLY A 134 ARG A 148 1 15 HELIX 6 AA6 GLU A 150 GLN A 153 5 4 HELIX 7 AA7 SER A 160 ASN A 172 1 13 SHEET 1 AA1 7 ILE A 15 LEU A 18 0 SHEET 2 AA1 7 HIS A 75 LYS A 81 -1 O ILE A 79 N THR A 16 SHEET 3 AA1 7 ILE A 93 TYR A 101 -1 O ILE A 97 N TYR A 78 SHEET 4 AA1 7 LEU A 119 ILE A 126 -1 O ASP A 123 N LYS A 98 SHEET 5 AA1 7 ALA A 155 ASP A 157 1 O ALA A 155 N ILE A 121 SHEET 6 AA1 7 PHE A 183 PHE A 186 -1 O VAL A 184 N ILE A 156 SHEET 7 AA1 7 THR A 176 VAL A 177 -1 N VAL A 177 O ILE A 185 SHEET 1 AA2 2 LEU A 104 LEU A 107 0 SHEET 2 AA2 2 HIS A 113 VAL A 116 -1 O VAL A 116 N LEU A 104 SITE 1 AC1 31 LYS A 56 GLN A 58 PHE A 124 TYR A 125 SITE 2 AC1 31 ILE A 126 GLU A 128 GLN A 131 ARG A 132 SITE 3 AC1 31 HIS A 133 GLY A 134 HIS A 135 GLY A 136 SITE 4 AC1 31 ARG A 137 ARG A 158 SER A 160 LYS A 162 SITE 5 AC1 31 LYS A 165 PHE A 166 LYS A 169 HIS A 170 SITE 6 AC1 31 HOH A 308 HOH A 310 HOH A 315 HOH A 325 SITE 7 AC1 31 HOH A 350 HOH A 366 HOH A 388 HOH A 391 SITE 8 AC1 31 HOH A 393 HOH A 395 HOH A 406 SITE 1 AC2 5 SER A 66 ARG A 69 MET A 70 HIS A 75 SITE 2 AC2 5 LYS A 98 CRYST1 42.849 121.938 37.397 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 0.023338 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008201 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026740 0.00000