HEADER DNA BINDING PROTEIN 01-JUN-18 6GO7 TITLE TDT CHIMERA (LOOP1 OF POL MU) - FULL DNA SYNAPSIS COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA NUCLEOTIDYLEXOTRANSFERASE,DNA-DIRECTED DNA/RNA COMPND 3 POLYMERASE MU,DNA NUCLEOTIDYLEXOTRANSFERASE; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: TERMINAL ADDITION ENZYME,TERMINAL COMPND 6 DEOXYNUCLEOTIDYLTRANSFERASE,TERMINAL TRANSFERASE,POL MU,TERMINAL COMPND 7 TRANSFERASE,TERMINAL ADDITION ENZYME,TERMINAL COMPND 8 DEOXYNUCLEOTIDYLTRANSFERASE,TERMINAL TRANSFERASE; COMPND 9 EC: 2.7.7.31,2.7.7.7,2.7.7.31; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: THERE IS AN INSERTION OF ONE RESIDUE BETWEEN LOOP1 OF COMPND 12 POL MU AND TDT (Q394). THIS INSERTION EXPLAIN THE NUMBERING SHIFT COMPND 13 WITH WT-TDT.,THERE IS AN INSERTION OF ONE RESIDUE BETWEEN LOOP1 OF COMPND 14 POL MU AND TDT (Q394). THIS INSERTION EXPLAIN THE NUMBERING SHIFT COMPND 15 WITH WT-TDT.,THERE IS AN INSERTION OF ONE RESIDUE BETWEEN LOOP1 OF COMPND 16 POL MU AND TDT (Q394). THIS INSERTION EXPLAIN THE NUMBERING SHIFT COMPND 17 WITH WT-TDT.; COMPND 18 MOL_ID: 2; COMPND 19 MOLECULE: DNA (5'-D(*AP*AP*AP*AP*AP*C)-3'); COMPND 20 CHAIN: F, G; COMPND 21 ENGINEERED: YES; COMPND 22 MOL_ID: 3; COMPND 23 MOLECULE: DNA (5'-D(*TP*TP*TP*TP*TP*GP*C)-3'); COMPND 24 CHAIN: E, H, I, J; COMPND 25 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, POLM, POLMU; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630 KEYWDS NHEJ PATHWAY, DNA BRIDGING, DNA POLYMERASE POLX, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.LOC'H,C.A.GERODIMOS,S.ROSARIO,M.R.LIEBER,M.DELARUE REVDAT 3 17-JAN-24 6GO7 1 LINK REVDAT 2 25-DEC-19 6GO7 1 JRNL REVDAT 1 05-JUN-19 6GO7 0 JRNL AUTH J.LOC'H,C.A.GERODIMOS,S.ROSARIO,M.TEKPINAR,M.R.LIEBER, JRNL AUTH 2 M.DELARUE JRNL TITL STRUCTURAL EVIDENCE FOR AN INTRANSBASE SELECTION MECHANISM JRNL TITL 2 INVOLVING LOOP1 IN POLYMERASE MU AT AN NHEJ DOUBLE-STRAND JRNL TITL 3 BREAK JUNCTION. JRNL REF J.BIOL.CHEM. V. 294 10579 2019 JRNL REFN ESSN 1083-351X JRNL PMID 31138645 JRNL DOI 10.1074/JBC.RA119.008739 REMARK 2 REMARK 2 RESOLUTION. 2.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 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) : 2.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 16484 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) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 825 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.55 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.73 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.80 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2953 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2347 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2805 REMARK 3 BIN R VALUE (WORKING SET) : 0.2325 REMARK 3 BIN FREE R VALUE : 0.2769 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.01 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 148 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 : 2665 REMARK 3 NUCLEIC ACID ATOMS : 774 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 180 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 60.47 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.24280 REMARK 3 B22 (A**2) : 7.24390 REMARK 3 B33 (A**2) : -11.48670 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -3.31320 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.330 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.795 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.269 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.689 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.269 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 : 0.921 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.877 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 3621 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 5042 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1147 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 62 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 449 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 3621 ; 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 : 463 ; 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 : 3883 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.05 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.73 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 19.54 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): -10.2355 -12.8645 -22.0701 REMARK 3 T TENSOR REMARK 3 T11: -0.0943 T22: -0.0729 REMARK 3 T33: -0.0688 T12: -0.0173 REMARK 3 T13: -0.0044 T23: 0.0329 REMARK 3 L TENSOR REMARK 3 L11: 0.5151 L22: 1.6513 REMARK 3 L33: 0.9723 L12: 0.0344 REMARK 3 L13: 0.0152 L23: 0.4629 REMARK 3 S TENSOR REMARK 3 S11: -0.0222 S12: -0.0366 S13: -0.0928 REMARK 3 S21: 0.0063 S22: 0.0548 S23: 0.0590 REMARK 3 S31: 0.1216 S32: 0.0580 S33: -0.0326 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { D|* } REMARK 3 ORIGIN FOR THE GROUP (A): -25.2525 -31.1246 -16.8800 REMARK 3 T TENSOR REMARK 3 T11: 0.0491 T22: -0.0005 REMARK 3 T33: -0.0577 T12: 0.0068 REMARK 3 T13: 0.0480 T23: 0.1608 REMARK 3 L TENSOR REMARK 3 L11: 1.9138 L22: 0.6246 REMARK 3 L33: -0.0356 L12: -0.1220 REMARK 3 L13: -1.2597 L23: -0.1291 REMARK 3 S TENSOR REMARK 3 S11: 0.0063 S12: 0.0356 S13: -0.0055 REMARK 3 S21: 0.0071 S22: 0.0027 S23: 0.0188 REMARK 3 S31: 0.0135 S32: 0.0042 S33: -0.0090 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: { E|* } REMARK 3 ORIGIN FOR THE GROUP (A): -31.0675 -33.2640 -17.2507 REMARK 3 T TENSOR REMARK 3 T11: 0.1178 T22: -0.0375 REMARK 3 T33: -0.1038 T12: 0.0086 REMARK 3 T13: -0.0398 T23: 0.1593 REMARK 3 L TENSOR REMARK 3 L11: -0.0637 L22: 0.2608 REMARK 3 L33: 2.1634 L12: -0.2407 REMARK 3 L13: 0.7076 L23: 0.0455 REMARK 3 S TENSOR REMARK 3 S11: -0.0062 S12: 0.0126 S13: 0.0305 REMARK 3 S21: -0.0116 S22: -0.0100 S23: 0.0528 REMARK 3 S31: 0.0307 S32: -0.0342 S33: 0.0162 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: { F|* } REMARK 3 ORIGIN FOR THE GROUP (A): -12.0010 0.0101 0.6464 REMARK 3 T TENSOR REMARK 3 T11: -0.0983 T22: 0.1021 REMARK 3 T33: -0.0139 T12: 0.0594 REMARK 3 T13: 0.0362 T23: -0.0665 REMARK 3 L TENSOR REMARK 3 L11: 0.2346 L22: 0.8679 REMARK 3 L33: 1.6781 L12: 0.1086 REMARK 3 L13: -0.0983 L23: 0.2817 REMARK 3 S TENSOR REMARK 3 S11: -0.0078 S12: 0.0496 S13: 0.0701 REMARK 3 S21: -0.0311 S22: -0.0020 S23: 0.0557 REMARK 3 S31: -0.0644 S32: 0.0059 S33: 0.0098 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: { G|* } REMARK 3 ORIGIN FOR THE GROUP (A): -17.5311 -4.5013 0.2239 REMARK 3 T TENSOR REMARK 3 T11: -0.0611 T22: 0.0179 REMARK 3 T33: 0.0487 T12: 0.0221 REMARK 3 T13: 0.1233 T23: -0.0846 REMARK 3 L TENSOR REMARK 3 L11: -0.7850 L22: 0.1792 REMARK 3 L33: 0.8222 L12: 1.3422 REMARK 3 L13: 1.2440 L23: 0.6897 REMARK 3 S TENSOR REMARK 3 S11: -0.0055 S12: -0.0871 S13: 0.0125 REMARK 3 S21: 0.0588 S22: 0.0538 S23: 0.0213 REMARK 3 S31: 0.0159 S32: -0.0416 S33: -0.0483 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: { K|* } REMARK 3 ORIGIN FOR THE GROUP (A): -22.6807 -24.6245 -13.6953 REMARK 3 T TENSOR REMARK 3 T11: 0.0303 T22: -0.1264 REMARK 3 T33: 0.0810 T12: -0.1027 REMARK 3 T13: 0.1644 T23: 0.1086 REMARK 3 L TENSOR REMARK 3 L11: 0.2637 L22: 2.2418 REMARK 3 L33: 0.6889 L12: -1.2882 REMARK 3 L13: 0.8257 L23: 0.0091 REMARK 3 S TENSOR REMARK 3 S11: -0.0157 S12: 0.0158 S13: 0.0450 REMARK 3 S21: 0.0218 S22: 0.0192 S23: 0.0138 REMARK 3 S31: -0.0020 S32: 0.0137 S33: -0.0035 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6GO7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1200010309. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8728 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 X 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16488 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550 REMARK 200 RESOLUTION RANGE LOW (A) : 44.990 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.13500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.76200 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 REMARK 200 STARTING MODEL: 1JMS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 19-25% PEG 4000, 100-400 MM LITHIUM REMARK 280 SULFATE, 100 MM TRIS, PH 8.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K 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 45.15500 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: HEPTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEPTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -61.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, F, E, H, G, I, J 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 VAL A 147 REMARK 465 LYS A 148 REMARK 465 HIS A 384 REMARK 465 LEU A 385 REMARK 465 ALA A 386 REMARK 465 ASP A 387 REMARK 465 SER A 388 REMARK 465 ALA A 389 REMARK 465 HIS A 390 REMARK 465 ASN A 391 REMARK 465 LEU A 392 REMARK 465 ARG A 393 REMARK 465 GLN A 394 REMARK 465 ARG A 395 REMARK 465 SER A 396 REMARK 465 SER A 397 REMARK 465 THR A 398 REMARK 465 MET A 399 REMARK 465 ASP A 400 REMARK 465 VAL A 401 REMARK 465 GLU A 419 REMARK 465 LYS A 420 REMARK 465 SER A 421 REMARK 465 GLY A 422 REMARK 465 GLN A 423 REMARK 465 GLN A 424 REMARK 465 GLU A 425 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 GLU A 183 CG CD OE1 OE2 REMARK 470 GLU A 185 CD OE1 OE2 REMARK 470 LYS A 209 CG CD CE NZ REMARK 470 ASP A 219 CG OD1 OD2 REMARK 470 GLU A 244 CD OE1 OE2 REMARK 470 GLU A 264 CG CD OE1 OE2 REMARK 470 ARG A 268 CG CD NE CZ NH1 NH2 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 GLU A 352 CG CD OE1 OE2 REMARK 470 THR A 354 OG1 CG2 REMARK 470 GLU A 355 CG CD OE1 OE2 REMARK 470 GLU A 358 CG CD OE1 OE2 REMARK 470 GLN A 359 CG CD OE1 NE2 REMARK 470 ARG A 382 CG CD NE CZ NH1 NH2 REMARK 470 SER A 383 OG REMARK 470 HIS A 417 CB CG ND1 CD2 CE1 NE2 REMARK 470 SER A 418 OG REMARK 470 ASP A 442 CG OD1 OD2 REMARK 470 LYS A 470 CD CE NZ REMARK 470 LYS A 483 CG CD CE NZ REMARK 470 DC F 6 O3' REMARK 470 DC E 7 O3' REMARK 470 DC H 7 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DC H 7 N1 C2 O2 N3 C4 N4 C5 REMARK 470 DC H 7 C6 REMARK 470 DC G 6 O3' REMARK 470 DC I 7 O3' REMARK 470 DC J 7 O3' 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 OE1 GLU A 505 CZ2 TRP A 507 2.08 REMARK 500 O HOH A 807 O HOH A 843 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 F 3 O3' DA F 3 C3' -0.038 REMARK 500 DC E 7 C1' DC E 7 N1 0.082 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 DA F 3 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DT E 1 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT H 5 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DA G 5 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC I 7 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG J 6 O4' - C1' - N9 ANGL. DEV. = 1.9 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 216 -1.24 63.07 REMARK 500 LEU A 323 79.16 -154.53 REMARK 500 THR A 331 -156.51 -109.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 858 DISTANCE = 6.12 ANGSTROMS REMARK 525 HOH A 859 DISTANCE = 6.92 ANGSTROMS REMARK 525 HOH A 860 DISTANCE = 8.25 ANGSTROMS REMARK 525 HOH E 106 DISTANCE = 7.10 ANGSTROMS 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 601 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 253 O REMARK 620 2 VAL A 255 O 77.9 REMARK 620 3 VAL A 258 O 87.4 76.6 REMARK 620 4 DG E 6 OP1 171.1 104.8 85.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 603 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 343 OD1 REMARK 620 2 ASP A 345 OD2 86.3 REMARK 620 3 DCT A 602 O3G 74.3 127.7 REMARK 620 4 HOH A 752 O 128.1 76.0 151.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DCT A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 603 DBREF 6GO7 A 132 377 UNP P09838 TDT_MOUSE 132 377 DBREF 6GO7 A 378 407 UNP Q9JIW4 DPOLM_MOUSE 363 392 DBREF 6GO7 A 408 511 UNP P09838 TDT_MOUSE 407 510 DBREF 6GO7 F 1 6 PDB 6GO7 6GO7 1 6 DBREF 6GO7 E 1 7 PDB 6GO7 6GO7 1 7 DBREF 6GO7 H 1 7 PDB 6GO7 6GO7 1 7 DBREF 6GO7 G 1 6 PDB 6GO7 6GO7 1 6 DBREF 6GO7 I 1 7 PDB 6GO7 6GO7 1 7 DBREF 6GO7 J 1 7 PDB 6GO7 6GO7 1 7 SEQADV 6GO7 MET A 111 UNP P09838 INITIATING METHIONINE SEQADV 6GO7 GLY A 112 UNP P09838 EXPRESSION TAG SEQADV 6GO7 SER A 113 UNP P09838 EXPRESSION TAG SEQADV 6GO7 SER A 114 UNP P09838 EXPRESSION TAG SEQADV 6GO7 HIS A 115 UNP P09838 EXPRESSION TAG SEQADV 6GO7 HIS A 116 UNP P09838 EXPRESSION TAG SEQADV 6GO7 HIS A 117 UNP P09838 EXPRESSION TAG SEQADV 6GO7 HIS A 118 UNP P09838 EXPRESSION TAG SEQADV 6GO7 HIS A 119 UNP P09838 EXPRESSION TAG SEQADV 6GO7 HIS A 120 UNP P09838 EXPRESSION TAG SEQADV 6GO7 SER A 121 UNP P09838 EXPRESSION TAG SEQADV 6GO7 SER A 122 UNP P09838 EXPRESSION TAG SEQADV 6GO7 GLY A 123 UNP P09838 EXPRESSION TAG SEQADV 6GO7 LEU A 124 UNP P09838 EXPRESSION TAG SEQADV 6GO7 VAL A 125 UNP P09838 EXPRESSION TAG SEQADV 6GO7 PRO A 126 UNP P09838 EXPRESSION TAG SEQADV 6GO7 ARG A 127 UNP P09838 EXPRESSION TAG SEQADV 6GO7 GLY A 128 UNP P09838 EXPRESSION TAG SEQADV 6GO7 SER A 129 UNP P09838 EXPRESSION TAG SEQADV 6GO7 HIS A 130 UNP P09838 EXPRESSION TAG SEQADV 6GO7 MET A 131 UNP P09838 EXPRESSION TAG SEQADV 6GO7 VAL A 401 UNP Q9JIW4 ALA 386 CONFLICT SEQRES 1 A 401 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 401 LEU VAL PRO ARG GLY SER HIS MET SER PRO SER PRO VAL SEQRES 3 A 401 PRO GLY SER GLN ASN VAL PRO ALA PRO ALA VAL LYS LYS SEQRES 4 A 401 ILE SER GLN TYR ALA CYS GLN ARG ARG THR THR LEU ASN SEQRES 5 A 401 ASN TYR ASN GLN LEU PHE THR ASP ALA LEU ASP ILE LEU SEQRES 6 A 401 ALA GLU ASN ASP GLU LEU ARG GLU ASN GLU GLY SER CYS SEQRES 7 A 401 LEU ALA PHE MET ARG ALA SER SER VAL LEU LYS SER LEU SEQRES 8 A 401 PRO PHE PRO ILE THR SER MET LYS ASP THR GLU GLY ILE SEQRES 9 A 401 PRO CYS LEU GLY ASP LYS VAL LYS SER ILE ILE GLU GLY SEQRES 10 A 401 ILE ILE GLU ASP GLY GLU SER SER GLU ALA LYS ALA VAL SEQRES 11 A 401 LEU ASN ASP GLU ARG TYR LYS SER PHE LYS LEU PHE THR SEQRES 12 A 401 SER VAL PHE GLY VAL GLY LEU LYS THR ALA GLU LYS TRP SEQRES 13 A 401 PHE ARG MET GLY PHE ARG THR LEU SER LYS ILE GLN SER SEQRES 14 A 401 ASP LYS SER LEU ARG PHE THR GLN MET GLN LYS ALA GLY SEQRES 15 A 401 PHE LEU TYR TYR GLU ASP LEU VAL SER CYS VAL ASN ARG SEQRES 16 A 401 PRO GLU ALA GLU ALA VAL SER MET LEU VAL LYS GLU ALA SEQRES 17 A 401 VAL VAL THR PHE LEU PRO ASP ALA LEU VAL THR MET THR SEQRES 18 A 401 GLY GLY PHE ARG ARG GLY LYS MET THR GLY HIS ASP VAL SEQRES 19 A 401 ASP PHE LEU ILE THR SER PRO GLU ALA THR GLU ASP GLU SEQRES 20 A 401 GLU GLN GLN LEU LEU HIS LYS VAL THR ASP PHE TRP LYS SEQRES 21 A 401 GLN GLN GLY LEU LEU LEU TYR HIS GLN TYR HIS ARG SER SEQRES 22 A 401 HIS LEU ALA ASP SER ALA HIS ASN LEU ARG GLN ARG SER SEQRES 23 A 401 SER THR MET ASP VAL PHE GLU ARG SER PHE CYS ILE LEU SEQRES 24 A 401 LYS LEU ASP HIS GLY ARG VAL HIS SER GLU LYS SER GLY SEQRES 25 A 401 GLN GLN GLU GLY LYS GLY TRP LYS ALA ILE ARG VAL ASP SEQRES 26 A 401 LEU VAL MET CYS PRO TYR ASP ARG ARG ALA PHE ALA LEU SEQRES 27 A 401 LEU GLY TRP THR GLY SER ARG GLN PHE GLU ARG ASP LEU SEQRES 28 A 401 ARG ARG TYR ALA THR HIS GLU ARG LYS MET MET LEU ASP SEQRES 29 A 401 ASN HIS ALA LEU TYR ASP ARG THR LYS ARG VAL PHE LEU SEQRES 30 A 401 GLU ALA GLU SER GLU GLU GLU ILE PHE ALA HIS LEU GLY SEQRES 31 A 401 LEU ASP TYR ILE GLU PRO TRP GLU ARG ASN ALA SEQRES 1 F 6 DA DA DA DA DA DC SEQRES 1 E 7 DT DT DT DT DT DG DC SEQRES 1 H 7 DT DT DT DT DT DG DC SEQRES 1 G 6 DA DA DA DA DA DC SEQRES 1 I 7 DT DT DT DT DT DG DC SEQRES 1 J 7 DT DT DT DT DT DG DC HET NA A 601 1 HET DCT A 602 27 HET MG A 603 1 HETNAM NA SODIUM ION HETNAM DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 8 NA NA 1+ FORMUL 9 DCT C9 H16 N3 O12 P3 FORMUL 10 MG MG 2+ FORMUL 11 HOH *180(H2 O) HELIX 1 AA1 TYR A 153 ARG A 157 5 5 HELIX 2 AA2 ASN A 165 ARG A 182 1 18 HELIX 3 AA3 ASN A 184 SER A 200 1 17 HELIX 4 AA4 SER A 207 GLU A 212 5 6 HELIX 5 AA5 GLY A 218 GLY A 232 1 15 HELIX 6 AA6 SER A 234 ASN A 242 1 9 HELIX 7 AA7 ASP A 243 SER A 254 1 12 HELIX 8 AA8 GLY A 259 ARG A 268 1 10 HELIX 9 AA9 THR A 273 ASP A 280 1 8 HELIX 10 AB1 THR A 286 TYR A 295 1 10 HELIX 11 AB2 TYR A 295 SER A 301 1 7 HELIX 12 AB3 ARG A 305 LEU A 323 1 19 HELIX 13 AB4 THR A 331 ARG A 336 1 6 HELIX 14 AB5 THR A 354 GLN A 359 1 6 HELIX 15 AB6 GLN A 360 GLN A 372 1 13 HELIX 16 AB7 GLY A 414 VAL A 416 5 3 HELIX 17 AB8 PRO A 440 ASP A 442 5 3 HELIX 18 AB9 ARG A 443 GLY A 453 1 11 HELIX 19 AC1 SER A 454 LYS A 470 1 17 HELIX 20 AC2 SER A 491 LEU A 499 1 9 HELIX 21 AC3 GLU A 505 ARG A 509 5 5 SHEET 1 AA1 2 VAL A 303 ASN A 304 0 SHEET 2 AA1 2 THR A 340 GLY A 341 -1 O GLY A 341 N VAL A 303 SHEET 1 AA2 5 LEU A 327 MET A 330 0 SHEET 2 AA2 5 VAL A 344 THR A 349 -1 O THR A 349 N LEU A 327 SHEET 3 AA2 5 TRP A 429 MET A 438 1 O VAL A 437 N ILE A 348 SHEET 4 AA2 5 ARG A 404 ASP A 412 -1 N LEU A 409 O ILE A 432 SHEET 5 AA2 5 LEU A 375 HIS A 381 -1 N GLN A 379 O PHE A 406 SHEET 1 AA3 3 MET A 471 LEU A 473 0 SHEET 2 AA3 3 LEU A 478 ASP A 480 -1 O TYR A 479 N MET A 472 SHEET 3 AA3 3 VAL A 485 LEU A 487 -1 O VAL A 485 N ASP A 480 LINK O THR A 253 NA NA A 601 1555 1555 2.50 LINK O VAL A 255 NA NA A 601 1555 1555 2.78 LINK O VAL A 258 NA NA A 601 1555 1555 2.94 LINK OD1 ASP A 343 MG MG A 603 1555 1555 2.19 LINK OD2 ASP A 345 MG MG A 603 1555 1555 2.18 LINK NA NA A 601 OP1 DG E 6 1555 1555 2.91 LINK O3G DCT A 602 MG MG A 603 1555 1555 2.35 LINK MG MG A 603 O HOH A 752 1555 1555 3.00 CISPEP 1 GLY A 453 SER A 454 0 -2.07 SITE 1 AC1 4 THR A 253 VAL A 255 VAL A 258 DG E 6 SITE 1 AC2 21 GLY A 332 GLY A 333 ARG A 336 LYS A 338 SITE 2 AC2 21 GLY A 341 HIS A 342 ASP A 343 ASP A 345 SITE 3 AC2 21 TRP A 451 GLY A 453 ARG A 455 GLU A 458 SITE 4 AC2 21 MG A 603 HOH A 704 HOH A 705 HOH A 719 SITE 5 AC2 21 HOH A 742 HOH A 760 HOH A 762 DC E 7 SITE 6 AC2 21 DG H 6 SITE 1 AC3 4 ASP A 343 ASP A 345 DCT A 602 HOH A 752 CRYST1 47.000 90.310 65.900 90.00 106.79 90.00 P 1 21 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 0.021277 0.000000 0.006420 0.00000 SCALE2 0.000000 0.011073 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015850 0.00000