HEADER TRANSFERASE 21-NOV-12 4I2J TITLE BINARY COMPLEX OF MOUSE TDT WITH DCTP 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 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 KEYWDS TERMINAL TRANSFERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.GOUGE,M.DELARUE REVDAT 5 20-SEP-23 4I2J 1 REMARK SEQADV LINK REVDAT 4 26-JUL-17 4I2J 1 SOURCE REMARK REVDAT 3 13-NOV-13 4I2J 1 JRNL REVDAT 2 31-JUL-13 4I2J 1 JRNL REVDAT 1 24-JUL-13 4I2J 0 JRNL AUTH J.GOUGE,S.ROSARIO,F.ROMAIN,P.BEGUIN,M.DELARUE JRNL TITL STRUCTURES OF INTERMEDIATES ALONG THE CATALYTIC CYCLE OF JRNL TITL 2 TERMINAL DEOXYNUCLEOTIDYLTRANSFERASE: DYNAMICAL ASPECTS OF JRNL TITL 3 THE TWO-METAL ION MECHANISM. JRNL REF J.MOL.BIOL. V. 425 4334 2013 JRNL REFN ISSN 0022-2836 JRNL PMID 23856622 JRNL DOI 10.1016/J.JMB.2013.07.009 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.2 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) : 19.42 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 12388 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) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.830 REMARK 3 FREE R VALUE TEST SET COUNT : 598 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 : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.96 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.02 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2783 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2099 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2641 REMARK 3 BIN R VALUE (WORKING SET) : 0.2056 REMARK 3 BIN FREE R VALUE : 0.2938 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 142 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 : 2747 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 163 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 64.59 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 61.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.24160 REMARK 3 B22 (A**2) : 6.46280 REMARK 3 B33 (A**2) : -7.70440 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.371 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.326 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 1.215 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.319 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 : 0.919 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.891 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 2831 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 3834 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1298 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 70 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 415 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 2831 ; 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 : 371 ; 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 : 3172 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.02 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.63 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 2.88 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: {A|149 - 184} REMARK 3 ORIGIN FOR THE GROUP (A): 48.6053 52.3180 64.1693 REMARK 3 T TENSOR REMARK 3 T11: -0.2116 T22: -0.1075 REMARK 3 T33: 0.2396 T12: 0.0140 REMARK 3 T13: 0.0584 T23: -0.0033 REMARK 3 L TENSOR REMARK 3 L11: 3.1437 L22: 1.4770 REMARK 3 L33: 0.0000 L12: 2.9060 REMARK 3 L13: 1.1513 L23: -1.1109 REMARK 3 S TENSOR REMARK 3 S11: 0.0342 S12: 0.0008 S13: 0.0123 REMARK 3 S21: -0.0885 S22: -0.1152 S23: -0.0409 REMARK 3 S31: -0.0842 S32: 0.0032 S33: 0.0809 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: {A|185 - 263} REMARK 3 ORIGIN FOR THE GROUP (A): 51.5398 59.5036 64.5282 REMARK 3 T TENSOR REMARK 3 T11: -0.2996 T22: -0.2616 REMARK 3 T33: 0.3040 T12: -0.0107 REMARK 3 T13: 0.0292 T23: 0.0741 REMARK 3 L TENSOR REMARK 3 L11: 0.9531 L22: 3.0158 REMARK 3 L33: 2.2313 L12: -0.5578 REMARK 3 L13: -0.6126 L23: 2.9051 REMARK 3 S TENSOR REMARK 3 S11: -0.0640 S12: 0.1761 S13: 0.2455 REMARK 3 S21: -0.2893 S22: 0.0117 S23: -0.1405 REMARK 3 S31: -0.4313 S32: 0.0319 S33: 0.0523 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: {A|264 - 307} REMARK 3 ORIGIN FOR THE GROUP (A): 42.2390 67.6705 87.3277 REMARK 3 T TENSOR REMARK 3 T11: -0.2078 T22: -0.2723 REMARK 3 T33: 0.3040 T12: 0.0276 REMARK 3 T13: 0.0261 T23: -0.0837 REMARK 3 L TENSOR REMARK 3 L11: 1.2311 L22: 3.9790 REMARK 3 L33: 0.5031 L12: 1.2904 REMARK 3 L13: 0.2466 L23: -0.5574 REMARK 3 S TENSOR REMARK 3 S11: -0.0210 S12: -0.1726 S13: 0.2221 REMARK 3 S21: 0.1128 S22: -0.1454 S23: -0.0872 REMARK 3 S31: -0.0641 S32: -0.3713 S33: 0.1665 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: {A|308 - 453} REMARK 3 ORIGIN FOR THE GROUP (A): 32.0752 45.6340 86.0884 REMARK 3 T TENSOR REMARK 3 T11: -0.3040 T22: -0.3040 REMARK 3 T33: 0.3040 T12: -0.0318 REMARK 3 T13: 0.1036 T23: 0.0281 REMARK 3 L TENSOR REMARK 3 L11: 3.7670 L22: 3.0585 REMARK 3 L33: 3.1496 L12: -0.7554 REMARK 3 L13: 1.2859 L23: 0.6539 REMARK 3 S TENSOR REMARK 3 S11: 0.1275 S12: -0.2943 S13: -0.0133 REMARK 3 S21: 0.2728 S22: -0.1589 S23: 0.3291 REMARK 3 S31: 0.0827 S32: -0.5269 S33: 0.0314 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: {A|454 - 510} REMARK 3 ORIGIN FOR THE GROUP (A): 31.5189 41.0435 63.5189 REMARK 3 T TENSOR REMARK 3 T11: -0.3040 T22: -0.2198 REMARK 3 T33: 0.3040 T12: 0.0160 REMARK 3 T13: 0.0188 T23: -0.0338 REMARK 3 L TENSOR REMARK 3 L11: 8.0159 L22: 1.9492 REMARK 3 L33: 1.2712 L12: -0.4532 REMARK 3 L13: 2.2744 L23: -0.6901 REMARK 3 S TENSOR REMARK 3 S11: -0.0090 S12: 0.2315 S13: -0.3380 REMARK 3 S21: -0.1508 S22: 0.0097 S23: 0.0827 REMARK 3 S31: 0.2545 S32: -0.2285 S33: -0.0007 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4I2J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-NOV-12. REMARK 100 THE DEPOSITION ID IS D_1000076222. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-APR-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0-7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9330 REMARK 200 MONOCHROMATOR : CHANNEL CUT SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12388 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 19.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL 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) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.33000 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 1JMS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20-26% PEG4000, 100 MM HEPES, 200 MM REMARK 280 LITHIUM CHLORIDE, PH 6.0-7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 23.56500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.93500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.62500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.93500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.56500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.62500 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 SER A 392 REMARK 465 ARG A 393 REMARK 465 LYS A 394 REMARK 465 VAL A 395 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 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 LYS A 149 CG CD CE NZ REMARK 470 ARG A 182 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 185 CG CD OE1 OE2 REMARK 470 LEU A 189 CG CD1 CD2 REMARK 470 LYS A 209 CG CD CE NZ REMARK 470 GLU A 212 CG CD OE1 OE2 REMARK 470 LYS A 220 CG CD CE NZ REMARK 470 VAL A 221 CG1 CG2 REMARK 470 SER A 223 OG REMARK 470 GLU A 233 CG CD OE1 OE2 REMARK 470 ARG A 245 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 261 CD CE NZ REMARK 470 GLU A 264 CG CD OE1 OE2 REMARK 470 LYS A 265 CG CD CE NZ REMARK 470 VAL A 300 CG1 CG2 REMARK 470 GLU A 352 CG CD OE1 OE2 REMARK 470 GLU A 355 CG CD OE1 OE2 REMARK 470 LYS A 364 CG CD CE NZ REMARK 470 ASP A 367 CG OD1 OD2 REMARK 470 LYS A 370 CG CD CE NZ REMARK 470 GLN A 371 CG CD OE1 NE2 REMARK 470 GLN A 372 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 LYS A 389 CG CD CE NZ REMARK 470 GLN A 390 CG CD OE1 NE2 REMARK 470 LYS A 419 CG CD CE NZ REMARK 470 LYS A 426 NZ REMARK 470 ARG A 468 CZ NH1 NH2 REMARK 470 LYS A 469 CE NZ REMARK 470 LYS A 482 CD CE NZ 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 -154.62 -111.61 REMARK 500 ASN A 509 46.59 -86.24 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 ZN A 604 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 343 OD2 REMARK 620 2 ASP A 345 OD2 85.5 REMARK 620 3 ASP A 434 OD2 78.4 90.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 605 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 343 OD1 REMARK 620 2 ASP A 345 OD1 91.0 REMARK 620 3 DCP A 601 O2B 158.7 90.4 REMARK 620 4 DCP A 601 O2A 74.0 72.9 86.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 603 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 473 OD2 REMARK 620 2 HIS A 475 ND1 95.7 REMARK 620 3 HOH A 715 O 90.4 97.4 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DCP A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 605 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4I27 RELATED DB: PDB REMARK 900 RELATED ID: 4I28 RELATED DB: PDB REMARK 900 RELATED ID: 4I29 RELATED DB: PDB REMARK 900 RELATED ID: 4I2A RELATED DB: PDB REMARK 900 RELATED ID: 4I2B RELATED DB: PDB REMARK 900 RELATED ID: 4I2C RELATED DB: PDB REMARK 900 RELATED ID: 4I2D RELATED DB: PDB REMARK 900 RELATED ID: 4I2E RELATED DB: PDB REMARK 900 RELATED ID: 4I2F RELATED DB: PDB REMARK 900 RELATED ID: 4I2G RELATED DB: PDB REMARK 900 RELATED ID: 4I2H RELATED DB: PDB REMARK 900 RELATED ID: 4I2I RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 PROTEIN FRAGMENT IS THE CATALYTIC CORE OF THE TDT-S (TDT-SMALL) REMARK 999 ISOFORM (UNP RESIDUES 132-482, 503-530). DBREF 4I2J A 132 482 UNP P09838 TDT_MOUSE 132 482 DBREF 4I2J A 483 510 UNP P09838 TDT_MOUSE 503 530 SEQADV 4I2J MET A 111 UNP P09838 EXPRESSION TAG SEQADV 4I2J GLY A 112 UNP P09838 EXPRESSION TAG SEQADV 4I2J SER A 113 UNP P09838 EXPRESSION TAG SEQADV 4I2J SER A 114 UNP P09838 EXPRESSION TAG SEQADV 4I2J HIS A 115 UNP P09838 EXPRESSION TAG SEQADV 4I2J HIS A 116 UNP P09838 EXPRESSION TAG SEQADV 4I2J HIS A 117 UNP P09838 EXPRESSION TAG SEQADV 4I2J HIS A 118 UNP P09838 EXPRESSION TAG SEQADV 4I2J HIS A 119 UNP P09838 EXPRESSION TAG SEQADV 4I2J HIS A 120 UNP P09838 EXPRESSION TAG SEQADV 4I2J SER A 121 UNP P09838 EXPRESSION TAG SEQADV 4I2J SER A 122 UNP P09838 EXPRESSION TAG SEQADV 4I2J GLY A 123 UNP P09838 EXPRESSION TAG SEQADV 4I2J LEU A 124 UNP P09838 EXPRESSION TAG SEQADV 4I2J VAL A 125 UNP P09838 EXPRESSION TAG SEQADV 4I2J PRO A 126 UNP P09838 EXPRESSION TAG SEQADV 4I2J ARG A 127 UNP P09838 EXPRESSION TAG SEQADV 4I2J GLY A 128 UNP P09838 EXPRESSION TAG SEQADV 4I2J SER A 129 UNP P09838 EXPRESSION TAG SEQADV 4I2J HIS A 130 UNP P09838 EXPRESSION TAG SEQADV 4I2J 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 HET DCP A 601 28 HET ZN A 602 1 HET ZN A 603 1 HET ZN A 604 1 HET ZN A 605 1 HETNAM DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE HETNAM ZN ZINC ION FORMUL 2 DCP C9 H16 N3 O13 P3 FORMUL 3 ZN 4(ZN 2+) FORMUL 7 HOH *163(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 LEU A 498 1 9 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 OD2 ASP A 343 ZN ZN A 604 1555 1555 2.34 LINK OD1 ASP A 343 ZN ZN A 605 1555 1555 2.15 LINK OD2 ASP A 345 ZN ZN A 604 1555 1555 2.07 LINK OD1 ASP A 345 ZN ZN A 605 1555 1555 2.55 LINK OD2 ASP A 434 ZN ZN A 604 1555 1555 2.17 LINK OD2 ASP A 473 ZN ZN A 603 1555 1555 2.12 LINK ND1 HIS A 475 ZN ZN A 603 1555 1555 1.89 LINK O2B DCP A 601 ZN ZN A 605 1555 1555 1.91 LINK O2A DCP A 601 ZN ZN A 605 1555 1555 2.52 LINK ZN ZN A 603 O HOH A 715 1555 1555 2.38 CISPEP 1 GLY A 452 SER A 453 0 -2.17 SITE 1 AC1 18 GLY A 332 GLY A 333 ARG A 336 LYS A 338 SITE 2 AC1 18 GLY A 341 HIS A 342 ASP A 343 ASP A 345 SITE 3 AC1 18 GLY A 449 TRP A 450 GLY A 452 ARG A 454 SITE 4 AC1 18 ASN A 474 ZN A 604 ZN A 605 HOH A 702 SITE 5 AC1 18 HOH A 800 HOH A 848 SITE 1 AC2 2 HIS A 416 HOH A 755 SITE 1 AC3 4 ASP A 399 ASP A 473 HIS A 475 HOH A 715 SITE 1 AC4 4 ASP A 343 ASP A 345 ASP A 434 DCP A 601 SITE 1 AC5 3 ASP A 343 ASP A 345 DCP A 601 CRYST1 47.130 85.250 111.870 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 0.021218 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011730 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008939 0.00000