PDB Short entry for 3VWE HEADER TRANSFERASE 22-AUG-12 3VWE TITLE CRYSTAL STRUCTURE OF ALPHA-TUBULIN ACETYLTRANSFERASE DOMAIN OF HUMAN TITLE 2 MEC-17 IN COMPLEX WITH COA (P21 FORM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-TUBULIN N-ACETYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ALPHA-TUBULIN ACETYLTRANSFERASE DOMAIN, UNP RESIDUES 1-194; COMPND 5 SYNONYM: ALPHA-TAT, 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; 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: PRSFDUET-1 KEYWDS GNAT FOLD, ACETYLTRANSFERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.YUZAWA,H.SUMIMOTO REVDAT 1 28-AUG-13 3VWE 0 JRNL AUTH S.YUZAWA,H.SUMIMOTO JRNL TITL CRYSTAL STRUCTURE OF ALPHA-TUBULIN ACETYLTRANSFERASE DOMAIN JRNL TITL 2 OF HUMAN MEC-17 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.96 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 13645 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 686 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 39.6294 - 3.3439 0.99 2678 147 0.1616 0.1833 REMARK 3 2 3.3439 - 2.6543 0.97 2539 135 0.1992 0.2684 REMARK 3 3 2.6543 - 2.3188 0.98 2570 134 0.1886 0.2504 REMARK 3 4 2.3188 - 2.1068 0.99 2629 121 0.1826 0.2392 REMARK 3 5 2.1068 - 1.9558 0.98 2543 149 0.2035 0.2799 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.900 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.11 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.01 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 : 0.006 1570 REMARK 3 ANGLE : 1.102 2127 REMARK 3 CHIRALITY : 0.068 234 REMARK 3 PLANARITY : 0.004 270 REMARK 3 DIHEDRAL : 17.898 591 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 3VWE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-SEP-12. REMARK 100 THE RCSB ID CODE IS RCSB095583. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.100 REMARK 200 MONOCHROMATOR : SI(111) CHANNEL-CUT MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13656 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 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 (%) : 98.2 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.14100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.50800 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS, 26% PEG 3350, PH 9.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 17.49900 REMARK 290 SMTRY3 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 GLY A -1 REMARK 465 ARG A 28 REMARK 465 PRO A 29 REMARK 465 GLY A 30 REMARK 465 THR A 31 REMARK 465 THR A 32 REMARK 465 PRO A 87 REMARK 465 HIS A 192 REMARK 465 GLN A 193 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 27 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 86 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 111 CD OE1 OE2 REMARK 470 GLU A 115 CD OE1 OE2 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 19 -165.13 -122.13 REMARK 500 GLU A 174 -52.26 -131.50 REMARK 500 ASN A 182 -1.29 75.94 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VWD RELATED DB: PDB DBREF 3VWE A 1 194 UNP Q5SQI0 ATAT_HUMAN 1 194 SEQADV 3VWE GLY A -3 UNP Q5SQI0 EXPRESSION TAG SEQADV 3VWE PRO A -2 UNP Q5SQI0 EXPRESSION TAG SEQADV 3VWE GLY A -1 UNP Q5SQI0 EXPRESSION TAG SEQADV 3VWE SER A 0 UNP Q5SQI0 EXPRESSION TAG SEQADV 3VWE GLU A 195 UNP Q5SQI0 EXPRESSION TAG SEQADV 3VWE PHE A 196 UNP Q5SQI0 EXPRESSION TAG SEQADV 3VWE 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 HETNAM COA COENZYME A FORMUL 2 COA C21 H36 N7 O16 P3 S FORMUL 3 HOH *100(H2 O) HELIX 1 1 ASP A 6 PHE A 11 1 6 HELIX 2 2 ALA A 35 GLN A 58 1 24 HELIX 3 3 SER A 66 ASN A 73 1 8 HELIX 4 4 GLU A 128 GLN A 131 5 4 HELIX 5 5 GLY A 134 ARG A 148 1 15 HELIX 6 6 GLU A 150 LEU A 154 5 5 HELIX 7 7 SER A 160 ASN A 172 1 13 SHEET 1 A 7 ILE A 15 LEU A 18 0 SHEET 2 A 7 VAL A 76 LYS A 81 -1 O ILE A 79 N THR A 16 SHEET 3 A 7 ILE A 93 TYR A 101 -1 O VAL A 99 N VAL A 76 SHEET 4 A 7 LEU A 119 ILE A 126 -1 O CYS A 120 N GLY A 100 SHEET 5 A 7 ALA A 155 ASP A 157 1 O ALA A 155 N ILE A 121 SHEET 6 A 7 PHE A 183 PHE A 186 -1 O VAL A 184 N ILE A 156 SHEET 7 A 7 THR A 176 VAL A 177 -1 N VAL A 177 O ILE A 185 SHEET 1 B 2 LEU A 104 LEU A 107 0 SHEET 2 B 2 HIS A 113 VAL A 116 -1 O ASN A 114 N VAL A 106 CISPEP 1 ALA A 26 ARG A 27 0 -4.12 SITE 1 AC1 19 GLN A 58 PHE A 124 TYR A 125 ILE A 126 SITE 2 AC1 19 GLN A 131 ARG A 132 HIS A 133 GLY A 134 SITE 3 AC1 19 GLY A 136 ARG A 137 SER A 160 LYS A 162 SITE 4 AC1 19 LYS A 165 PHE A 166 LYS A 169 HIS A 170 SITE 5 AC1 19 HOH A 308 HOH A 355 HOH A 389 CRYST1 43.726 34.998 63.981 90.00 103.24 90.00 P 1 21 1 2 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 0.022870 0.000000 0.005381 0.00000 SCALE2 0.000000 0.028573 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016056 0.00000