HEADER HYDROLASE/DNA 23-APR-14 4PE8 TITLE CRYSTAL STRUCTURE OF TATD IN COMPLEX WITH TRINUCLEOTIDE DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: TAT-LINKED QUALITY CONTROL PROTEIN TATD; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DEOXYRIBONUCLEASE TATD,DNASE TATD; COMPND 5 EC: 3.1.15.-; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*GP*CP*T)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: TATD, MTTC, YIGW, YIGX, B4483, JW5931; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS(DE3)-RIPL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET22B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630 KEYWDS DNA REPAIR, DNA PROCESSING, EXONUCLEASE, TIM BARREL, HYDROLASE-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.CHEN,C.-L.LI,Y.-Y.HSIAO,Y.DUH,H.S.YUAN REVDAT 5 27-SEP-23 4PE8 1 REMARK REVDAT 4 17-APR-19 4PE8 1 REMARK REVDAT 3 22-NOV-17 4PE8 1 SOURCE JRNL REMARK REVDAT 2 01-OCT-14 4PE8 1 JRNL REVDAT 1 27-AUG-14 4PE8 0 JRNL AUTH Y.C.CHEN,C.L.LI,Y.Y.HSIAO,Y.DUH,H.S.YUAN JRNL TITL STRUCTURE AND FUNCTION OF TATD EXONUCLEASE IN DNA REPAIR. JRNL REF NUCLEIC ACIDS RES. V. 42 10776 2014 JRNL REFN ESSN 1362-4962 JRNL PMID 25114049 JRNL DOI 10.1093/NAR/GKU732 REMARK 2 REMARK 2 RESOLUTION. 2.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) 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) : 2.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 5513 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.980 REMARK 3 FREE R VALUE TEST SET COUNT : 550 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 28.4208 - 4.5890 0.99 1308 145 0.1873 0.2232 REMARK 3 2 4.5890 - 3.6448 1.00 1241 137 0.1764 0.1878 REMARK 3 3 3.6448 - 3.1848 0.99 1214 136 0.1998 0.2861 REMARK 3 4 3.1848 - 2.8940 0.99 1200 132 0.2438 0.3306 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) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.940 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.15 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 : 0.003 2159 REMARK 3 ANGLE : 0.718 2950 REMARK 3 CHIRALITY : 0.048 327 REMARK 3 PLANARITY : 0.003 380 REMARK 3 DIHEDRAL : 14.901 789 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 4PE8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-MAY-14. REMARK 100 THE DEPOSITION ID IS D_1000200768. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-MAR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4 - 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL13B1 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 : LN2-COOLED, FIXED-EXIT DOUBLE REMARK 200 CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-2000, SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5539 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.894 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.11700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.89 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.42800 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: PHENIX REMARK 200 STARTING MODEL: 1XWY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4% TACSIMATE PH 4 AND 12% PEG3350, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 21.72500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.55350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.43550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.55350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.72500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.43550 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: 810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 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 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 O5' DG B -1 O HOH B 101 1.98 REMARK 500 OG1 THR A 254 O HOH A 301 2.03 REMARK 500 O GLN A 83 O HOH A 302 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 DC B 0 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES REMARK 500 DC B 0 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES 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 16 44.96 -143.70 REMARK 500 ARG A 98 -167.66 -112.50 REMARK 500 ASN A 99 11.05 -142.96 REMARK 500 ALA A 131 32.52 -148.76 REMARK 500 THR A 174 -162.11 -107.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4P5U RELATED DB: PDB REMARK 900 TATD APOPROTEIN DBREF 4PE8 A 1 260 UNP P27859 TATD_ECOLI 1 260 DBREF 4PE8 B -1 1 PDB 4PE8 4PE8 -1 1 SEQRES 1 A 260 MET PHE ASP ILE GLY VAL ASN LEU THR SER SER GLN PHE SEQRES 2 A 260 ALA LYS ASP ARG ASP ASP VAL VAL ALA CYS ALA PHE ASP SEQRES 3 A 260 ALA GLY VAL ASN GLY LEU LEU ILE THR GLY THR ASN LEU SEQRES 4 A 260 ARG GLU SER GLN GLN ALA GLN LYS LEU ALA ARG GLN TYR SEQRES 5 A 260 SER SER CYS TRP SER THR ALA GLY VAL HIS PRO HIS ASP SEQRES 6 A 260 SER SER GLN TRP GLN ALA ALA THR GLU GLU ALA ILE ILE SEQRES 7 A 260 GLU LEU ALA ALA GLN PRO GLU VAL VAL ALA ILE GLY GLU SEQRES 8 A 260 CYS GLY LEU ASP PHE ASN ARG ASN PHE SER THR PRO GLU SEQRES 9 A 260 GLU GLN GLU ARG ALA PHE VAL ALA GLN LEU ARG ILE ALA SEQRES 10 A 260 ALA ASP LEU ASN MET PRO VAL PHE MET HIS CYS ARG ASP SEQRES 11 A 260 ALA HIS GLU ARG PHE MET THR LEU LEU GLU PRO TRP LEU SEQRES 12 A 260 ASP LYS LEU PRO GLY ALA VAL LEU HIS CYS PHE THR GLY SEQRES 13 A 260 THR ARG GLU GLU MET GLN ALA CYS VAL ALA HIS GLY ILE SEQRES 14 A 260 TYR ILE GLY ILE THR GLY TRP VAL CYS ASP GLU ARG ARG SEQRES 15 A 260 GLY LEU GLU LEU ARG GLU LEU LEU PRO LEU ILE PRO ALA SEQRES 16 A 260 GLU LYS LEU LEU ILE GLU THR ASP ALA PRO TYR LEU LEU SEQRES 17 A 260 PRO ARG ASP LEU THR PRO LYS PRO SER SER ARG ARG ASN SEQRES 18 A 260 GLU PRO ALA HIS LEU PRO HIS ILE LEU GLN ARG ILE ALA SEQRES 19 A 260 HIS TRP ARG GLY GLU ASP ALA ALA TRP LEU ALA ALA THR SEQRES 20 A 260 THR ASP ALA ASN VAL LYS THR LEU PHE GLY ILE ALA PHE SEQRES 1 B 3 DG DC DT FORMUL 3 HOH *39(H2 O) HELIX 1 AA1 SER A 10 ALA A 14 5 5 HELIX 2 AA2 ASP A 16 ASP A 26 1 11 HELIX 3 AA3 ASN A 38 TYR A 52 1 15 HELIX 4 AA4 ASP A 65 TRP A 69 5 5 HELIX 5 AA5 GLN A 70 ALA A 82 1 13 HELIX 6 AA6 THR A 102 ASN A 121 1 20 HELIX 7 AA7 ALA A 131 GLU A 140 1 10 HELIX 8 AA8 TRP A 142 LEU A 146 5 5 HELIX 9 AA9 THR A 157 ALA A 166 1 10 HELIX 10 AB1 THR A 174 ASP A 179 5 6 HELIX 11 AB2 GLY A 183 LEU A 190 1 8 HELIX 12 AB3 GLU A 222 ALA A 224 5 3 HELIX 13 AB4 HIS A 225 TRP A 236 1 12 HELIX 14 AB5 ASP A 240 GLY A 257 1 18 SHEET 1 AA1 8 ASP A 3 VAL A 6 0 SHEET 2 AA1 8 LEU A 32 ILE A 34 1 O LEU A 33 N ASP A 3 SHEET 3 AA1 8 CYS A 55 THR A 58 1 O TRP A 56 N ILE A 34 SHEET 4 AA1 8 VAL A 86 ASP A 95 1 O VAL A 87 N SER A 57 SHEET 5 AA1 8 VAL A 124 ARG A 129 1 O PHE A 125 N CYS A 92 SHEET 6 AA1 8 ALA A 149 LEU A 151 1 O VAL A 150 N MET A 126 SHEET 7 AA1 8 ILE A 169 ILE A 173 1 O TYR A 170 N LEU A 151 SHEET 8 AA1 8 LEU A 198 ILE A 200 1 O LEU A 199 N ILE A 173 CISPEP 1 GLY A 90 GLU A 91 0 5.69 CISPEP 2 ALA A 204 PRO A 205 0 2.53 CISPEP 3 THR A 213 PRO A 214 0 -4.57 CRYST1 43.450 52.871 101.107 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 0.023015 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018914 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009891 0.00000