PDB Short entry for 4I2A HEADER TRANSFERASE/DNA 21-NOV-12 4I2A TITLE BINARY COMPLEX OF MOUSE TDT WITH SSDNA IN ABSENCE OF DIVALENT TITLE 2 TRANSITION METAL ION 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*(BRU)P*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 4I2A 1 REMARK SEQADV LINK REVDAT 4 26-JUL-17 4I2A 1 SOURCE REMARK REVDAT 3 13-NOV-13 4I2A 1 JRNL REVDAT 2 31-JUL-13 4I2A 1 JRNL REVDAT 1 24-JUL-13 4I2A 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. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.65 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 35260 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) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1759 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 : 18 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.96 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.50 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2915 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2194 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2761 REMARK 3 BIN R VALUE (WORKING SET) : 0.2174 REMARK 3 BIN FREE R VALUE : 0.2551 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.28 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 154 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 : 2889 REMARK 3 NUCLEIC ACID ATOMS : 101 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 457 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.74 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.36990 REMARK 3 B22 (A**2) : 5.61680 REMARK 3 B33 (A**2) : -8.98680 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) : 0.234 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.151 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.139 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.136 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.132 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 : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.929 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 3068 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 4145 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1450 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 78 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 447 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 3068 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 1 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 391 ; 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 : 3834 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 0.89 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.94 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 2.70 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: {A|149 - 237} REMARK 3 ORIGIN FOR THE GROUP (A): -27.3245 -11.4922 5.3107 REMARK 3 T TENSOR REMARK 3 T11: -0.0690 T22: -0.0350 REMARK 3 T33: -0.0404 T12: -0.0096 REMARK 3 T13: -0.0024 T23: -0.0196 REMARK 3 L TENSOR REMARK 3 L11: 2.6199 L22: 2.8401 REMARK 3 L33: 1.5299 L12: 0.6327 REMARK 3 L13: -0.0181 L23: -0.5743 REMARK 3 S TENSOR REMARK 3 S11: -0.0360 S12: 0.2212 S13: -0.1380 REMARK 3 S21: -0.2292 S22: 0.0283 S23: -0.0890 REMARK 3 S31: 0.2108 S32: -0.0274 S33: 0.0077 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: {A|238 - 301} REMARK 3 ORIGIN FOR THE GROUP (A): -19.4360 -27.9237 27.7069 REMARK 3 T TENSOR REMARK 3 T11: -0.0310 T22: -0.0874 REMARK 3 T33: 0.0486 T12: -0.0091 REMARK 3 T13: 0.0104 T23: 0.0374 REMARK 3 L TENSOR REMARK 3 L11: 0.2735 L22: 1.9209 REMARK 3 L33: 1.1268 L12: 0.1065 REMARK 3 L13: -0.0370 L23: -0.0798 REMARK 3 S TENSOR REMARK 3 S11: -0.0191 S12: -0.0522 S13: -0.0012 REMARK 3 S21: -0.1210 S22: 0.0529 S23: -0.0493 REMARK 3 S31: -0.0491 S32: 0.0665 S33: -0.0338 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: {A|302 - 451} REMARK 3 ORIGIN FOR THE GROUP (A): -8.8741 -3.9119 31.1773 REMARK 3 T TENSOR REMARK 3 T11: -0.0626 T22: -0.0805 REMARK 3 T33: 0.0012 T12: -0.0150 REMARK 3 T13: -0.0526 T23: -0.0185 REMARK 3 L TENSOR REMARK 3 L11: 1.5669 L22: 1.5210 REMARK 3 L33: 1.4024 L12: -0.0839 REMARK 3 L13: -0.6720 L23: -0.7353 REMARK 3 S TENSOR REMARK 3 S11: -0.0679 S12: -0.1882 S13: -0.0144 REMARK 3 S21: 0.2685 S22: -0.0479 S23: -0.2526 REMARK 3 S31: -0.0581 S32: 0.1778 S33: 0.1157 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: {A|452 - 510} REMARK 3 ORIGIN FOR THE GROUP (A): -7.1984 1.1816 8.8108 REMARK 3 T TENSOR REMARK 3 T11: -0.0838 T22: -0.0340 REMARK 3 T33: 0.0618 T12: 0.0107 REMARK 3 T13: 0.0027 T23: 0.0379 REMARK 3 L TENSOR REMARK 3 L11: 4.4431 L22: 0.5605 REMARK 3 L33: 0.6497 L12: -0.2711 REMARK 3 L13: -0.6470 L23: -0.2584 REMARK 3 S TENSOR REMARK 3 S11: 0.0392 S12: 0.2846 S13: 0.2230 REMARK 3 S21: -0.0437 S22: -0.1073 S23: -0.1879 REMARK 3 S31: 0.0422 S32: 0.0158 S33: 0.0681 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: {C|1 - 5} REMARK 3 ORIGIN FOR THE GROUP (A): -6.8045 -20.2529 23.7723 REMARK 3 T TENSOR REMARK 3 T11: 0.0058 T22: -0.1033 REMARK 3 T33: 0.0785 T12: -0.1314 REMARK 3 T13: 0.0121 T23: -0.0121 REMARK 3 L TENSOR REMARK 3 L11: 0.4754 L22: 0.1548 REMARK 3 L33: 0.0000 L12: 0.0318 REMARK 3 L13: -0.9531 L23: 0.6239 REMARK 3 S TENSOR REMARK 3 S11: 0.0048 S12: 0.0230 S13: -0.0037 REMARK 3 S21: -0.0085 S22: -0.0080 S23: 0.0060 REMARK 3 S31: 0.0005 S32: 0.0600 S33: 0.0032 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4I2A 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_1000076213. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUN-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) : 0.9194 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 : 35301 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 47.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.07800 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) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.60900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 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 (%): 49.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20-26% PEG4000, 100 MM HEPES, 200 MM REMARK 280 AMMONIUM FORMATE, 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 23.46750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 57.34350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.44650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.34350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.46750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.44650 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 ALA A 146 REMARK 465 VAL A 147 REMARK 465 LYS A 148 REMARK 465 GLY A 421 REMARK 465 GLN A 422 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 LYS A 238 CD CE NZ REMARK 470 GLU A 264 OE1 OE2 REMARK 470 GLU A 352 CG CD OE1 OE2 REMARK 470 GLU A 355 CG CD OE1 OE2 REMARK 470 VAL A 395 CG1 CG2 REMARK 470 ASP A 396 CG OD1 OD2 REMARK 470 SER A 420 OG REMARK 470 GLN A 423 CG CD OE1 NE2 REMARK 470 GLU A 424 CG CD OE1 OE2 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 4 O4' - C4' - C3' ANGL. DEV. = -2.9 DEGREES REMARK 500 DA C 4 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DA C 5 C1' - O4' - C4' ANGL. DEV. = -7.5 DEGREES REMARK 500 DA C 5 O4' - C1' - N9 ANGL. DEV. = 7.5 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 -152.62 -113.70 REMARK 500 ASN A 509 46.39 -84.41 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 84.8 REMARK 620 3 VAL A 258 O 101.5 94.0 REMARK 620 4 HOH A 967 O 78.8 89.2 176.8 REMARK 620 5 DA C 4 OP1 167.7 92.0 90.6 89.3 REMARK 620 6 HOH C 101 O 95.3 178.5 84.5 92.2 88.2 REMARK 620 N 1 2 3 4 5 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 HOH A 916 O 88.3 REMARK 620 3 HOH A 965 O 146.6 113.5 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 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 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: 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 4I2A A 132 482 UNP P09838 TDT_MOUSE 132 482 DBREF 4I2A A 483 510 UNP P09838 TDT_MOUSE 503 530 DBREF 4I2A C 1 5 PDB 4I2A 4I2A 1 5 SEQADV 4I2A MET A 111 UNP P09838 EXPRESSION TAG SEQADV 4I2A GLY A 112 UNP P09838 EXPRESSION TAG SEQADV 4I2A SER A 113 UNP P09838 EXPRESSION TAG SEQADV 4I2A SER A 114 UNP P09838 EXPRESSION TAG SEQADV 4I2A HIS A 115 UNP P09838 EXPRESSION TAG SEQADV 4I2A HIS A 116 UNP P09838 EXPRESSION TAG SEQADV 4I2A HIS A 117 UNP P09838 EXPRESSION TAG SEQADV 4I2A HIS A 118 UNP P09838 EXPRESSION TAG SEQADV 4I2A HIS A 119 UNP P09838 EXPRESSION TAG SEQADV 4I2A HIS A 120 UNP P09838 EXPRESSION TAG SEQADV 4I2A SER A 121 UNP P09838 EXPRESSION TAG SEQADV 4I2A SER A 122 UNP P09838 EXPRESSION TAG SEQADV 4I2A GLY A 123 UNP P09838 EXPRESSION TAG SEQADV 4I2A LEU A 124 UNP P09838 EXPRESSION TAG SEQADV 4I2A VAL A 125 UNP P09838 EXPRESSION TAG SEQADV 4I2A PRO A 126 UNP P09838 EXPRESSION TAG SEQADV 4I2A ARG A 127 UNP P09838 EXPRESSION TAG SEQADV 4I2A GLY A 128 UNP P09838 EXPRESSION TAG SEQADV 4I2A SER A 129 UNP P09838 EXPRESSION TAG SEQADV 4I2A HIS A 130 UNP P09838 EXPRESSION TAG SEQADV 4I2A 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 BRU DA DA MODRES 4I2A BRU C 3 DU HET BRU C 3 20 HET MG A 601 1 HET NA A 602 1 HETNAM BRU 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION FORMUL 2 BRU C9 H12 BR N2 O8 P FORMUL 3 MG MG 2+ FORMUL 4 NA NA 1+ FORMUL 5 HOH *457(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 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 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 PHE A 485 -1 O VAL A 484 N ASP A 479 LINK O3' DA C 2 P BRU C 3 1555 1555 1.55 LINK O3' BRU C 3 P DA C 4 1555 1555 1.59 LINK O THR A 253 NA NA A 602 1555 1555 2.31 LINK O VAL A 255 NA NA A 602 1555 1555 2.64 LINK O VAL A 258 NA NA A 602 1555 1555 2.43 LINK OD1 ASP A 343 MG MG A 601 1555 1555 2.96 LINK MG MG A 601 O HOH A 916 1555 1555 2.42 LINK MG MG A 601 O HOH A 965 1555 1555 2.18 LINK NA NA A 602 O HOH A 967 1555 1555 2.56 LINK NA NA A 602 OP1 DA C 4 1555 1555 2.56 LINK NA NA A 602 O HOH C 101 1555 1555 2.40 CISPEP 1 GLY A 452 SER A 453 0 -2.39 SITE 1 AC1 5 GLY A 333 ASP A 343 ASP A 345 HOH A 916 SITE 2 AC1 5 HOH A 965 SITE 1 AC2 6 THR A 253 VAL A 255 VAL A 258 HOH A 967 SITE 2 AC2 6 DA C 4 HOH C 101 CRYST1 46.935 84.893 114.687 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 0.021306 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011780 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008719 0.00000