PDB Short entry for 4I2I HEADER TRANSFERASE 21-NOV-12 4I2I TITLE BINARY COMPLEX OF MOUSE TDT WITH AP5A 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 4I2I 1 REMARK SEQADV LINK REVDAT 4 26-JUL-17 4I2I 1 SOURCE REMARK REVDAT 3 13-NOV-13 4I2I 1 JRNL REVDAT 2 31-JUL-13 4I2I 1 JRNL REVDAT 1 24-JUL-13 4I2I 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. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.9.3 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 14581 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) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 733 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 7 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.70 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.83 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2837 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2906 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2693 REMARK 3 BIN R VALUE (WORKING SET) : 0.2863 REMARK 3 BIN FREE R VALUE : 0.3695 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.08 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 144 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 : 2627 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 47 REMARK 3 SOLVENT ATOMS : 165 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 53.52 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.69 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.32430 REMARK 3 B22 (A**2) : 5.96100 REMARK 3 B33 (A**2) : -12.28530 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) : 0.339 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.556 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.270 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.462 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.265 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 : 0.926 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.897 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 2737 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 3714 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 926 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 61 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 406 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 2737 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 2 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 358 ; 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 : 3093 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.10 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.81 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 17.57 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: {A|148 - 241} REMARK 3 ORIGIN FOR THE GROUP (A): 51.8264 53.3537 54.4891 REMARK 3 T TENSOR REMARK 3 T11: -0.1317 T22: -0.0236 REMARK 3 T33: -0.0818 T12: 0.0146 REMARK 3 T13: 0.0709 T23: 0.0511 REMARK 3 L TENSOR REMARK 3 L11: 4.3138 L22: 4.7156 REMARK 3 L33: 2.1907 L12: -0.0356 REMARK 3 L13: -0.3435 L23: 0.4846 REMARK 3 S TENSOR REMARK 3 S11: 0.0968 S12: 0.2478 S13: 0.3465 REMARK 3 S21: -0.1913 S22: 0.0035 S23: -0.2055 REMARK 3 S31: -0.2120 S32: 0.0892 S33: -0.1004 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: {A|242 - 303} REMARK 3 ORIGIN FOR THE GROUP (A): 42.4095 69.7745 77.5235 REMARK 3 T TENSOR REMARK 3 T11: 0.0347 T22: -0.0542 REMARK 3 T33: -0.0130 T12: -0.0116 REMARK 3 T13: -0.0846 T23: -0.0170 REMARK 3 L TENSOR REMARK 3 L11: 1.0412 L22: 5.9926 REMARK 3 L33: 1.4238 L12: 1.8964 REMARK 3 L13: -0.8343 L23: -2.3655 REMARK 3 S TENSOR REMARK 3 S11: 0.0276 S12: -0.0344 S13: 0.0995 REMARK 3 S21: -0.2383 S22: -0.1127 S23: -0.0007 REMARK 3 S31: 0.0878 S32: -0.0932 S33: 0.0851 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: {A|304 - 442} REMARK 3 ORIGIN FOR THE GROUP (A): 33.3168 45.7074 83.0675 REMARK 3 T TENSOR REMARK 3 T11: -0.0226 T22: -0.0623 REMARK 3 T33: -0.1150 T12: -0.0699 REMARK 3 T13: 0.0264 T23: 0.0497 REMARK 3 L TENSOR REMARK 3 L11: 2.6710 L22: 2.2605 REMARK 3 L33: 2.5080 L12: 0.0888 REMARK 3 L13: 0.3043 L23: 0.7855 REMARK 3 S TENSOR REMARK 3 S11: 0.0424 S12: -0.1995 S13: 0.0611 REMARK 3 S21: 0.2919 S22: -0.0198 S23: 0.2694 REMARK 3 S31: 0.1694 S32: -0.3928 S33: -0.0226 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: {A|443 - 510} REMARK 3 ORIGIN FOR THE GROUP (A): 31.1381 40.5792 59.0880 REMARK 3 T TENSOR REMARK 3 T11: -0.0447 T22: -0.0167 REMARK 3 T33: -0.0542 T12: 0.0319 REMARK 3 T13: -0.0049 T23: -0.0285 REMARK 3 L TENSOR REMARK 3 L11: 5.5772 L22: 0.7737 REMARK 3 L33: 2.1835 L12: 0.4201 REMARK 3 L13: 1.5768 L23: 0.4275 REMARK 3 S TENSOR REMARK 3 S11: 0.1403 S12: 0.0479 S13: -0.2688 REMARK 3 S21: -0.0165 S22: -0.1435 S23: 0.0400 REMARK 3 S31: -0.0310 S32: -0.0531 S33: 0.0032 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4I2I 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_1000076221. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-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 : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14589 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 24.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.10100 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) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.34000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.700 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 (%): 44.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 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 23.37500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.94500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.05000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.94500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.37500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.05000 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 LEU A 381 REMARK 465 GLU A 382 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 ASP A 399 REMARK 465 SER A 420 REMARK 465 GLY A 421 REMARK 465 GLN A 422 REMARK 465 GLN A 423 REMARK 465 GLU A 424 REMARK 465 GLY 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 LYS A 148 CG CD CE NZ REMARK 470 LYS A 149 CG CD CE NZ REMARK 470 GLU A 177 CG CD OE1 OE2 REMARK 470 GLU A 185 CG CD OE1 OE2 REMARK 470 LYS A 209 CE NZ REMARK 470 ASP A 219 CG OD1 OD2 REMARK 470 LYS A 220 CG CD CE NZ REMARK 470 GLU A 233 CG CD OE1 OE2 REMARK 470 LYS A 238 CD CE NZ REMARK 470 GLU A 244 CG CD OE1 OE2 REMARK 470 LYS A 247 CG CD CE NZ REMARK 470 LYS A 250 CD CE NZ REMARK 470 LEU A 260 CG CD1 CD2 REMARK 470 LYS A 261 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 297 CG CD OE1 OE2 REMARK 470 GLU A 352 CG CD OE1 OE2 REMARK 470 GLU A 355 CG CD OE1 OE2 REMARK 470 ASP A 356 CG OD1 OD2 REMARK 470 GLU A 358 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 370 CG CD CE NZ REMARK 470 ASP A 379 CG OD1 OD2 REMARK 470 GLU A 418 CG CD OE1 OE2 REMARK 470 LYS A 419 CG CD CE NZ REMARK 470 LYS A 426 CG CD CE NZ REMARK 470 LYS A 469 CG CD CE NZ REMARK 470 GLU A 487 CG CD OE1 OE2 REMARK 470 GLU A 489 CG CD OE1 OE2 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 ASN A 178 62.55 -117.15 REMARK 500 ASP A 231 10.93 -143.17 REMARK 500 THR A 331 -154.07 -114.69 REMARK 500 ASN A 509 43.34 -82.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 AP5 A 601 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 608 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 179 OD2 REMARK 620 2 CYS A 188 SG 102.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 606 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 264 OE2 REMARK 620 2 HOH A 796 O 86.6 REMARK 620 N 1 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 GLU A 307 OE2 REMARK 620 2 HIS A 412 NE2 128.7 REMARK 620 3 HOH A 798 O 112.1 103.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 602 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 343 OD2 REMARK 620 2 ASP A 345 OD1 98.7 REMARK 620 3 ASP A 434 OD2 78.7 93.3 REMARK 620 4 AP5 A 601 N7B 146.7 114.6 99.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 609 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 343 OD1 REMARK 620 2 ASP A 345 OD2 108.9 REMARK 620 3 AP5 A 601 O2E 159.9 91.3 REMARK 620 4 AP5 A 601 O3G 83.0 149.6 79.3 REMARK 620 5 HOH A 730 O 91.4 101.6 84.4 106.0 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 HIS A 416 ND1 REMARK 620 2 HOH A 802 O 120.4 REMARK 620 3 HOH A 803 O 115.5 92.0 REMARK 620 4 HOH A 804 O 90.0 116.8 125.1 REMARK 620 N 1 2 3 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 HIS A 466 NE2 REMARK 620 2 HOH A 807 O 102.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 607 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 473 OD2 REMARK 620 2 HIS A 475 ND1 111.4 REMARK 620 3 HOH A 775 O 125.4 108.0 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 AP5 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 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 607 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 608 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 609 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: 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 4I2I A 132 482 UNP P09838 TDT_MOUSE 132 482 DBREF 4I2I A 483 510 UNP P09838 TDT_MOUSE 503 530 SEQADV 4I2I MET A 111 UNP P09838 EXPRESSION TAG SEQADV 4I2I GLY A 112 UNP P09838 EXPRESSION TAG SEQADV 4I2I SER A 113 UNP P09838 EXPRESSION TAG SEQADV 4I2I SER A 114 UNP P09838 EXPRESSION TAG SEQADV 4I2I HIS A 115 UNP P09838 EXPRESSION TAG SEQADV 4I2I HIS A 116 UNP P09838 EXPRESSION TAG SEQADV 4I2I HIS A 117 UNP P09838 EXPRESSION TAG SEQADV 4I2I HIS A 118 UNP P09838 EXPRESSION TAG SEQADV 4I2I HIS A 119 UNP P09838 EXPRESSION TAG SEQADV 4I2I HIS A 120 UNP P09838 EXPRESSION TAG SEQADV 4I2I SER A 121 UNP P09838 EXPRESSION TAG SEQADV 4I2I SER A 122 UNP P09838 EXPRESSION TAG SEQADV 4I2I GLY A 123 UNP P09838 EXPRESSION TAG SEQADV 4I2I LEU A 124 UNP P09838 EXPRESSION TAG SEQADV 4I2I VAL A 125 UNP P09838 EXPRESSION TAG SEQADV 4I2I PRO A 126 UNP P09838 EXPRESSION TAG SEQADV 4I2I ARG A 127 UNP P09838 EXPRESSION TAG SEQADV 4I2I GLY A 128 UNP P09838 EXPRESSION TAG SEQADV 4I2I SER A 129 UNP P09838 EXPRESSION TAG SEQADV 4I2I HIS A 130 UNP P09838 EXPRESSION TAG SEQADV 4I2I 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 AP5 A 601 39 HET ZN A 602 1 HET ZN A 603 1 HET ZN A 604 1 HET ZN A 605 1 HET ZN A 606 1 HET ZN A 607 1 HET ZN A 608 1 HET MG A 609 1 HETNAM AP5 BIS(ADENOSINE)-5'-PENTAPHOSPHATE HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION FORMUL 2 AP5 C20 H29 N10 O22 P5 FORMUL 3 ZN 7(ZN 2+) FORMUL 10 MG MG 2+ FORMUL 11 HOH *165(H2 O) HELIX 1 1 TYR A 153 ARG A 157 5 5 HELIX 2 2 ASN A 165 ASN A 178 1 14 HELIX 3 3 SER A 187 LEU A 201 1 15 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 ASN A 242 1 9 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 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 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 LEU A 486 -1 O VAL A 484 N ASP A 479 LINK OD2 ASP A 179 ZN ZN A 608 1555 1555 1.88 LINK SG CYS A 188 ZN ZN A 608 1555 1555 2.44 LINK OE2 GLU A 264 ZN ZN A 606 1555 1555 2.24 LINK OE2 GLU A 307 ZN ZN A 604 1555 1555 2.07 LINK OD2 ASP A 343 ZN ZN A 602 1555 1555 2.29 LINK OD1 ASP A 343 MG MG A 609 1555 1555 2.20 LINK OD1 ASP A 345 ZN ZN A 602 1555 1555 2.10 LINK OD2 ASP A 345 MG MG A 609 1555 1555 2.28 LINK NE2AHIS A 412 ZN ZN A 604 1555 1555 1.86 LINK ND1 HIS A 416 ZN ZN A 603 1555 1555 2.22 LINK OD2 ASP A 434 ZN ZN A 602 1555 1555 2.12 LINK NE2 HIS A 466 ZN ZN A 605 1555 1555 2.06 LINK OD2 ASP A 473 ZN ZN A 607 1555 1555 2.05 LINK ND1 HIS A 475 ZN ZN A 607 1555 1555 2.09 LINK N7B AP5 A 601 ZN ZN A 602 1555 1555 2.11 LINK O2E AP5 A 601 MG MG A 609 1555 1555 2.49 LINK O3G AP5 A 601 MG MG A 609 1555 1555 2.79 LINK ZN ZN A 603 O HOH A 802 1555 1555 2.39 LINK ZN ZN A 603 O HOH A 803 1555 1555 2.20 LINK ZN ZN A 603 O HOH A 804 1555 1555 2.23 LINK ZN ZN A 604 O HOH A 798 1555 1555 2.33 LINK ZN ZN A 605 O HOH A 807 1555 1555 2.14 LINK ZN ZN A 606 O HOH A 796 1555 1555 2.31 LINK ZN ZN A 607 O HOH A 775 1555 1555 2.10 LINK MG MG A 609 O HOH A 730 1555 1555 2.66 CISPEP 1 GLY A 452 SER A 453 0 -1.93 SITE 1 AC1 18 GLY A 332 GLY A 333 ARG A 336 GLY A 341 SITE 2 AC1 18 HIS A 342 ASP A 343 ASP A 345 PHE A 405 SITE 3 AC1 18 ASP A 434 GLY A 449 TRP A 450 ARG A 454 SITE 4 AC1 18 GLU A 457 ZN A 602 MG A 609 HOH A 730 SITE 5 AC1 18 HOH A 747 HOH A 800 SITE 1 AC2 5 ASP A 343 ASP A 345 ASP A 434 AP5 A 601 SITE 2 AC2 5 MG A 609 SITE 1 AC3 4 HIS A 416 HOH A 802 HOH A 803 HOH A 804 SITE 1 AC4 4 GLU A 307 HIS A 412 HOH A 798 HOH A 863 SITE 1 AC5 3 GLU A 183 HIS A 466 HOH A 807 SITE 1 AC6 2 GLU A 264 HOH A 796 SITE 1 AC7 3 ASP A 473 HIS A 475 HOH A 775 SITE 1 AC8 3 ASP A 179 CYS A 188 GLU A 230 SITE 1 AC9 5 ASP A 343 ASP A 345 AP5 A 601 ZN A 602 SITE 2 AC9 5 HOH A 730 CRYST1 46.750 84.100 103.890 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 0.021390 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011891 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009626 0.00000