PDB Short entry for 4I2H HEADER TRANSFERASE/DNA 21-NOV-12 4I2H TITLE TERNARY COMPLEX OF MOUSE TDT WITH SSDNA AND AMPCPP 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(P*AP*AP*AP*AP*A)-3'; COMPND 11 CHAIN: C; COMPND 12 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 KEYWDS TERMINAL TRANSFERASE, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.GOUGE,M.DELARUE REVDAT 5 20-SEP-23 4I2H 1 REMARK SEQADV LINK REVDAT 4 26-JUL-17 4I2H 1 SOURCE REMARK REVDAT 3 13-NOV-13 4I2H 1 JRNL REVDAT 2 31-JUL-13 4I2H 1 JRNL REVDAT 1 24-JUL-13 4I2H 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. 2.75 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) : 2.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 12564 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.860 REMARK 3 FREE R VALUE TEST SET COUNT : 611 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) : 2.75 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 3.01 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.89 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2927 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2156 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2780 REMARK 3 BIN R VALUE (WORKING SET) : 0.2120 REMARK 3 BIN FREE R VALUE : 0.2780 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.02 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 : 2616 REMARK 3 NUCLEIC ACID ATOMS : 17 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 154 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 83.79 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 67.77 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 9.76490 REMARK 3 B22 (A**2) : 8.11350 REMARK 3 B33 (A**2) : -17.87840 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) : 0.347 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 1.470 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.308 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.789 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.302 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 : 0.883 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 2718 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 3688 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1237 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 63 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 399 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 2718 ; 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 : 361 ; 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 : 2995 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 0.99 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.86 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 2.62 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: {A|149 - 190} REMARK 3 ORIGIN FOR THE GROUP (A): 24.8037 -11.2279 -8.6703 REMARK 3 T TENSOR REMARK 3 T11: -0.0970 T22: 0.0894 REMARK 3 T33: -0.1563 T12: -0.0002 REMARK 3 T13: -0.0568 T23: -0.0113 REMARK 3 L TENSOR REMARK 3 L11: 5.8712 L22: 2.1581 REMARK 3 L33: 3.7349 L12: -1.8806 REMARK 3 L13: -1.3005 L23: 0.3742 REMARK 3 S TENSOR REMARK 3 S11: 0.0170 S12: -0.3493 S13: -0.0458 REMARK 3 S21: 0.0806 S22: -0.0865 S23: 0.0153 REMARK 3 S31: 0.2708 S32: 0.0592 S33: 0.0695 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: {A|191 - 315} REMARK 3 ORIGIN FOR THE GROUP (A): 24.1162 -19.6580 -19.7828 REMARK 3 T TENSOR REMARK 3 T11: -0.0891 T22: -0.1452 REMARK 3 T33: -0.0943 T12: 0.0567 REMARK 3 T13: -0.0070 T23: -0.0008 REMARK 3 L TENSOR REMARK 3 L11: 1.5561 L22: 2.2943 REMARK 3 L33: 1.6861 L12: 0.3757 REMARK 3 L13: -0.1674 L23: 1.1172 REMARK 3 S TENSOR REMARK 3 S11: -0.0122 S12: -0.1135 S13: -0.3022 REMARK 3 S21: 0.0394 S22: -0.0074 S23: -0.1186 REMARK 3 S31: 0.2986 S32: 0.0721 S33: 0.0196 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: {A|316 - 456} REMARK 3 ORIGIN FOR THE GROUP (A): 9.4512 -3.8454 -31.5342 REMARK 3 T TENSOR REMARK 3 T11: -0.0027 T22: -0.1307 REMARK 3 T33: -0.0694 T12: 0.0585 REMARK 3 T13: -0.1167 T23: 0.0352 REMARK 3 L TENSOR REMARK 3 L11: 3.4512 L22: 2.4185 REMARK 3 L33: 4.1943 L12: -0.7562 REMARK 3 L13: -0.2769 L23: 1.5183 REMARK 3 S TENSOR REMARK 3 S11: 0.1896 S12: 0.3822 S13: -0.0504 REMARK 3 S21: -0.5442 S22: -0.2772 S23: 0.5220 REMARK 3 S31: -0.2658 S32: -0.5442 S33: 0.0876 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: {A|457 - 510} REMARK 3 ORIGIN FOR THE GROUP (A): 7.8220 1.2900 -8.0767 REMARK 3 T TENSOR REMARK 3 T11: -0.1305 T22: 0.0177 REMARK 3 T33: -0.0527 T12: 0.0057 REMARK 3 T13: -0.0007 T23: -0.1408 REMARK 3 L TENSOR REMARK 3 L11: 8.1966 L22: 1.1305 REMARK 3 L33: 2.9642 L12: 0.6093 REMARK 3 L13: -1.7466 L23: 0.2658 REMARK 3 S TENSOR REMARK 3 S11: -0.0157 S12: -0.5437 S13: 0.4848 REMARK 3 S21: -0.1137 S22: -0.1464 S23: 0.1271 REMARK 3 S31: -0.0143 S32: -0.1890 S33: 0.1621 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4I2H 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_1000076220. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUL-12 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 : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8726 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12624 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.750 REMARK 200 RESOLUTION RANGE LOW (A) : 47.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.73500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200 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 (%): 49.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20-26% PEG4000, 100 MM HEPES, 200 MM REMARK 280 AMMONIUM ACETATE, 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 23.55600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 57.54250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.63200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.54250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.55600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.63200 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 383 REMARK 465 THR A 384 REMARK 465 PHE A 385 REMARK 465 GLU A 386 REMARK 465 LYS A 387 REMARK 465 PHE A 388 REMARK 465 LYS A 389 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 DA C 5 REMARK 465 DA C 6 REMARK 465 DA C 7 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 LEU A 181 CG CD1 CD2 REMARK 470 GLU A 183 CG CD OE1 OE2 REMARK 470 ASN A 184 CG OD1 ND2 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 ASP A 219 CG OD1 OD2 REMARK 470 LYS A 220 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 261 CG CD CE NZ REMARK 470 LYS A 265 CG CD CE NZ REMARK 470 ARG A 268 CD NE CZ NH1 NH2 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 GLN A 359 CG CD OE1 NE2 REMARK 470 GLN A 360 CG CD OE1 NE2 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 ASP A 379 CG OD1 OD2 REMARK 470 GLU A 382 CG CD OE1 OE2 REMARK 470 HIS A 400 CG ND1 CD2 CE1 NE2 REMARK 470 SER A 417 OG REMARK 470 GLU A 424 CG CD OE1 OE2 REMARK 470 LYS A 426 CG CD CE NZ REMARK 470 ARG A 442 NE CZ NH1 NH2 REMARK 470 ARG A 454 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 461 CZ NH1 NH2 REMARK 470 LYS A 469 CD CE NZ REMARK 470 LYS A 482 CD CE NZ REMARK 470 GLU A 487 CG CD OE1 OE2 REMARK 470 GLU A 489 CG CD OE1 OE2 REMARK 470 DA C 3 C8 N7 C5 C6 N6 N1 C2 REMARK 470 DA C 3 N3 C4 REMARK 470 DA C 4 C4' O4' C3' O3' C2' C1' N9 REMARK 470 DA C 4 C8 N7 C5 C6 N6 N1 C2 REMARK 470 DA C 4 N3 C4 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 -151.63 -112.60 REMARK 500 ILE A 380 74.50 -101.90 REMARK 500 ASN A 509 48.28 -86.32 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 86.3 REMARK 620 3 VAL A 258 O 102.8 93.9 REMARK 620 4 DA C 4 OP1 165.4 86.6 90.4 REMARK 620 N 1 2 3 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 79.9 REMARK 620 3 APC A 605 O3B 114.7 150.2 REMARK 620 4 APC A 605 O1A 59.7 77.3 87.8 REMARK 620 5 HOH A 726 O 85.7 116.9 90.9 140.6 REMARK 620 N 1 2 3 4 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 343 OD2 REMARK 620 2 ASP A 345 OD1 90.6 REMARK 620 3 ASP A 434 OD2 79.6 88.7 REMARK 620 4 APC A 605 O1A 79.7 112.3 150.5 REMARK 620 N 1 2 3 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 473 OD2 REMARK 620 2 HIS A 475 ND1 87.4 REMARK 620 N 1 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 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 APC 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: 4I2I RELATED DB: PDB REMARK 900 RELATED ID: 4I2J 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 4I2H A 132 482 UNP P09838 TDT_MOUSE 132 482 DBREF 4I2H A 483 510 UNP P09838 TDT_MOUSE 503 530 DBREF 4I2H C 3 7 PDB 4I2H 4I2H 3 7 SEQADV 4I2H MET A 111 UNP P09838 EXPRESSION TAG SEQADV 4I2H GLY A 112 UNP P09838 EXPRESSION TAG SEQADV 4I2H SER A 113 UNP P09838 EXPRESSION TAG SEQADV 4I2H SER A 114 UNP P09838 EXPRESSION TAG SEQADV 4I2H HIS A 115 UNP P09838 EXPRESSION TAG SEQADV 4I2H HIS A 116 UNP P09838 EXPRESSION TAG SEQADV 4I2H HIS A 117 UNP P09838 EXPRESSION TAG SEQADV 4I2H HIS A 118 UNP P09838 EXPRESSION TAG SEQADV 4I2H HIS A 119 UNP P09838 EXPRESSION TAG SEQADV 4I2H HIS A 120 UNP P09838 EXPRESSION TAG SEQADV 4I2H SER A 121 UNP P09838 EXPRESSION TAG SEQADV 4I2H SER A 122 UNP P09838 EXPRESSION TAG SEQADV 4I2H GLY A 123 UNP P09838 EXPRESSION TAG SEQADV 4I2H LEU A 124 UNP P09838 EXPRESSION TAG SEQADV 4I2H VAL A 125 UNP P09838 EXPRESSION TAG SEQADV 4I2H PRO A 126 UNP P09838 EXPRESSION TAG SEQADV 4I2H ARG A 127 UNP P09838 EXPRESSION TAG SEQADV 4I2H GLY A 128 UNP P09838 EXPRESSION TAG SEQADV 4I2H SER A 129 UNP P09838 EXPRESSION TAG SEQADV 4I2H HIS A 130 UNP P09838 EXPRESSION TAG SEQADV 4I2H 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 C 5 DA DA DA DA DA HET MG A 601 1 HET NA A 602 1 HET ZN A 603 1 HET ZN A 604 1 HET APC A 605 31 HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM ZN ZINC ION HETNAM APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER HETSYN APC ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE FORMUL 3 MG MG 2+ FORMUL 4 NA NA 1+ FORMUL 5 ZN 2(ZN 2+) FORMUL 7 APC C11 H18 N5 O12 P3 FORMUL 8 HOH *154(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 SER A 279 1 7 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 ASP A 379 -1 N LEU A 376 O ILE A 407 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 2.36 LINK O VAL A 255 NA NA A 602 1555 1555 2.74 LINK O VAL A 258 NA NA A 602 1555 1555 2.45 LINK OD1 ASP A 343 MG MG A 601 1555 1555 2.71 LINK OD2 ASP A 343 ZN ZN A 603 1555 1555 2.00 LINK OD2 ASP A 345 MG MG A 601 1555 1555 2.57 LINK OD1 ASP A 345 ZN ZN A 603 1555 1555 2.13 LINK OD2 ASP A 434 ZN ZN A 603 1555 1555 2.05 LINK OD2 ASP A 473 ZN ZN A 604 1555 1555 2.26 LINK ND1 HIS A 475 ZN ZN A 604 1555 1555 2.11 LINK MG MG A 601 O3B APC A 605 1555 1555 2.20 LINK MG MG A 601 O1A APC A 605 1555 1555 2.63 LINK MG MG A 601 O HOH A 726 1555 1555 2.40 LINK NA NA A 602 OP1 DA C 4 1555 1555 2.47 LINK ZN ZN A 603 O1A APC A 605 1555 1555 2.61 CISPEP 1 GLY A 452 SER A 453 0 -0.16 SITE 1 AC1 4 ASP A 343 ASP A 345 APC A 605 HOH A 726 SITE 1 AC2 4 THR A 253 VAL A 255 VAL A 258 DA C 4 SITE 1 AC3 4 ASP A 343 ASP A 345 ASP A 434 APC A 605 SITE 1 AC4 2 ASP A 473 HIS A 475 SITE 1 AC5 19 GLY A 333 ARG A 336 GLY A 341 HIS A 342 SITE 2 AC5 19 ASP A 343 ASP A 345 ASP A 399 GLY A 449 SITE 3 AC5 19 TRP A 450 GLY A 452 GLU A 457 ASN A 474 SITE 4 AC5 19 MG A 601 ZN A 603 HOH A 706 HOH A 726 SITE 5 AC5 19 HOH A 784 HOH A 820 HOH A 841 CRYST1 47.112 85.264 115.085 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 0.021226 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011728 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008689 0.00000