HEADER TRANSFERASE/DNA 27-JUL-14 4QZD TITLE MOUSE TDT, F405A MUTANT, IN COMPLEX WITH A DSB SUBSTRATE, C-C BASE TITLE 2 PAIR COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA NUCLEOTIDYLEXOTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEE REMARK 999; COMPND 5 SYNONYM: TERMINAL ADDITION ENZYME, TERMINAL COMPND 6 DEOXYNUCLEOTIDYLTRANSFERASE, TDT, TERMINAL TRANSFERASE; COMPND 7 EC: 2.7.7.31; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: 5'-D(*AP*AP*AP*AP*AP*C)-3'; COMPND 12 CHAIN: D, U; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: 5'-D(*TP*TP*TP*TP*TP*GP*C)-3'; COMPND 16 CHAIN: T; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: DNTT, TDT; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 MOL_ID: 3; SOURCE 11 SYNTHETIC: YES KEYWDS TERMINAL DEOXYNUCLEOTIDYLTRANSFERASE, NUCLEUS, TRANSFERASE-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.GOUGE,M.DELARUE REVDAT 3 20-SEP-23 4QZD 1 REMARK SEQADV LINK REVDAT 2 26-JUL-17 4QZD 1 SOURCE REMARK REVDAT 1 10-JUN-15 4QZD 0 JRNL AUTH J.GOUGE,S.ROSARIO,F.ROMAIN,F.POITEVIN,P.BEGUIN,M.DELARUE JRNL TITL STRUCTURAL BASIS FOR A NOVEL MECHANISM OF DNA BRIDGING AND JRNL TITL 2 ALIGNMENT IN EUKARYOTIC DSB DNA REPAIR. JRNL REF EMBO J. V. 34 1126 2015 JRNL REFN ISSN 0261-4189 JRNL PMID 25762590 JRNL DOI 10.15252/EMBJ.201489643 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.1 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.56 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 14133 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 710 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 7 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.92 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.28 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2854 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2263 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2707 REMARK 3 BIN R VALUE (WORKING SET) : 0.2246 REMARK 3 BIN FREE R VALUE : 0.2574 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.15 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 147 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2642 REMARK 3 NUCLEIC ACID ATOMS : 329 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 63 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 83.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 83.86 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.00930 REMARK 3 B22 (A**2) : 10.05740 REMARK 3 B33 (A**2) : -8.04800 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -6.81360 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.455 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.666 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.302 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.690 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.307 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.937 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.914 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 3094 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 4263 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1312 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 59 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 426 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 3094 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 0 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 412 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 3403 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 0.96 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.79 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 2.81 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: {A|147 - 243} REMARK 3 ORIGIN FOR THE GROUP (A): 9.2882 -8.9842 19.8952 REMARK 3 T TENSOR REMARK 3 T11: -0.1764 T22: -0.0317 REMARK 3 T33: 0.0992 T12: 0.1445 REMARK 3 T13: -0.0557 T23: -0.1322 REMARK 3 L TENSOR REMARK 3 L11: 2.4065 L22: 4.8468 REMARK 3 L33: 2.4624 L12: -0.5110 REMARK 3 L13: 0.8014 L23: 1.3807 REMARK 3 S TENSOR REMARK 3 S11: 0.0108 S12: 0.4583 S13: -0.5295 REMARK 3 S21: -0.0686 S22: 0.0389 S23: -0.5604 REMARK 3 S31: 0.0859 S32: 0.6181 S33: -0.0497 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: {A|244 - 431} REMARK 3 ORIGIN FOR THE GROUP (A): 4.1248 5.5566 45.2571 REMARK 3 T TENSOR REMARK 3 T11: 0.2625 T22: -0.2650 REMARK 3 T33: -0.2625 T12: -0.0992 REMARK 3 T13: 0.1817 T23: -0.0506 REMARK 3 L TENSOR REMARK 3 L11: 4.4339 L22: 2.2890 REMARK 3 L33: 1.1785 L12: 1.4410 REMARK 3 L13: -0.1360 L23: -0.0099 REMARK 3 S TENSOR REMARK 3 S11: 0.2046 S12: -0.5471 S13: 0.4590 REMARK 3 S21: 0.5519 S22: -0.1757 S23: -0.0113 REMARK 3 S31: 0.0572 S32: -0.0211 S33: -0.0290 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: {A|432 - 510} REMARK 3 ORIGIN FOR THE GROUP (A): -12.4924 0.6782 28.2503 REMARK 3 T TENSOR REMARK 3 T11: 0.0095 T22: -0.2064 REMARK 3 T33: 0.1812 T12: 0.1629 REMARK 3 T13: 0.1328 T23: -0.0627 REMARK 3 L TENSOR REMARK 3 L11: 1.2862 L22: 0.3217 REMARK 3 L33: 2.5301 L12: 1.1990 REMARK 3 L13: 0.8405 L23: -1.4739 REMARK 3 S TENSOR REMARK 3 S11: 0.1789 S12: -0.3557 S13: -0.0698 REMARK 3 S21: 0.4586 S22: -0.0840 S23: 0.6182 REMARK 3 S31: -0.3045 S32: -0.6022 S33: -0.0948 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: {T|1 - 7} REMARK 3 ORIGIN FOR THE GROUP (A): 0.2044 8.4664 12.3741 REMARK 3 T TENSOR REMARK 3 T11: 0.1966 T22: -0.0437 REMARK 3 T33: -0.1276 T12: 0.1488 REMARK 3 T13: 0.0873 T23: 0.0324 REMARK 3 L TENSOR REMARK 3 L11: 1.6024 L22: 2.0931 REMARK 3 L33: 1.2068 L12: 2.4140 REMARK 3 L13: -1.1383 L23: 3.3000 REMARK 3 S TENSOR REMARK 3 S11: 0.0015 S12: 0.2192 S13: 0.0619 REMARK 3 S21: -0.1102 S22: 0.0648 S23: 0.3784 REMARK 3 S31: -0.4024 S32: 0.1565 S33: -0.0663 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: {U|1 - 5} REMARK 3 ORIGIN FOR THE GROUP (A): 6.2804 15.7520 35.3426 REMARK 3 T TENSOR REMARK 3 T11: 0.0420 T22: -0.0294 REMARK 3 T33: 0.0289 T12: -0.1147 REMARK 3 T13: 0.0576 T23: 0.0112 REMARK 3 L TENSOR REMARK 3 L11: 0.3713 L22: 0.0554 REMARK 3 L33: -0.0829 L12: -0.8501 REMARK 3 L13: -0.2903 L23: 0.0915 REMARK 3 S TENSOR REMARK 3 S11: -0.0055 S12: 0.0092 S13: 0.0077 REMARK 3 S21: -0.0170 S22: -0.0022 S23: 0.0339 REMARK 3 S31: -0.0231 S32: -0.0621 S33: 0.0077 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: {D|1 - 6} REMARK 3 ORIGIN FOR THE GROUP (A): 1.4682 1.6974 8.4143 REMARK 3 T TENSOR REMARK 3 T11: -0.0118 T22: 0.1316 REMARK 3 T33: -0.1028 T12: 0.1164 REMARK 3 T13: -0.0026 T23: -0.0924 REMARK 3 L TENSOR REMARK 3 L11: 1.7792 L22: 3.2780 REMARK 3 L33: 6.0685 L12: 2.6249 REMARK 3 L13: -3.6911 L23: -2.5532 REMARK 3 S TENSOR REMARK 3 S11: 0.0125 S12: 0.1587 S13: -0.0868 REMARK 3 S21: 0.0671 S22: 0.1244 S23: 0.1969 REMARK 3 S31: -0.0084 S32: -0.2251 S33: -0.1369 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4QZD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-AUG-14. REMARK 100 THE DEPOSITION ID IS D_1000086704. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUL-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.915010 REMARK 200 MONOCHROMATOR : CHANNEL CUT CRYOGENICALLY COOLED REMARK 200 CRYSTAL REMARK 200 OPTICS : KIRKPATRICK-BAEZ PAIR OF BI REMARK 200 -MORPH MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS, SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14140 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 45.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.83000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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: PDB ENTRY 4I2A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12-17% PEG4000, 9-12% ISOPROPANOL, 100 REMARK 280 MM SODIUM ACETATE, 100 MM HEPES, PH 7.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 27.96650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.46000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 27.96650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 37.46000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -57.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, T, U 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 111 REMARK 465 GLY A 112 REMARK 465 SER A 113 REMARK 465 SER A 114 REMARK 465 HIS A 115 REMARK 465 HIS A 116 REMARK 465 HIS A 117 REMARK 465 HIS A 118 REMARK 465 HIS A 119 REMARK 465 HIS A 120 REMARK 465 SER A 121 REMARK 465 SER A 122 REMARK 465 GLY A 123 REMARK 465 LEU A 124 REMARK 465 VAL A 125 REMARK 465 PRO A 126 REMARK 465 ARG A 127 REMARK 465 GLY A 128 REMARK 465 SER A 129 REMARK 465 HIS A 130 REMARK 465 MET A 131 REMARK 465 SER A 132 REMARK 465 PRO A 133 REMARK 465 SER A 134 REMARK 465 PRO A 135 REMARK 465 VAL A 136 REMARK 465 PRO A 137 REMARK 465 GLY A 138 REMARK 465 SER A 139 REMARK 465 GLN A 140 REMARK 465 ASN A 141 REMARK 465 VAL A 142 REMARK 465 PRO A 143 REMARK 465 ALA A 144 REMARK 465 PRO A 145 REMARK 465 ALA A 146 REMARK 465 GLN A 390 REMARK 465 PRO A 391 REMARK 465 SER A 392 REMARK 465 ARG A 393 REMARK 465 LYS A 394 REMARK 465 VAL A 395 REMARK 465 ASP A 396 REMARK 465 ALA A 397 REMARK 465 LEU A 398 REMARK 465 GLU A 418 REMARK 465 LYS A 419 REMARK 465 SER A 420 REMARK 465 GLY A 421 REMARK 465 GLN A 422 REMARK 465 GLN A 423 REMARK 465 GLU A 424 REMARK 465 DA U 0 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 VAL A 147 CG1 CG2 REMARK 470 LYS A 148 CG CD CE NZ REMARK 470 LYS A 149 CG CD CE NZ REMARK 470 GLU A 180 CG CD OE1 OE2 REMARK 470 GLU A 183 CG CD OE1 OE2 REMARK 470 GLU A 185 CG CD OE1 OE2 REMARK 470 SER A 187 OG REMARK 470 LYS A 209 CG CD CE NZ REMARK 470 GLU A 212 CG CD OE1 OE2 REMARK 470 VAL A 221 CG1 CG2 REMARK 470 SER A 223 OG REMARK 470 GLU A 230 CG CD OE1 OE2 REMARK 470 LYS A 238 CG CD CE NZ REMARK 470 GLU A 244 CG CD OE1 OE2 REMARK 470 LYS A 261 CG CD CE NZ REMARK 470 LYS A 276 CG CD CE NZ REMARK 470 LYS A 281 CG CD CE NZ REMARK 470 ARG A 284 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 290 CG CD CE NZ REMARK 470 GLU A 309 CG CD OE1 OE2 REMARK 470 GLU A 317 CG CD OE1 OE2 REMARK 470 LEU A 323 CG CD1 CD2 REMARK 470 GLU A 352 CG CD OE1 OE2 REMARK 470 GLU A 355 CG CD OE1 OE2 REMARK 470 ASP A 356 CG OD1 OD2 REMARK 470 GLU A 357 CG CD OE1 OE2 REMARK 470 GLN A 360 CG CD OE1 NE2 REMARK 470 LEU A 361 CG CD1 CD2 REMARK 470 LEU A 362 CG CD1 CD2 REMARK 470 LYS A 364 CG CD CE NZ REMARK 470 LYS A 370 CG CD CE NZ REMARK 470 GLN A 371 CG CD OE1 NE2 REMARK 470 PHE A 385 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 386 CG CD OE1 OE2 REMARK 470 LYS A 387 CG CD CE NZ REMARK 470 PHE A 388 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 389 CG CD CE NZ REMARK 470 ASP A 399 CG OD1 OD2 REMARK 470 GLN A 402 CG CD OE1 NE2 REMARK 470 LYS A 403 CG CD CE NZ REMARK 470 LYS A 409 CG CD CE NZ REMARK 470 LEU A 410 CG CD1 CD2 REMARK 470 VAL A 415 CG1 CG2 REMARK 470 LYS A 426 CG CD CE NZ REMARK 470 LYS A 429 CG CD CE NZ REMARK 470 GLU A 487 CG CD OE1 OE2 REMARK 470 GLU A 489 CG CD OE1 OE2 REMARK 470 DC D 6 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DC D 6 N1 C2 O2 N3 C4 N4 C5 REMARK 470 DC D 6 C6 REMARK 470 DA U 1 P OP1 OP2 REMARK 470 DC U 5 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DC U 5 N1 C2 O2 N3 C4 N4 C5 REMARK 470 DC U 5 C6 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 DA D 4 O3' DA D 4 C3' -0.046 REMARK 500 DC T 7 C1' DC T 7 N1 0.109 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 DT T 5 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DA U 3 O4' - C1' - N9 ANGL. DEV. = 2.1 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 CYS A 302 -168.57 72.72 REMARK 500 THR A 331 -153.50 -114.35 REMARK 500 ASN A 509 46.60 -86.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 603 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 253 O REMARK 620 2 VAL A 255 O 81.2 REMARK 620 3 VAL A 258 O 83.5 95.6 REMARK 620 4 HOH A 723 O 78.4 84.6 161.6 REMARK 620 5 DA U 4 OP1 163.0 110.9 106.5 90.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 601 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 343 OD1 REMARK 620 2 ASP A 345 OD2 96.4 REMARK 620 3 DCT A 604 O3G 81.5 153.5 REMARK 620 4 DCT A 604 O2B 156.1 100.1 76.1 REMARK 620 5 DCT A 604 O2A 83.6 71.5 82.1 85.2 REMARK 620 6 HOH A 724 O 108.3 126.3 78.6 75.3 155.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 602 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 343 OD1 REMARK 620 2 ASP A 343 OD2 50.2 REMARK 620 3 ASP A 345 OD1 78.4 125.1 REMARK 620 4 ASP A 345 OD2 72.4 117.3 46.7 REMARK 620 5 ASP A 434 OD2 132.2 113.1 85.5 124.4 REMARK 620 6 DCT A 604 O2A 72.0 77.0 107.6 61.5 155.3 REMARK 620 7 DC U 5 OP1 114.8 64.8 152.6 157.7 67.8 99.5 REMARK 620 8 HOH U 101 O 142.8 134.1 97.6 78.1 83.5 74.3 85.6 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DCT A 604 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4I27 RELATED DB: PDB REMARK 900 RELATED ID: 1JMS RELATED DB: PDB REMARK 900 RELATED ID: 4QZ8 RELATED DB: PDB REMARK 900 RELATED ID: 4QZ9 RELATED DB: PDB REMARK 900 RELATED ID: 4QZA RELATED DB: PDB REMARK 900 RELATED ID: 4QZB RELATED DB: PDB REMARK 900 RELATED ID: 4QZC RELATED DB: PDB REMARK 900 RELATED ID: 4QZE RELATED DB: PDB REMARK 900 RELATED ID: 4QZF RELATED DB: PDB REMARK 900 RELATED ID: 4QZG RELATED DB: PDB REMARK 900 RELATED ID: 4QZH RELATED DB: PDB REMARK 900 RELATED ID: 4QZI RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 PROTEIN COMPRISES UNP RESIDUES 132-482 AND 503-530 WITH 483-502 REMARK 999 DELETED. DBREF 4QZD A 132 482 UNP P09838 TDT_MOUSE 132 482 DBREF 4QZD A 483 510 UNP P09838 TDT_MOUSE 503 530 DBREF 4QZD D 1 6 PDB 4QZD 4QZD 1 6 DBREF 4QZD U 0 5 PDB 4QZD 4QZD 0 5 DBREF 4QZD T 1 7 PDB 4QZD 4QZD 1 7 SEQADV 4QZD MET A 111 UNP P09838 EXPRESSION TAG SEQADV 4QZD GLY A 112 UNP P09838 EXPRESSION TAG SEQADV 4QZD SER A 113 UNP P09838 EXPRESSION TAG SEQADV 4QZD SER A 114 UNP P09838 EXPRESSION TAG SEQADV 4QZD HIS A 115 UNP P09838 EXPRESSION TAG SEQADV 4QZD HIS A 116 UNP P09838 EXPRESSION TAG SEQADV 4QZD HIS A 117 UNP P09838 EXPRESSION TAG SEQADV 4QZD HIS A 118 UNP P09838 EXPRESSION TAG SEQADV 4QZD HIS A 119 UNP P09838 EXPRESSION TAG SEQADV 4QZD HIS A 120 UNP P09838 EXPRESSION TAG SEQADV 4QZD SER A 121 UNP P09838 EXPRESSION TAG SEQADV 4QZD SER A 122 UNP P09838 EXPRESSION TAG SEQADV 4QZD GLY A 123 UNP P09838 EXPRESSION TAG SEQADV 4QZD LEU A 124 UNP P09838 EXPRESSION TAG SEQADV 4QZD VAL A 125 UNP P09838 EXPRESSION TAG SEQADV 4QZD PRO A 126 UNP P09838 EXPRESSION TAG SEQADV 4QZD ARG A 127 UNP P09838 EXPRESSION TAG SEQADV 4QZD GLY A 128 UNP P09838 EXPRESSION TAG SEQADV 4QZD SER A 129 UNP P09838 EXPRESSION TAG SEQADV 4QZD HIS A 130 UNP P09838 EXPRESSION TAG SEQADV 4QZD MET A 131 UNP P09838 EXPRESSION TAG SEQADV 4QZD ALA A 405 UNP P09838 PHE 405 ENGINEERED MUTATION SEQRES 1 A 400 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 400 LEU VAL PRO ARG GLY SER HIS MET SER PRO SER PRO VAL SEQRES 3 A 400 PRO GLY SER GLN ASN VAL PRO ALA PRO ALA VAL LYS LYS SEQRES 4 A 400 ILE SER GLN TYR ALA CYS GLN ARG ARG THR THR LEU ASN SEQRES 5 A 400 ASN TYR ASN GLN LEU PHE THR ASP ALA LEU ASP ILE LEU SEQRES 6 A 400 ALA GLU ASN ASP GLU LEU ARG GLU ASN GLU GLY SER CYS SEQRES 7 A 400 LEU ALA PHE MET ARG ALA SER SER VAL LEU LYS SER LEU SEQRES 8 A 400 PRO PHE PRO ILE THR SER MET LYS ASP THR GLU GLY ILE SEQRES 9 A 400 PRO CYS LEU GLY ASP LYS VAL LYS SER ILE ILE GLU GLY SEQRES 10 A 400 ILE ILE GLU ASP GLY GLU SER SER GLU ALA LYS ALA VAL SEQRES 11 A 400 LEU ASN ASP GLU ARG TYR LYS SER PHE LYS LEU PHE THR SEQRES 12 A 400 SER VAL PHE GLY VAL GLY LEU LYS THR ALA GLU LYS TRP SEQRES 13 A 400 PHE ARG MET GLY PHE ARG THR LEU SER LYS ILE GLN SER SEQRES 14 A 400 ASP LYS SER LEU ARG PHE THR GLN MET GLN LYS ALA GLY SEQRES 15 A 400 PHE LEU TYR TYR GLU ASP LEU VAL SER CYS VAL ASN ARG SEQRES 16 A 400 PRO GLU ALA GLU ALA VAL SER MET LEU VAL LYS GLU ALA SEQRES 17 A 400 VAL VAL THR PHE LEU PRO ASP ALA LEU VAL THR MET THR SEQRES 18 A 400 GLY GLY PHE ARG ARG GLY LYS MET THR GLY HIS ASP VAL SEQRES 19 A 400 ASP PHE LEU ILE THR SER PRO GLU ALA THR GLU ASP GLU SEQRES 20 A 400 GLU GLN GLN LEU LEU HIS LYS VAL THR ASP PHE TRP LYS SEQRES 21 A 400 GLN GLN GLY LEU LEU LEU TYR CYS ASP ILE LEU GLU SER SEQRES 22 A 400 THR PHE GLU LYS PHE LYS GLN PRO SER ARG LYS VAL ASP SEQRES 23 A 400 ALA LEU ASP HIS PHE GLN LYS CYS ALA LEU ILE LEU LYS SEQRES 24 A 400 LEU ASP HIS GLY ARG VAL HIS SER GLU LYS SER GLY GLN SEQRES 25 A 400 GLN GLU GLY LYS GLY TRP LYS ALA ILE ARG VAL ASP LEU SEQRES 26 A 400 VAL MET CYS PRO TYR ASP ARG ARG ALA PHE ALA LEU LEU SEQRES 27 A 400 GLY TRP THR GLY SER ARG GLN PHE GLU ARG ASP LEU ARG SEQRES 28 A 400 ARG TYR ALA THR HIS GLU ARG LYS MET MET LEU ASP ASN SEQRES 29 A 400 HIS ALA LEU TYR ASP ARG THR LYS ARG VAL PHE LEU GLU SEQRES 30 A 400 ALA GLU SER GLU GLU GLU ILE PHE ALA HIS LEU GLY LEU SEQRES 31 A 400 ASP TYR ILE GLU PRO TRP GLU ARG ASN ALA SEQRES 1 D 6 DA DA DA DA DA DC SEQRES 1 T 7 DT DT DT DT DT DG DC SEQRES 1 U 6 DA DA DA DA DA DC HET MG A 601 1 HET MG A 602 1 HET NA A 603 1 HET DCT A 604 27 HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE FORMUL 5 MG 2(MG 2+) FORMUL 7 NA NA 1+ FORMUL 8 DCT C9 H16 N3 O12 P3 FORMUL 9 HOH *63(H2 O) HELIX 1 1 TYR A 153 ARG A 157 5 5 HELIX 2 2 ASN A 165 ARG A 182 1 18 HELIX 3 3 ASN A 184 SER A 200 1 17 HELIX 4 4 SER A 207 GLU A 212 5 6 HELIX 5 5 GLY A 218 GLY A 232 1 15 HELIX 6 6 SER A 234 ASP A 243 1 10 HELIX 7 7 ASP A 243 SER A 254 1 12 HELIX 8 8 GLY A 259 MET A 269 1 11 HELIX 9 9 THR A 273 ASP A 280 1 8 HELIX 10 10 THR A 286 TYR A 295 1 10 HELIX 11 11 TYR A 295 SER A 301 1 7 HELIX 12 12 ARG A 305 LEU A 323 1 19 HELIX 13 13 THR A 331 ARG A 336 1 6 HELIX 14 14 THR A 354 GLY A 373 1 20 HELIX 15 15 GLY A 413 VAL A 415 5 3 HELIX 16 16 PRO A 439 ASP A 441 5 3 HELIX 17 17 ARG A 442 GLY A 452 1 11 HELIX 18 18 SER A 453 LYS A 469 1 17 HELIX 19 19 SER A 490 GLY A 499 1 10 HELIX 20 20 GLU A 504 ARG A 508 5 5 SHEET 1 A 2 VAL A 303 ASN A 304 0 SHEET 2 A 2 THR A 340 GLY A 341 -1 O GLY A 341 N VAL A 303 SHEET 1 B 5 LEU A 327 MET A 330 0 SHEET 2 B 5 VAL A 344 THR A 349 -1 O THR A 349 N LEU A 327 SHEET 3 B 5 TRP A 428 MET A 437 1 O VAL A 436 N ILE A 348 SHEET 4 B 5 GLN A 402 ASP A 411 -1 N LEU A 406 O VAL A 433 SHEET 5 B 5 LEU A 375 LEU A 381 -1 N LEU A 381 O LYS A 403 SHEET 1 C 3 MET A 470 LEU A 472 0 SHEET 2 C 3 LEU A 477 ASP A 479 -1 O TYR A 478 N MET A 471 SHEET 3 C 3 VAL A 484 LEU A 486 -1 O LEU A 486 N LEU A 477 LINK O THR A 253 NA NA A 603 1555 1555 2.80 LINK O VAL A 255 NA NA A 603 1555 1555 2.34 LINK O VAL A 258 NA NA A 603 1555 1555 2.60 LINK OD1 ASP A 343 MG MG A 601 1555 1555 1.97 LINK OD1 ASP A 343 MG MG A 602 1555 1555 2.54 LINK OD2 ASP A 343 MG MG A 602 1555 1555 2.66 LINK OD2 ASP A 345 MG MG A 601 1555 1555 2.42 LINK OD1 ASP A 345 MG MG A 602 1555 1555 2.09 LINK OD2 ASP A 345 MG MG A 602 1555 1555 2.99 LINK OD2 ASP A 434 MG MG A 602 1555 1555 2.20 LINK MG MG A 601 O3G DCT A 604 1555 1555 2.09 LINK MG MG A 601 O2B DCT A 604 1555 1555 2.19 LINK MG MG A 601 O2A DCT A 604 1555 1555 2.45 LINK MG MG A 601 O HOH A 724 1555 1555 2.24 LINK MG MG A 602 O2A DCT A 604 1555 1555 2.52 LINK MG MG A 602 OP1 DC U 5 1555 1555 2.86 LINK MG MG A 602 O HOH U 101 1555 1555 2.18 LINK NA NA A 603 O HOH A 723 1555 1555 2.47 LINK NA NA A 603 OP1 DA U 4 1555 1555 2.36 CISPEP 1 GLY A 452 SER A 453 0 -1.24 SITE 1 AC1 5 ASP A 343 ASP A 345 MG A 602 DCT A 604 SITE 2 AC1 5 HOH A 724 SITE 1 AC2 7 ASP A 343 ASP A 345 ASP A 434 MG A 601 SITE 2 AC2 7 DCT A 604 DC U 5 HOH U 101 SITE 1 AC3 6 THR A 253 VAL A 255 GLY A 257 VAL A 258 SITE 2 AC3 6 HOH A 723 DA U 4 SITE 1 AC4 19 GLY A 332 GLY A 333 ARG A 336 LYS A 338 SITE 2 AC4 19 GLY A 341 HIS A 342 ASP A 343 ASP A 345 SITE 3 AC4 19 GLY A 449 TRP A 450 GLY A 452 ARG A 454 SITE 4 AC4 19 GLU A 457 MG A 601 MG A 602 HOH A 724 SITE 5 AC4 19 DG T 6 DC U 5 HOH U 101 CRYST1 55.933 74.920 125.633 90.00 98.43 90.00 C 1 2 1 8 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 0.017879 0.000000 0.002650 0.00000 SCALE2 0.000000 0.013348 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008047 0.00000