PDB Short entry for 4QZB HEADER TRANSFERASE/DNA 27-JUL-14 4QZB TITLE MOUSE TDT IN COMPLEX WITH A DSB SUBSTRATE, C-T BASE 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 MOL_ID: 2; COMPND 10 MOLECULE: 5'-D(*AP*AP*AP*AP*AP*C)-3'; COMPND 11 CHAIN: D, U; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: 5'-D(*TP*TP*TP*TP*TP*GP*T)-3'; COMPND 15 CHAIN: T; COMPND 16 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 4QZB 1 REMARK SEQADV LINK REVDAT 2 26-JUL-17 4QZB 1 SOURCE REMARK REVDAT 1 10-JUN-15 4QZB 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. 2.15 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 28971 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) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 1467 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 : 15 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.23 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.71 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2821 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2147 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2672 REMARK 3 BIN R VALUE (WORKING SET) : 0.2133 REMARK 3 BIN FREE R VALUE : 0.2407 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.28 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 149 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 : 2851 REMARK 3 NUCLEIC ACID ATOMS : 365 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 250 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 50.25 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.60440 REMARK 3 B22 (A**2) : 4.82300 REMARK 3 B33 (A**2) : -4.21860 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -4.90590 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.301 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.200 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.165 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.194 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.164 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 : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.936 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 3367 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 4627 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1459 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 75 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 446 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 3367 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 1 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 432 ; 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 : 3814 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 0.98 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.82 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 3.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: {A|148 - 233} REMARK 3 ORIGIN FOR THE GROUP (A): -20.8964 -9.9846 19.9919 REMARK 3 T TENSOR REMARK 3 T11: -0.0624 T22: -0.0507 REMARK 3 T33: -0.0324 T12: 0.1518 REMARK 3 T13: 0.0660 T23: 0.0141 REMARK 3 L TENSOR REMARK 3 L11: 2.0013 L22: 4.4927 REMARK 3 L33: 1.3686 L12: -1.2137 REMARK 3 L13: -0.3066 L23: 0.3941 REMARK 3 S TENSOR REMARK 3 S11: 0.0450 S12: 0.0444 S13: -0.1188 REMARK 3 S21: -0.1839 S22: -0.0529 S23: -0.4699 REMARK 3 S31: 0.0215 S32: 0.2806 S33: 0.0079 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: {A|234 - 398} REMARK 3 ORIGIN FOR THE GROUP (A): -25.5847 4.8705 43.3860 REMARK 3 T TENSOR REMARK 3 T11: -0.0622 T22: -0.1011 REMARK 3 T33: -0.0044 T12: 0.0538 REMARK 3 T13: 0.0498 T23: 0.0799 REMARK 3 L TENSOR REMARK 3 L11: 1.9396 L22: 1.2261 REMARK 3 L33: 0.8550 L12: 0.1784 REMARK 3 L13: -0.3197 L23: 0.4362 REMARK 3 S TENSOR REMARK 3 S11: 0.1792 S12: -0.1369 S13: 0.2481 REMARK 3 S21: 0.0751 S22: -0.1115 S23: -0.2424 REMARK 3 S31: -0.1051 S32: 0.0510 S33: -0.0677 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: {A|399 - 510} REMARK 3 ORIGIN FOR THE GROUP (A): -37.9030 -0.7114 34.4007 REMARK 3 T TENSOR REMARK 3 T11: -0.0642 T22: -0.1103 REMARK 3 T33: -0.0334 T12: 0.0726 REMARK 3 T13: 0.0621 T23: 0.0327 REMARK 3 L TENSOR REMARK 3 L11: 0.9640 L22: 1.3062 REMARK 3 L33: 1.8368 L12: 0.0329 REMARK 3 L13: 0.0744 L23: -0.0360 REMARK 3 S TENSOR REMARK 3 S11: 0.0853 S12: -0.0019 S13: -0.0466 REMARK 3 S21: -0.0226 S22: -0.1367 S23: 0.1271 REMARK 3 S31: 0.0168 S32: 0.0004 S33: 0.0513 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: {T|1 - 7} REMARK 3 ORIGIN FOR THE GROUP (A): -30.0150 7.5171 14.4856 REMARK 3 T TENSOR REMARK 3 T11: 0.1130 T22: -0.0163 REMARK 3 T33: -0.1003 T12: 0.1402 REMARK 3 T13: 0.0703 T23: 0.0795 REMARK 3 L TENSOR REMARK 3 L11: 0.1806 L22: 0.4197 REMARK 3 L33: 3.6817 L12: 1.9089 REMARK 3 L13: -0.2888 L23: 2.8485 REMARK 3 S TENSOR REMARK 3 S11: -0.0938 S12: 0.3053 S13: 0.1716 REMARK 3 S21: -0.3824 S22: 0.3354 S23: 0.1296 REMARK 3 S31: -0.4875 S32: 0.2675 S33: -0.2416 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: {U|1 - 6} REMARK 3 ORIGIN FOR THE GROUP (A): -23.9985 15.6895 36.8690 REMARK 3 T TENSOR REMARK 3 T11: -0.1146 T22: -0.2192 REMARK 3 T33: 0.3261 T12: -0.0199 REMARK 3 T13: 0.0843 T23: 0.1079 REMARK 3 L TENSOR REMARK 3 L11: 3.1820 L22: 0.2456 REMARK 3 L33: 1.8362 L12: -2.4609 REMARK 3 L13: -2.8414 L23: -1.9096 REMARK 3 S TENSOR REMARK 3 S11: 0.0075 S12: -0.0224 S13: 0.1715 REMARK 3 S21: -0.1613 S22: -0.1027 S23: 0.0713 REMARK 3 S31: -0.1875 S32: -0.0314 S33: 0.0952 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: {D|1 - 6} REMARK 3 ORIGIN FOR THE GROUP (A): -27.2243 0.8170 8.6176 REMARK 3 T TENSOR REMARK 3 T11: -0.0189 T22: 0.0015 REMARK 3 T33: -0.0011 T12: 0.0950 REMARK 3 T13: 0.0328 T23: 0.0147 REMARK 3 L TENSOR REMARK 3 L11: -0.2056 L22: 2.0629 REMARK 3 L33: 7.4280 L12: 0.3108 REMARK 3 L13: 0.4294 L23: -2.7812 REMARK 3 S TENSOR REMARK 3 S11: 0.0288 S12: 0.1096 S13: -0.2444 REMARK 3 S21: -0.1849 S22: 0.1539 S23: 0.1249 REMARK 3 S31: 0.0896 S32: -0.3045 S33: -0.1827 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4QZB 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_1000086702. 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) : 0.919600 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 : 28987 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 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 : 3.700 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.60800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300 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 (%): 53.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 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 28.55500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.60000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 28.55500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 37.60000 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: 4420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 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 GLU A 418 REMARK 465 LYS A 419 REMARK 465 SER A 420 REMARK 465 GLY A 421 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 LYS A 209 CG CD CE NZ REMARK 470 GLU A 230 CG CD OE1 OE2 REMARK 470 LYS A 238 CG CD CE NZ REMARK 470 LYS A 281 CG CD CE NZ REMARK 470 GLU A 317 CG CD OE1 OE2 REMARK 470 GLU A 355 CG CD OE1 OE2 REMARK 470 GLU A 386 CG CD OE1 OE2 REMARK 470 LYS A 387 CG CD CE NZ REMARK 470 LYS A 389 CG CD CE NZ REMARK 470 SER A 392 OG REMARK 470 ARG A 393 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 394 CG CD CE NZ REMARK 470 VAL A 395 CG1 CG2 REMARK 470 ASP A 396 CG OD1 OD2 REMARK 470 GLN A 422 CG CD OE1 NE2 REMARK 470 GLN A 423 CG CD OE1 NE2 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 DC U 6 O3' 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 DT T 7 C1' DT T 7 N1 0.097 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. = 1.9 DEGREES REMARK 500 DT T 7 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 DT T 7 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DA U 2 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 THR A 331 -152.85 -116.28 REMARK 500 SER A 392 -38.91 69.02 REMARK 500 ASN A 509 44.30 -84.25 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 602 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 253 O REMARK 620 2 VAL A 255 O 87.0 REMARK 620 3 VAL A 258 O 102.8 97.9 REMARK 620 4 DA U 5 OP1 166.5 97.1 89.5 REMARK 620 5 HOH U 106 O 99.6 171.3 86.3 75.3 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 85.4 REMARK 620 3 DCT A 603 O2B 169.9 104.5 REMARK 620 4 DCT A 603 O3G 82.2 165.7 88.3 REMARK 620 5 DCT A 603 O2A 87.1 76.8 97.5 95.4 REMARK 620 6 HOH A 892 O 85.5 103.6 89.7 82.6 172.5 REMARK 620 N 1 2 3 4 5 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 NA A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DCT A 603 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: 4QZC RELATED DB: PDB REMARK 900 RELATED ID: 4QZD 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 4QZB A 132 482 UNP P09838 TDT_MOUSE 132 482 DBREF 4QZB A 483 510 UNP P09838 TDT_MOUSE 503 530 DBREF 4QZB D 1 6 PDB 4QZB 4QZB 1 6 DBREF 4QZB U 1 6 PDB 4QZB 4QZB 1 6 DBREF 4QZB T 1 7 PDB 4QZB 4QZB 1 7 SEQADV 4QZB MET A 111 UNP P09838 EXPRESSION TAG SEQADV 4QZB GLY A 112 UNP P09838 EXPRESSION TAG SEQADV 4QZB SER A 113 UNP P09838 EXPRESSION TAG SEQADV 4QZB SER A 114 UNP P09838 EXPRESSION TAG SEQADV 4QZB HIS A 115 UNP P09838 EXPRESSION TAG SEQADV 4QZB HIS A 116 UNP P09838 EXPRESSION TAG SEQADV 4QZB HIS A 117 UNP P09838 EXPRESSION TAG SEQADV 4QZB HIS A 118 UNP P09838 EXPRESSION TAG SEQADV 4QZB HIS A 119 UNP P09838 EXPRESSION TAG SEQADV 4QZB HIS A 120 UNP P09838 EXPRESSION TAG SEQADV 4QZB SER A 121 UNP P09838 EXPRESSION TAG SEQADV 4QZB SER A 122 UNP P09838 EXPRESSION TAG SEQADV 4QZB GLY A 123 UNP P09838 EXPRESSION TAG SEQADV 4QZB LEU A 124 UNP P09838 EXPRESSION TAG SEQADV 4QZB VAL A 125 UNP P09838 EXPRESSION TAG SEQADV 4QZB PRO A 126 UNP P09838 EXPRESSION TAG SEQADV 4QZB ARG A 127 UNP P09838 EXPRESSION TAG SEQADV 4QZB GLY A 128 UNP P09838 EXPRESSION TAG SEQADV 4QZB SER A 129 UNP P09838 EXPRESSION TAG SEQADV 4QZB HIS A 130 UNP P09838 EXPRESSION TAG SEQADV 4QZB MET A 131 UNP P09838 EXPRESSION TAG 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 PHE 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 DT SEQRES 1 U 6 DA DA DA DA DA DC HET MG A 601 1 HET NA A 602 1 HET DCT A 603 27 HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE FORMUL 5 MG MG 2+ FORMUL 6 NA NA 1+ FORMUL 7 DCT C9 H16 N3 O12 P3 FORMUL 8 HOH *250(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 LEU A 201 1 18 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 GLN A 372 1 19 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 PHE A 485 -1 O VAL A 484 N ASP A 479 LINK O THR A 253 NA NA A 602 1555 1555 2.39 LINK O VAL A 255 NA NA A 602 1555 1555 2.50 LINK O VAL A 258 NA NA A 602 1555 1555 2.24 LINK OD1 ASP A 343 MG MG A 601 1555 1555 2.13 LINK OD2 ASP A 345 MG MG A 601 1555 1555 2.72 LINK MG MG A 601 O2B DCT A 603 1555 1555 2.03 LINK MG MG A 601 O3G DCT A 603 1555 1555 2.04 LINK MG MG A 601 O2A DCT A 603 1555 1555 2.11 LINK MG MG A 601 O HOH A 892 1555 1555 2.22 LINK NA NA A 602 OP1 DA U 5 1555 1555 2.58 LINK NA NA A 602 O HOH U 106 1555 1555 2.33 CISPEP 1 GLY A 452 SER A 453 0 -3.67 SITE 1 AC1 4 ASP A 343 ASP A 345 DCT A 603 HOH A 892 SITE 1 AC2 5 THR A 253 VAL A 255 VAL A 258 DA U 5 SITE 2 AC2 5 HOH U 106 SITE 1 AC3 22 GLY A 332 GLY A 333 ARG A 336 LYS A 338 SITE 2 AC3 22 GLY A 341 HIS A 342 ASP A 343 ASP A 345 SITE 3 AC3 22 GLY A 449 TRP A 450 GLY A 452 ARG A 454 SITE 4 AC3 22 GLU A 457 MG A 601 HOH A 707 HOH A 760 SITE 5 AC3 22 HOH A 819 HOH A 861 HOH A 892 DG T 6 SITE 6 AC3 22 DT T 7 DC U 6 CRYST1 57.110 75.200 127.620 90.00 99.58 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 0.017510 0.000000 0.002955 0.00000 SCALE2 0.000000 0.013298 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007947 0.00000