HEADER TRANSFERASE/DNA 21-NOV-12 4I27 TITLE TERNARY COMPLEX OF MOUSE TDT WITH SSDNA AND INCOMING NUCLEOTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA NUCLEOTIDYLEXOTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEE REMARK 999; COMPND 5 SYNONYM: TERMINAL ADDITION ENZYME, TERMINAL COMPND 6 DEOXYNUCLEOTIDYLTRANSFERASE, TDT, TERMINAL TRANSFERASE; COMPND 7 EC: 2.7.7.31; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: 5'-D(*AP*AP*AP*AP*AP*T)-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 4I27 1 REMARK SEQADV LINK REVDAT 4 26-JUL-17 4I27 1 SOURCE REMARK REVDAT 3 13-NOV-13 4I27 1 JRNL REVDAT 2 31-JUL-13 4I27 1 JRNL REVDAT 1 24-JUL-13 4I27 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. 2.60 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.95 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 12229 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) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.770 REMARK 3 FREE R VALUE TEST SET COUNT : 583 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.85 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.40 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2899 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2067 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2756 REMARK 3 BIN R VALUE (WORKING SET) : 0.2014 REMARK 3 BIN FREE R VALUE : 0.3101 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.93 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 143 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 : 2869 REMARK 3 NUCLEIC ACID ATOMS : 121 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 205 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.65 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.25 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.72690 REMARK 3 B22 (A**2) : -5.90640 REMARK 3 B33 (A**2) : 1.17950 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.80910 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.288 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.310 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL 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 : 0.922 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.871 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 3092 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 4198 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1461 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 75 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 441 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 3092 ; 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 : 393 ; 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 : 3510 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.09 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.85 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 3.13 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: {A|146 - 164} REMARK 3 ORIGIN FOR THE GROUP (A): 7.2976 13.4161 2.5131 REMARK 3 T TENSOR REMARK 3 T11: -0.0593 T22: 0.0609 REMARK 3 T33: -0.0562 T12: -0.0491 REMARK 3 T13: 0.0006 T23: 0.0606 REMARK 3 L TENSOR REMARK 3 L11: 3.0512 L22: 0.0025 REMARK 3 L33: -1.5391 L12: -3.5180 REMARK 3 L13: -1.9266 L23: 1.9298 REMARK 3 S TENSOR REMARK 3 S11: 0.0502 S12: 0.1783 S13: -0.0701 REMARK 3 S21: -0.0779 S22: 0.0621 S23: -0.0820 REMARK 3 S31: -0.1165 S32: 0.2162 S33: -0.1123 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: {A|166 - 195} REMARK 3 ORIGIN FOR THE GROUP (A): 6.5254 13.1651 20.5440 REMARK 3 T TENSOR REMARK 3 T11: 0.0143 T22: 0.0108 REMARK 3 T33: -0.0576 T12: 0.0415 REMARK 3 T13: -0.0142 T23: 0.0157 REMARK 3 L TENSOR REMARK 3 L11: -0.8235 L22: 1.9544 REMARK 3 L33: 2.6780 L12: -0.1699 REMARK 3 L13: 1.9269 L23: 2.2795 REMARK 3 S TENSOR REMARK 3 S11: -0.0273 S12: 0.1204 S13: -0.0138 REMARK 3 S21: 0.1507 S22: -0.0713 S23: 0.0360 REMARK 3 S31: 0.1924 S32: -0.2140 S33: 0.0985 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: {A|196 - 368} REMARK 3 ORIGIN FOR THE GROUP (A): 1.9588 -1.3477 18.9462 REMARK 3 T TENSOR REMARK 3 T11: -0.0472 T22: 0.0042 REMARK 3 T33: -0.0836 T12: -0.0108 REMARK 3 T13: 0.0130 T23: 0.0145 REMARK 3 L TENSOR REMARK 3 L11: 0.2193 L22: 0.2268 REMARK 3 L33: 0.3717 L12: -0.1180 REMARK 3 L13: -0.0336 L23: 0.0185 REMARK 3 S TENSOR REMARK 3 S11: 0.0193 S12: -0.0425 S13: -0.0368 REMARK 3 S21: 0.0452 S22: -0.0269 S23: 0.0135 REMARK 3 S31: 0.0363 S32: -0.0208 S33: 0.0075 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: {A|369 - 424} REMARK 3 ORIGIN FOR THE GROUP (A): -6.9029 -11.6583 14.8176 REMARK 3 T TENSOR REMARK 3 T11: -0.0168 T22: 0.0584 REMARK 3 T33: -0.0966 T12: -0.0227 REMARK 3 T13: -0.0064 T23: -0.0472 REMARK 3 L TENSOR REMARK 3 L11: 1.1874 L22: 0.0035 REMARK 3 L33: 1.2136 L12: 0.8459 REMARK 3 L13: 1.0105 L23: -1.5044 REMARK 3 S TENSOR REMARK 3 S11: 0.0186 S12: 0.2435 S13: -0.2558 REMARK 3 S21: 0.2300 S22: -0.0691 S23: 0.0686 REMARK 3 S31: 0.1013 S32: 0.0096 S33: 0.0505 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: {A|425 - 510} REMARK 3 ORIGIN FOR THE GROUP (A): -8.3406 4.7191 4.1635 REMARK 3 T TENSOR REMARK 3 T11: -0.0503 T22: 0.0253 REMARK 3 T33: -0.0757 T12: 0.0028 REMARK 3 T13: 0.0117 T23: -0.0071 REMARK 3 L TENSOR REMARK 3 L11: 0.2003 L22: 1.1108 REMARK 3 L33: 0.2940 L12: -0.1407 REMARK 3 L13: -0.3600 L23: -0.0054 REMARK 3 S TENSOR REMARK 3 S11: -0.0434 S12: -0.0482 S13: -0.0273 REMARK 3 S21: 0.0733 S22: 0.1223 S23: 0.0658 REMARK 3 S31: -0.0327 S32: -0.1425 S33: -0.0789 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: {C|1 - 6} REMARK 3 ORIGIN FOR THE GROUP (A): -11.9212 -0.4556 27.3894 REMARK 3 T TENSOR REMARK 3 T11: 0.0333 T22: 0.3017 REMARK 3 T33: -0.2315 T12: 0.0522 REMARK 3 T13: 0.1438 T23: -0.0350 REMARK 3 L TENSOR REMARK 3 L11: 2.4493 L22: 0.0000 REMARK 3 L33: -0.4396 L12: -0.5087 REMARK 3 L13: -0.3654 L23: 1.8851 REMARK 3 S TENSOR REMARK 3 S11: 0.0030 S12: 0.0721 S13: 0.1179 REMARK 3 S21: 0.0635 S22: 0.0562 S23: 0.3576 REMARK 3 S31: -0.0330 S32: -0.1721 S33: -0.0592 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4I27 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_1000076210. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-APR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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 : 12246 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 47.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.13700 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) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.46100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 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 (%): 42.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG4000, 20% ISOPROPANOL, 100 MM REMARK 280 SODIUM CITRATE, PH 8.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 47.95000 REMARK 290 SMTRY3 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 KCAL/MOL 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 ARG A 393 REMARK 465 LYS A 394 REMARK 465 VAL A 395 REMARK 465 ASP A 396 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 VAL A 147 CG1 CG2 REMARK 470 LYS A 148 CG CD CE NZ REMARK 470 LYS A 149 CG CD CE NZ REMARK 470 GLU A 185 CG CD OE1 OE2 REMARK 470 LYS A 281 CG CD CE NZ REMARK 470 ARG A 284 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 317 CG CD OE1 OE2 REMARK 470 GLU A 418 CG CD OE1 OE2 REMARK 470 GLN A 422 CG CD OE1 NE2 REMARK 470 ARG A 454 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 469 CG CD CE NZ REMARK 470 LYS A 482 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DA C 1 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 DA C 2 C3' - O3' - P ANGL. DEV. = 8.4 DEGREES REMARK 500 DA C 4 C3' - O3' - P ANGL. DEV. = 9.8 DEGREES REMARK 500 DA C 5 O4' - C1' - N9 ANGL. DEV. = 7.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 THR A 331 -154.08 -111.99 REMARK 500 PRO A 391 -7.21 -55.24 REMARK 500 GLU A 418 -20.60 61.94 REMARK 500 ASN A 509 45.41 -83.02 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 603 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 253 O REMARK 620 2 VAL A 255 O 90.3 REMARK 620 3 VAL A 258 O 92.9 88.1 REMARK 620 4 DA C 5 OP1 177.5 91.4 89.0 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 94.0 REMARK 620 3 D3T A 602 O1A 93.1 93.7 REMARK 620 4 D3T A 602 O2B 168.0 97.9 87.4 REMARK 620 5 D3T A 602 O3G 90.6 175.4 85.5 77.5 REMARK 620 6 HOH A 897 O 99.5 99.1 161.3 77.4 80.6 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE D3T A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 603 REMARK 900 REMARK 900 RELATED ENTRIES 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 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 4I27 A 132 482 UNP P09838 TDT_MOUSE 132 482 DBREF 4I27 A 483 510 UNP P09838 TDT_MOUSE 503 530 DBREF 4I27 C 1 6 PDB 4I27 4I27 1 6 SEQADV 4I27 MET A 111 UNP P09838 EXPRESSION TAG SEQADV 4I27 GLY A 112 UNP P09838 EXPRESSION TAG SEQADV 4I27 SER A 113 UNP P09838 EXPRESSION TAG SEQADV 4I27 SER A 114 UNP P09838 EXPRESSION TAG SEQADV 4I27 HIS A 115 UNP P09838 EXPRESSION TAG SEQADV 4I27 HIS A 116 UNP P09838 EXPRESSION TAG SEQADV 4I27 HIS A 117 UNP P09838 EXPRESSION TAG SEQADV 4I27 HIS A 118 UNP P09838 EXPRESSION TAG SEQADV 4I27 HIS A 119 UNP P09838 EXPRESSION TAG SEQADV 4I27 HIS A 120 UNP P09838 EXPRESSION TAG SEQADV 4I27 SER A 121 UNP P09838 EXPRESSION TAG SEQADV 4I27 SER A 122 UNP P09838 EXPRESSION TAG SEQADV 4I27 GLY A 123 UNP P09838 EXPRESSION TAG SEQADV 4I27 LEU A 124 UNP P09838 EXPRESSION TAG SEQADV 4I27 VAL A 125 UNP P09838 EXPRESSION TAG SEQADV 4I27 PRO A 126 UNP P09838 EXPRESSION TAG SEQADV 4I27 ARG A 127 UNP P09838 EXPRESSION TAG SEQADV 4I27 GLY A 128 UNP P09838 EXPRESSION TAG SEQADV 4I27 SER A 129 UNP P09838 EXPRESSION TAG SEQADV 4I27 HIS A 130 UNP P09838 EXPRESSION TAG SEQADV 4I27 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 6 DA DA DA DA DA 2DT MODRES 4I27 2DT C 6 DT 3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE HET 2DT C 6 19 HET MG A 601 1 HET D3T A 602 28 HET NA A 603 1 HETNAM 2DT 3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE HETNAM NA SODIUM ION HETSYN 2DT 2',3'-DIDEOXYTHYMIDINE-5'-MONOPHOSPHATE FORMUL 2 2DT C10 H15 N2 O7 P FORMUL 3 MG MG 2+ FORMUL 4 D3T C10 H17 N2 O13 P3 FORMUL 5 NA NA 1+ FORMUL 6 HOH *205(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 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 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 408 O ILE A 431 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 O3' DA C 5 P 2DT C 6 1555 1555 1.62 LINK O THR A 253 NA NA A 603 1555 1555 2.31 LINK O VAL A 255 NA NA A 603 1555 1555 2.57 LINK O VAL A 258 NA NA A 603 1555 1555 2.57 LINK OD1 ASP A 343 MG MG A 601 1555 1555 2.34 LINK OD2 ASP A 345 MG MG A 601 1555 1555 2.65 LINK MG MG A 601 O1A D3T A 602 1555 1555 2.30 LINK MG MG A 601 O2B D3T A 602 1555 1555 2.62 LINK MG MG A 601 O3G D3T A 602 1555 1555 2.78 LINK MG MG A 601 O HOH A 897 1555 1555 2.71 LINK NA NA A 603 OP1 DA C 5 1555 1555 2.50 CISPEP 1 GLY A 452 SER A 453 0 -0.62 SITE 1 AC1 4 ASP A 343 ASP A 345 D3T A 602 HOH A 897 SITE 1 AC2 15 GLY A 332 GLY A 333 ARG A 336 LYS A 338 SITE 2 AC2 15 GLY A 341 HIS A 342 ASP A 343 ASP A 345 SITE 3 AC2 15 GLY A 449 TRP A 450 GLY A 452 MG A 601 SITE 4 AC2 15 HOH A 750 HOH A 865 2DT C 6 SITE 1 AC3 4 THR A 253 VAL A 255 VAL A 258 DA C 5 CRYST1 46.940 95.900 47.230 90.00 107.75 90.00 P 1 21 1 2 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 0.021304 0.000000 0.006819 0.00000 SCALE2 0.000000 0.010428 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022231 0.00000