HEADER DNA BINDING PROTEIN 18-SEP-18 6IF4 TITLE CRYSTAL STRUCTURE OF TBTUDOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE ACETYLTRANSFERASE; COMPND 3 CHAIN: B, A; COMPND 4 SYNONYM: TBTUDOR; COMPND 5 EC: 2.3.1.48; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRYPANOSOMA BRUCEI BRUCEI (STRAIN 927/4 SOURCE 3 GUTAT10.1); SOURCE 4 ORGANISM_TAXID: 185431; SOURCE 5 STRAIN: 927/4 GUTAT10.1; SOURCE 6 GENE: TB927.7.4560; SOURCE 7 EXPRESSION_SYSTEM: ENTEROBACTERIA PHAGE L1; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 268588 KEYWDS TUDOR, DNA, TRANSCRIPTION, METHYLATION, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.GAO,K.YE,Y.DIWU,S.LIAO,X.TU REVDAT 4 22-NOV-23 6IF4 1 REMARK REVDAT 3 30-SEP-20 6IF4 1 JRNL REVDAT 2 06-NOV-19 6IF4 1 COMPND REMARK SHEET SCALE REVDAT 2 2 1 ATOM REVDAT 1 18-SEP-19 6IF4 0 JRNL AUTH J.GAO,K.YE,Y.DIWU,C.XU,X.ZHANG,S.LIAO,X.TU JRNL TITL CRYSTAL STRUCTURE OF TBESA1 PRESUMED TUDOR DOMAIN FROM JRNL TITL 2 TRYPANOSOMA BRUCEI. JRNL REF J.STRUCT.BIOL. V. 209 07406 2020 JRNL REFN ESSN 1095-8657 JRNL PMID 31747559 JRNL DOI 10.1016/J.JSB.2019.107406 REMARK 2 REMARK 2 RESOLUTION. 1.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.980 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 3 NUMBER OF REFLECTIONS : 8622 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 429 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 32.7100 - 2.7887 0.93 2757 135 0.1837 0.2108 REMARK 3 2 2.7887 - 2.2136 0.94 2755 147 0.2367 0.2894 REMARK 3 3 2.2136 - 1.9340 0.91 2681 147 0.2416 0.3025 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.700 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.91 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL 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 : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: (CHAIN A AND (RESID 2 THROUGH 14 OR REMARK 3 (RESID 15 AND (NAME N OR NAME CA OR NAME REMARK 3 C OR NAME O OR NAME CB )) OR RESID 16 REMARK 3 THROUGH 44 OR (RESID 45 AND (NAME N OR REMARK 3 NAME CA OR NAME C OR NAME O OR NAME CB )) REMARK 3 OR RESID 46 OR (RESID 47 AND (NAME N OR REMARK 3 NAME CA OR NAME C OR NAME O OR NAME CB )) REMARK 3 OR RESID 48 THROUGH 61)) REMARK 3 SELECTION : (CHAIN B AND (RESID 2 THROUGH 30 OR REMARK 3 (RESID 31 AND (NAME N OR NAME CA OR NAME REMARK 3 C OR NAME O OR NAME CB )) OR RESID 32 REMARK 3 THROUGH 60 OR (RESID 61 AND (NAME N OR REMARK 3 NAME CA OR NAME C OR NAME O OR NAME CB ))) REMARK 3 ) REMARK 3 ATOM PAIRS NUMBER : 538 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6IF4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-OCT-18. REMARK 100 THE DEPOSITION ID IS D_1300009084. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JAN-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9789 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8625 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 REMARK 200 RESOLUTION RANGE LOW (A) : 32.710 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.11500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.04 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.65200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 4PL6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS, 3M NACL PH6.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 GLN B 62 REMARK 465 GLY B 63 REMARK 465 LEU B 64 REMARK 465 GLU B 65 REMARK 465 HIS B 66 REMARK 465 HIS B 67 REMARK 465 HIS B 68 REMARK 465 HIS B 69 REMARK 465 HIS B 70 REMARK 465 HIS B 71 REMARK 465 MET A 1 REMARK 465 GLN A 62 REMARK 465 GLY A 63 REMARK 465 LEU A 64 REMARK 465 GLU A 65 REMARK 465 HIS A 66 REMARK 465 HIS A 67 REMARK 465 HIS A 68 REMARK 465 HIS A 69 REMARK 465 HIS A 70 REMARK 465 HIS A 71 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 MET B 1 CG SD CE REMARK 470 HIS B 15 CG ND1 CD2 CE1 NE2 REMARK 470 ASP B 45 CG OD1 OD2 REMARK 470 ARG B 47 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 61 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 31 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 61 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU B 43 CD GLU B 43 OE1 -0.071 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 ARG B 7 -2.97 82.34 REMARK 500 HIS B 15 -105.02 66.90 REMARK 500 ARG A 7 -2.31 81.86 REMARK 500 REMARK 500 REMARK: NULL DBREF 6IF4 B 1 63 UNP D6XIY7 D6XIY7_TRYB2 1 63 DBREF 6IF4 A 1 63 UNP D6XIY7 D6XIY7_TRYB2 1 63 SEQADV 6IF4 LEU B 64 UNP D6XIY7 EXPRESSION TAG SEQADV 6IF4 GLU B 65 UNP D6XIY7 EXPRESSION TAG SEQADV 6IF4 HIS B 66 UNP D6XIY7 EXPRESSION TAG SEQADV 6IF4 HIS B 67 UNP D6XIY7 EXPRESSION TAG SEQADV 6IF4 HIS B 68 UNP D6XIY7 EXPRESSION TAG SEQADV 6IF4 HIS B 69 UNP D6XIY7 EXPRESSION TAG SEQADV 6IF4 HIS B 70 UNP D6XIY7 EXPRESSION TAG SEQADV 6IF4 HIS B 71 UNP D6XIY7 EXPRESSION TAG SEQADV 6IF4 LEU A 64 UNP D6XIY7 EXPRESSION TAG SEQADV 6IF4 GLU A 65 UNP D6XIY7 EXPRESSION TAG SEQADV 6IF4 HIS A 66 UNP D6XIY7 EXPRESSION TAG SEQADV 6IF4 HIS A 67 UNP D6XIY7 EXPRESSION TAG SEQADV 6IF4 HIS A 68 UNP D6XIY7 EXPRESSION TAG SEQADV 6IF4 HIS A 69 UNP D6XIY7 EXPRESSION TAG SEQADV 6IF4 HIS A 70 UNP D6XIY7 EXPRESSION TAG SEQADV 6IF4 HIS A 71 UNP D6XIY7 EXPRESSION TAG SEQRES 1 B 71 MET VAL MET PHE GLU VAL ARG GLN LYS VAL TYR ALA THR SEQRES 2 B 71 LEU HIS GLU THR PHE HIS ALA ALA ILE ILE GLN GLU VAL SEQRES 3 B 71 ALA HIS ASP ALA HIS THR GLY GLN LEU LEU TYR TYR VAL SEQRES 4 B 71 HIS TYR VAL GLU GLN ASP SER ARG MET ASP ARG TRP LEU SEQRES 5 B 71 PRO GLY SER ALA LEU ARG GLU ARG ARG GLN GLY LEU GLU SEQRES 6 B 71 HIS HIS HIS HIS HIS HIS SEQRES 1 A 71 MET VAL MET PHE GLU VAL ARG GLN LYS VAL TYR ALA THR SEQRES 2 A 71 LEU HIS GLU THR PHE HIS ALA ALA ILE ILE GLN GLU VAL SEQRES 3 A 71 ALA HIS ASP ALA HIS THR GLY GLN LEU LEU TYR TYR VAL SEQRES 4 A 71 HIS TYR VAL GLU GLN ASP SER ARG MET ASP ARG TRP LEU SEQRES 5 A 71 PRO GLY SER ALA LEU ARG GLU ARG ARG GLN GLY LEU GLU SEQRES 6 A 71 HIS HIS HIS HIS HIS HIS FORMUL 3 HOH *74(H2 O) HELIX 1 AA1 ASP B 45 ASP B 49 5 5 HELIX 2 AA2 HIS A 31 GLY A 33 5 3 HELIX 3 AA3 ASP A 45 ASP A 49 5 5 SHEET 1 AA1 6 ARG B 50 PRO B 53 0 SHEET 2 AA1 6 LEU B 35 TYR B 41 -1 N TYR B 37 O LEU B 52 SHEET 3 AA1 6 THR B 17 HIS B 28 -1 N ALA B 27 O LEU B 36 SHEET 4 AA1 6 PHE A 18 ASP A 29 1 O HIS A 28 N PHE B 18 SHEET 5 AA1 6 LEU A 35 TYR A 41 -1 O TYR A 38 N GLN A 24 SHEET 6 AA1 6 ARG A 50 PRO A 53 -1 O LEU A 52 N TYR A 37 SHEET 1 AA2 6 LEU B 57 GLU B 59 0 SHEET 2 AA2 6 LYS B 9 LEU B 14 -1 N TYR B 11 O ARG B 58 SHEET 3 AA2 6 THR B 17 HIS B 28 -1 O ALA B 21 N VAL B 10 SHEET 4 AA2 6 PHE A 18 ASP A 29 1 O HIS A 28 N PHE B 18 SHEET 5 AA2 6 LYS A 9 THR A 13 -1 N VAL A 10 O ALA A 21 SHEET 6 AA2 6 LEU A 57 GLU A 59 -1 O ARG A 58 N TYR A 11 CRYST1 29.389 34.274 37.470 113.58 100.53 102.90 P 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 0.034026 0.007795 0.011164 0.00000 SCALE2 0.000000 0.029932 0.015507 0.00000 SCALE3 0.000000 0.000000 0.030572 0.00000