PDB Short entry for 4I2E HEADER TRANSFERASE/DNA 21-NOV-12 4I2E 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(*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 4 26-JUL-17 4I2E 1 SOURCE REMARK REVDAT 3 13-NOV-13 4I2E 1 JRNL REVDAT 2 31-JUL-13 4I2E 1 JRNL REVDAT 1 24-JUL-13 4I2E 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. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.39 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 31724 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) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 1608 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 : 16 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.07 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.33 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2928 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2097 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2762 REMARK 3 BIN R VALUE (WORKING SET) : 0.2094 REMARK 3 BIN FREE R VALUE : 0.2150 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.67 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 166 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 : 2833 REMARK 3 NUCLEIC ACID ATOMS : 33 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 404 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.09 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.31 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.43730 REMARK 3 B22 (A**2) : 3.68950 REMARK 3 B33 (A**2) : -10.12690 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) : 0.253 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.179 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.155 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.161 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.147 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 : 0.938 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.914 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 2957 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 3998 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1390 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 76 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 422 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 2957 ; 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 : 384 ; 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 : 3621 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 0.90 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.96 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 2.66 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 - 240} REMARK 3 ORIGIN FOR THE GROUP (A): 27.3969 11.8147 5.8937 REMARK 3 T TENSOR REMARK 3 T11: -0.0351 T22: -0.0282 REMARK 3 T33: -0.0689 T12: -0.0071 REMARK 3 T13: 0.0143 T23: 0.0051 REMARK 3 L TENSOR REMARK 3 L11: 2.2586 L22: 2.4199 REMARK 3 L33: 1.4008 L12: 0.2865 REMARK 3 L13: -0.1636 L23: 0.3744 REMARK 3 S TENSOR REMARK 3 S11: 0.0405 S12: 0.1886 S13: 0.0974 REMARK 3 S21: -0.1646 S22: -0.0205 S23: -0.0375 REMARK 3 S31: -0.1781 S32: 0.0220 S33: -0.0200 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: {A|241 - 347} REMARK 3 ORIGIN FOR THE GROUP (A): 17.2878 16.9875 29.9673 REMARK 3 T TENSOR REMARK 3 T11: -0.0221 T22: -0.0518 REMARK 3 T33: -0.0144 T12: -0.0073 REMARK 3 T13: 0.0156 T23: -0.0091 REMARK 3 L TENSOR REMARK 3 L11: 0.2501 L22: 2.1388 REMARK 3 L33: 0.4193 L12: -0.0697 REMARK 3 L13: -0.0205 L23: 0.4935 REMARK 3 S TENSOR REMARK 3 S11: -0.0283 S12: -0.1232 S13: 0.0136 REMARK 3 S21: 0.1010 S22: 0.0475 S23: 0.0571 REMARK 3 S31: -0.0037 S32: -0.0309 S33: -0.0192 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: {A|348 - 450} REMARK 3 ORIGIN FOR THE GROUP (A): 5.6198 5.5995 31.1883 REMARK 3 T TENSOR REMARK 3 T11: -0.0695 T22: -0.0601 REMARK 3 T33: -0.0107 T12: -0.0052 REMARK 3 T13: 0.0692 T23: 0.0067 REMARK 3 L TENSOR REMARK 3 L11: 1.7212 L22: 1.8059 REMARK 3 L33: 1.6262 L12: 0.2692 REMARK 3 L13: 0.7297 L23: 0.9334 REMARK 3 S TENSOR REMARK 3 S11: -0.0733 S12: -0.2178 S13: 0.0498 REMARK 3 S21: 0.1680 S22: -0.0840 S23: 0.3773 REMARK 3 S31: 0.0011 S32: -0.2200 S33: 0.1573 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: {A|451 - 510} REMARK 3 ORIGIN FOR THE GROUP (A): 7.1426 -1.0400 9.5355 REMARK 3 T TENSOR REMARK 3 T11: -0.0616 T22: -0.0495 REMARK 3 T33: 0.0167 T12: -0.0016 REMARK 3 T13: 0.0022 T23: -0.0380 REMARK 3 L TENSOR REMARK 3 L11: 4.9842 L22: 0.7152 REMARK 3 L33: 0.8582 L12: -0.5144 REMARK 3 L13: 0.8715 L23: 0.1202 REMARK 3 S TENSOR REMARK 3 S11: 0.0677 S12: 0.2753 S13: -0.2438 REMARK 3 S21: -0.0165 S22: -0.1059 S23: 0.1320 REMARK 3 S31: -0.0165 S32: -0.0309 S33: 0.0382 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4I2E 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_1000076217. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-SEP-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 : 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) : 0.9196 REMARK 200 MONOCHROMATOR : CHANNEL CUT REMARK 200 OPTICS : NULL 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 : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31783 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 48.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.09600 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) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.70500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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 (%): 49.95 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 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 23.54000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.14850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.39150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.14850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.54000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.39150 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 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 465 DA C 5 REMARK 465 DA C 6 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 CE NZ REMARK 470 ARG A 182 NE CZ NH1 NH2 REMARK 470 GLU A 185 CG CD OE1 OE2 REMARK 470 LYS A 209 CG CD CE NZ REMARK 470 GLU A 230 CG CD OE1 OE2 REMARK 470 LYS A 238 CD CE NZ REMARK 470 LYS A 261 CD CE NZ REMARK 470 ARG A 268 CZ NH1 NH2 REMARK 470 GLU A 355 CG CD OE1 OE2 REMARK 470 LYS A 370 CD CE NZ REMARK 470 GLN A 371 CD OE1 NE2 REMARK 470 LYS A 387 CD CE NZ REMARK 470 LYS A 389 CD CE NZ REMARK 470 LYS A 394 CD CE NZ REMARK 470 ASP A 396 CG OD1 OD2 REMARK 470 LYS A 419 CG CD CE NZ REMARK 470 LYS A 469 CD CE NZ REMARK 470 DA C 2 C8 N7 C5 C6 N6 N1 C2 REMARK 470 DA C 2 N3 C4 REMARK 470 DA C 3 C8 N7 C5 C6 N6 N1 C2 REMARK 470 DA C 3 N3 C4 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 CYS A 302 162.18 68.89 REMARK 500 THR A 331 -150.81 -114.01 REMARK 500 ASN A 509 46.70 -85.52 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 CO A 601 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 343 OD1 REMARK 620 2 APC A 603 O2A 95.9 REMARK 620 3 APC A 603 O2B 168.9 92.5 REMARK 620 4 APC A 603 O3G 84.1 95.9 87.8 REMARK 620 5 ASP A 345 OD2 93.4 83.4 94.9 177.3 REMARK 620 6 HOH A 971 O 80.0 173.0 92.4 89.4 91.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO A 604 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 343 OD2 REMARK 620 2 ASP A 434 OD2 87.3 REMARK 620 3 ASP A 345 OD1 95.4 89.5 REMARK 620 4 APC A 603 N7 169.6 90.7 94.8 REMARK 620 5 APC A 603 O2A 89.0 174.4 95.0 92.2 REMARK 620 6 HOH A 972 O 84.4 93.0 177.4 85.5 82.4 REMARK 620 N 1 2 3 4 5 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 258 O 102.8 REMARK 620 3 VAL A 255 O 86.8 94.2 REMARK 620 4 DA C 4 OP1 164.8 92.4 92.5 REMARK 620 5 HOH A 978 O 74.6 173.6 91.4 90.2 REMARK 620 6 HOH C 101 O 97.4 80.7 174.0 84.6 93.8 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 CO 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 APC A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO A 604 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: 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 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 4I2E A 132 482 UNP P09838 TDT_MOUSE 132 482 DBREF 4I2E A 483 510 UNP P09838 TDT_MOUSE 503 530 DBREF 4I2E C 2 6 PDB 4I2E 4I2E 2 6 SEQADV 4I2E MET A 111 UNP P09838 EXPRESSION TAG SEQADV 4I2E GLY A 112 UNP P09838 EXPRESSION TAG SEQADV 4I2E SER A 113 UNP P09838 EXPRESSION TAG SEQADV 4I2E SER A 114 UNP P09838 EXPRESSION TAG SEQADV 4I2E HIS A 115 UNP P09838 EXPRESSION TAG SEQADV 4I2E HIS A 116 UNP P09838 EXPRESSION TAG SEQADV 4I2E HIS A 117 UNP P09838 EXPRESSION TAG SEQADV 4I2E HIS A 118 UNP P09838 EXPRESSION TAG SEQADV 4I2E HIS A 119 UNP P09838 EXPRESSION TAG SEQADV 4I2E HIS A 120 UNP P09838 EXPRESSION TAG SEQADV 4I2E SER A 121 UNP P09838 EXPRESSION TAG SEQADV 4I2E SER A 122 UNP P09838 EXPRESSION TAG SEQADV 4I2E GLY A 123 UNP P09838 EXPRESSION TAG SEQADV 4I2E LEU A 124 UNP P09838 EXPRESSION TAG SEQADV 4I2E VAL A 125 UNP P09838 EXPRESSION TAG SEQADV 4I2E PRO A 126 UNP P09838 EXPRESSION TAG SEQADV 4I2E ARG A 127 UNP P09838 EXPRESSION TAG SEQADV 4I2E GLY A 128 UNP P09838 EXPRESSION TAG SEQADV 4I2E SER A 129 UNP P09838 EXPRESSION TAG SEQADV 4I2E HIS A 130 UNP P09838 EXPRESSION TAG SEQADV 4I2E 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 CO A 601 1 HET NA A 602 1 HET APC A 603 31 HET CO A 604 1 HETNAM CO COBALT (II) ION HETNAM NA SODIUM ION HETNAM APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER HETSYN APC ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE FORMUL 3 CO 2(CO 2+) FORMUL 4 NA NA 1+ FORMUL 5 APC C11 H18 N5 O12 P3 FORMUL 7 HOH *404(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 SER A 200 1 17 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 OD1 ASP A 343 CO CO A 601 1555 1555 2.00 LINK OD2 ASP A 343 CO CO A 604 1555 1555 2.03 LINK CO CO A 601 O2A APC A 603 1555 1555 2.10 LINK OD2 ASP A 434 CO CO A 604 1555 1555 2.11 LINK OD1 ASP A 345 CO CO A 604 1555 1555 2.12 LINK N7 APC A 603 CO CO A 604 1555 1555 2.13 LINK CO CO A 601 O2B APC A 603 1555 1555 2.16 LINK CO CO A 601 O3G APC A 603 1555 1555 2.16 LINK OD2 ASP A 345 CO CO A 601 1555 1555 2.18 LINK O2A APC A 603 CO CO A 604 1555 1555 2.24 LINK O THR A 253 NA NA A 602 1555 1555 2.36 LINK O VAL A 258 NA NA A 602 1555 1555 2.43 LINK O VAL A 255 NA NA A 602 1555 1555 2.69 LINK OP1 DA C 4 NA NA A 602 1555 1555 2.87 LINK CO CO A 604 O HOH A 972 1555 1555 2.24 LINK CO CO A 601 O HOH A 971 1555 1555 2.27 LINK NA NA A 602 O HOH A 978 1555 1555 2.44 LINK NA NA A 602 O HOH C 101 1555 1555 2.61 CISPEP 1 GLY A 452 SER A 453 0 -2.38 SITE 1 AC1 5 ASP A 343 ASP A 345 APC A 603 CO A 604 SITE 2 AC1 5 HOH A 971 SITE 1 AC2 6 THR A 253 VAL A 255 VAL A 258 HOH A 978 SITE 2 AC2 6 DA C 4 HOH C 101 SITE 1 AC3 25 GLY A 332 GLY A 333 ARG A 336 GLY A 341 SITE 2 AC3 25 HIS A 342 ASP A 343 ASP A 345 PHE A 405 SITE 3 AC3 25 ASP A 434 GLY A 449 TRP A 450 GLY A 452 SITE 4 AC3 25 CO A 601 CO A 604 HOH A 906 HOH A 929 SITE 5 AC3 25 HOH A 971 HOH A 972 HOH A 979 HOH A1031 SITE 6 AC3 25 HOH A1050 HOH A1060 HOH A1087 HOH A1096 SITE 7 AC3 25 DA C 4 SITE 1 AC4 6 ASP A 343 ASP A 345 ASP A 434 CO A 601 SITE 2 AC4 6 APC A 603 HOH A 972 CRYST1 47.080 84.783 116.297 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 0.021240 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011795 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008599 0.00000