HEADER DNA BINDING PROTEIN 01-JUN-18 6GO6 TITLE TDT CHIMERA (LOOP1 OF POL MU) - TERNARY COMPLEX WITH DOWNSTREAM DSDNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA NUCLEOTIDYLEXOTRANSFERASE,DNA-DIRECTED DNA/RNA COMPND 3 POLYMERASE MU,DNA NUCLEOTIDYLEXOTRANSFERASE; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: TERMINAL ADDITION ENZYME,TERMINAL COMPND 6 DEOXYNUCLEOTIDYLTRANSFERASE,TERMINAL TRANSFERASE,POL MU,TERMINAL COMPND 7 TRANSFERASE,TERMINAL ADDITION ENZYME,TERMINAL COMPND 8 DEOXYNUCLEOTIDYLTRANSFERASE,TERMINAL TRANSFERASE; COMPND 9 EC: 2.7.7.31,2.7.7.7,2.7.7.31; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: THERE IS AN INSERTION OF ONE RESIDUE BETWEEN LOOP1 OF COMPND 12 POL MU AND TDT (Q394). THIS INSERTION EXPLAIN THE NUMBERING SHIFT COMPND 13 WITH WT-TDT.,THERE IS AN INSERTION OF ONE RESIDUE BETWEEN LOOP1 OF COMPND 14 POL MU AND TDT (Q394). THIS INSERTION EXPLAIN THE NUMBERING SHIFT COMPND 15 WITH WT-TDT.,THERE IS AN INSERTION OF ONE RESIDUE BETWEEN LOOP1 OF COMPND 16 POL MU AND TDT (Q394). THIS INSERTION EXPLAIN THE NUMBERING SHIFT COMPND 17 WITH WT-TDT.; COMPND 18 MOL_ID: 2; COMPND 19 MOLECULE: DNA (5'-D(*TP*TP*TP*TP*TP*GP*GP*C)-3'); COMPND 20 CHAIN: G, F; COMPND 21 ENGINEERED: YES; COMPND 22 MOL_ID: 3; COMPND 23 MOLECULE: DNA (5'-D(*AP*AP*AP*AP*AP*C)-3'); COMPND 24 CHAIN: E; COMPND 25 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, POLM, POLMU; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630 KEYWDS NHEJ PATHWAY, DNA BRIDGING, DNA POLYMERASE POLX, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.LOC'H,C.A.GERODIMOS,S.ROSARIO,M.R.LIEBER,M.DELARUE REVDAT 3 17-JAN-24 6GO6 1 LINK REVDAT 2 25-DEC-19 6GO6 1 JRNL REVDAT 1 05-JUN-19 6GO6 0 JRNL AUTH J.LOC'H,C.A.GERODIMOS,S.ROSARIO,M.TEKPINAR,M.R.LIEBER, JRNL AUTH 2 M.DELARUE JRNL TITL STRUCTURAL EVIDENCE FOR AN INTRANSBASE SELECTION MECHANISM JRNL TITL 2 INVOLVING LOOP1 IN POLYMERASE MU AT AN NHEJ DOUBLE-STRAND JRNL TITL 3 BREAK JUNCTION. JRNL REF J.BIOL.CHEM. V. 294 10579 2019 JRNL REFN ESSN 1083-351X JRNL PMID 31138645 JRNL DOI 10.1074/JBC.RA119.008739 REMARK 2 REMARK 2 RESOLUTION. 2.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 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) : 2.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.46 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 45742 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) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2288 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 : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.09 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.14 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.48 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2839 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2805 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2697 REMARK 3 BIN R VALUE (WORKING SET) : 0.2806 REMARK 3 BIN FREE R VALUE : 0.2789 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 142 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 : 2872 REMARK 3 NUCLEIC ACID ATOMS : 424 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 329 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 58.43 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 61.89 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 11.87820 REMARK 3 B22 (A**2) : -14.44000 REMARK 3 B33 (A**2) : 2.56180 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) : 0.300 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.155 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.143 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.145 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.137 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 : 0.929 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 : 3439 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 4728 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1163 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 71 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 462 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 3439 ; 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 : 437 ; 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 : 3575 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 0.97 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.70 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 17.21 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): -7.5153 38.6958 -8.0063 REMARK 3 T TENSOR REMARK 3 T11: 0.0095 T22: -0.1093 REMARK 3 T33: -0.1668 T12: -0.0072 REMARK 3 T13: 0.0039 T23: 0.0470 REMARK 3 L TENSOR REMARK 3 L11: 0.9769 L22: 0.7859 REMARK 3 L33: 1.1398 L12: 0.4044 REMARK 3 L13: -0.1167 L23: 0.1150 REMARK 3 S TENSOR REMARK 3 S11: -0.0725 S12: -0.0176 S13: 0.0879 REMARK 3 S21: -0.1123 S22: 0.0248 S23: 0.0294 REMARK 3 S31: 0.0454 S32: -0.0530 S33: 0.0477 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { C|* } REMARK 3 ORIGIN FOR THE GROUP (A): 0.0121 18.9098 -16.5525 REMARK 3 T TENSOR REMARK 3 T11: 0.2336 T22: -0.2772 REMARK 3 T33: -0.2963 T12: 0.0668 REMARK 3 T13: 0.0923 T23: 0.0117 REMARK 3 L TENSOR REMARK 3 L11: 3.3997 L22: 1.3812 REMARK 3 L33: 7.2051 L12: 2.1977 REMARK 3 L13: -0.8045 L23: 0.6544 REMARK 3 S TENSOR REMARK 3 S11: -0.0472 S12: 0.5311 S13: -0.2001 REMARK 3 S21: -0.1636 S22: -0.0066 S23: -0.4993 REMARK 3 S31: 0.5323 S32: 0.2767 S33: 0.0538 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: { D|* } REMARK 3 ORIGIN FOR THE GROUP (A): -0.8008 12.8780 -8.1746 REMARK 3 T TENSOR REMARK 3 T11: 0.2851 T22: -0.3040 REMARK 3 T33: -0.2361 T12: 0.0296 REMARK 3 T13: -0.0381 T23: 0.0033 REMARK 3 L TENSOR REMARK 3 L11: 6.0242 L22: 7.7408 REMARK 3 L33: 5.7588 L12: -1.4593 REMARK 3 L13: -2.8542 L23: -2.9104 REMARK 3 S TENSOR REMARK 3 S11: 0.0587 S12: -0.0089 S13: -0.5372 REMARK 3 S21: -0.2434 S22: -0.1043 S23: 0.3315 REMARK 3 S31: 0.2157 S32: -0.4031 S33: 0.0456 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: { F|* } REMARK 3 ORIGIN FOR THE GROUP (A): 0.2794 6.8577 -6.8643 REMARK 3 T TENSOR REMARK 3 T11: 0.3040 T22: -0.2994 REMARK 3 T33: 0.2253 T12: 0.1520 REMARK 3 T13: -0.1127 T23: -0.0469 REMARK 3 L TENSOR REMARK 3 L11: 4.9532 L22: 8.1301 REMARK 3 L33: 8.3154 L12: -2.9104 REMARK 3 L13: -1.1135 L23: -2.8891 REMARK 3 S TENSOR REMARK 3 S11: 0.0166 S12: -0.4012 S13: -0.5009 REMARK 3 S21: -0.2455 S22: -0.1394 S23: 0.4060 REMARK 3 S31: 0.4194 S32: 0.0211 S33: 0.1227 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6GO6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1200010308. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-FEB-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9724 REMARK 200 MONOCHROMATOR : NULL 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 : 45742 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.090 REMARK 200 RESOLUTION RANGE LOW (A) : 47.460 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.7900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.09 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.22 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.07000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 1JMS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 19-25% PEG 4000, 100-400 MM LITHIUM REMARK 280 SULFATE, 100 MM TRIS, PH 8.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 43.21000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 94.91500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 43.21000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 94.91500 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -42.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, G, F, E 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 420 REMARK 465 SER A 421 REMARK 465 GLY A 422 REMARK 465 GLN A 423 REMARK 465 GLN A 424 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 CD CE NZ REMARK 470 ASP A 219 OD1 OD2 REMARK 470 GLU A 244 CD OE1 OE2 REMARK 470 ARG A 284 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 352 CG CD OE1 OE2 REMARK 470 GLU A 355 CG CD OE1 OE2 REMARK 470 GLN A 359 CG CD OE1 NE2 REMARK 470 ARG A 382 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 419 CG CD OE1 OE2 REMARK 470 GLU A 425 CG CD OE1 OE2 REMARK 470 DC G 8 O3' REMARK 470 DC F 8 O3' REMARK 470 DC E 6 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DC E 6 N1 C2 O2 N3 C4 N4 C5 REMARK 470 DC E 6 C6 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 N2 DG G 7 N2 DG G 7 2555 1.84 REMARK 500 REMARK 500 REMARK: NULL 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 DT F 5 O4' - C1' - N1 ANGL. DEV. = 2.2 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 -157.64 -115.42 REMARK 500 SER A 383 59.80 -117.39 REMARK 500 HIS A 384 -58.65 -131.06 REMARK 500 LEU A 385 85.88 68.07 REMARK 500 ASN A 510 38.32 -86.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 994 DISTANCE = 6.77 ANGSTROMS REMARK 525 HOH A 995 DISTANCE = 6.85 ANGSTROMS REMARK 525 HOH A 996 DISTANCE = 7.71 ANGSTROMS REMARK 525 HOH A 997 DISTANCE = 11.30 ANGSTROMS REMARK 525 HOH A 998 DISTANCE = 11.67 ANGSTROMS REMARK 525 HOH A 999 DISTANCE = 19.33 ANGSTROMS REMARK 525 HOH F 117 DISTANCE = 13.82 ANGSTROMS REMARK 525 HOH F 118 DISTANCE = 16.35 ANGSTROMS REMARK 525 HOH F 119 DISTANCE = 17.87 ANGSTROMS REMARK 525 HOH F 120 DISTANCE = 27.68 ANGSTROMS 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 601 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 253 O REMARK 620 2 VAL A 258 O 100.3 REMARK 620 3 HOH A 841 O 137.9 109.4 REMARK 620 4 HOH A 912 O 94.0 102.7 107.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 602 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 343 OD1 REMARK 620 2 ASP A 345 OD2 94.1 REMARK 620 3 DCT A 603 O1B 170.5 92.5 REMARK 620 4 DCT A 603 O2A 85.9 92.6 87.1 REMARK 620 5 DCT A 603 O1G 85.8 175.0 87.0 82.3 REMARK 620 6 HOH A 779 O 93.8 90.8 92.9 176.6 94.3 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 NA A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DCT A 603 DBREF 6GO6 A 132 377 UNP P09838 TDT_MOUSE 132 377 DBREF 6GO6 A 378 407 UNP Q9JIW4 DPOLM_MOUSE 363 392 DBREF 6GO6 A 408 511 UNP P09838 TDT_MOUSE 407 530 DBREF 6GO6 G 1 8 PDB 6GO6 6GO6 1 8 DBREF 6GO6 F 1 8 PDB 6GO6 6GO6 1 8 DBREF 6GO6 E 1 6 PDB 6GO6 6GO6 1 6 SEQADV 6GO6 MET A 111 UNP P09838 INITIATING METHIONINE SEQADV 6GO6 GLY A 112 UNP P09838 EXPRESSION TAG SEQADV 6GO6 SER A 113 UNP P09838 EXPRESSION TAG SEQADV 6GO6 SER A 114 UNP P09838 EXPRESSION TAG SEQADV 6GO6 HIS A 115 UNP P09838 EXPRESSION TAG SEQADV 6GO6 HIS A 116 UNP P09838 EXPRESSION TAG SEQADV 6GO6 HIS A 117 UNP P09838 EXPRESSION TAG SEQADV 6GO6 HIS A 118 UNP P09838 EXPRESSION TAG SEQADV 6GO6 HIS A 119 UNP P09838 EXPRESSION TAG SEQADV 6GO6 HIS A 120 UNP P09838 EXPRESSION TAG SEQADV 6GO6 SER A 121 UNP P09838 EXPRESSION TAG SEQADV 6GO6 SER A 122 UNP P09838 EXPRESSION TAG SEQADV 6GO6 GLY A 123 UNP P09838 EXPRESSION TAG SEQADV 6GO6 LEU A 124 UNP P09838 EXPRESSION TAG SEQADV 6GO6 VAL A 125 UNP P09838 EXPRESSION TAG SEQADV 6GO6 PRO A 126 UNP P09838 EXPRESSION TAG SEQADV 6GO6 ARG A 127 UNP P09838 EXPRESSION TAG SEQADV 6GO6 GLY A 128 UNP P09838 EXPRESSION TAG SEQADV 6GO6 SER A 129 UNP P09838 EXPRESSION TAG SEQADV 6GO6 HIS A 130 UNP P09838 EXPRESSION TAG SEQADV 6GO6 MET A 131 UNP P09838 EXPRESSION TAG SEQADV 6GO6 VAL A 401 UNP Q9JIW4 ALA 386 CONFLICT SEQRES 1 A 401 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 401 LEU VAL PRO ARG GLY SER HIS MET SER PRO SER PRO VAL SEQRES 3 A 401 PRO GLY SER GLN ASN VAL PRO ALA PRO ALA VAL LYS LYS SEQRES 4 A 401 ILE SER GLN TYR ALA CYS GLN ARG ARG THR THR LEU ASN SEQRES 5 A 401 ASN TYR ASN GLN LEU PHE THR ASP ALA LEU ASP ILE LEU SEQRES 6 A 401 ALA GLU ASN ASP GLU LEU ARG GLU ASN GLU GLY SER CYS SEQRES 7 A 401 LEU ALA PHE MET ARG ALA SER SER VAL LEU LYS SER LEU SEQRES 8 A 401 PRO PHE PRO ILE THR SER MET LYS ASP THR GLU GLY ILE SEQRES 9 A 401 PRO CYS LEU GLY ASP LYS VAL LYS SER ILE ILE GLU GLY SEQRES 10 A 401 ILE ILE GLU ASP GLY GLU SER SER GLU ALA LYS ALA VAL SEQRES 11 A 401 LEU ASN ASP GLU ARG TYR LYS SER PHE LYS LEU PHE THR SEQRES 12 A 401 SER VAL PHE GLY VAL GLY LEU LYS THR ALA GLU LYS TRP SEQRES 13 A 401 PHE ARG MET GLY PHE ARG THR LEU SER LYS ILE GLN SER SEQRES 14 A 401 ASP LYS SER LEU ARG PHE THR GLN MET GLN LYS ALA GLY SEQRES 15 A 401 PHE LEU TYR TYR GLU ASP LEU VAL SER CYS VAL ASN ARG SEQRES 16 A 401 PRO GLU ALA GLU ALA VAL SER MET LEU VAL LYS GLU ALA SEQRES 17 A 401 VAL VAL THR PHE LEU PRO ASP ALA LEU VAL THR MET THR SEQRES 18 A 401 GLY GLY PHE ARG ARG GLY LYS MET THR GLY HIS ASP VAL SEQRES 19 A 401 ASP PHE LEU ILE THR SER PRO GLU ALA THR GLU ASP GLU SEQRES 20 A 401 GLU GLN GLN LEU LEU HIS LYS VAL THR ASP PHE TRP LYS SEQRES 21 A 401 GLN GLN GLY LEU LEU LEU TYR HIS GLN TYR HIS ARG SER SEQRES 22 A 401 HIS LEU ALA ASP SER ALA HIS ASN LEU ARG GLN ARG SER SEQRES 23 A 401 SER THR MET ASP VAL PHE GLU ARG SER PHE CYS ILE LEU SEQRES 24 A 401 LYS LEU ASP HIS GLY ARG VAL HIS SER GLU LYS SER GLY SEQRES 25 A 401 GLN GLN GLU GLY LYS GLY TRP LYS ALA ILE ARG VAL ASP SEQRES 26 A 401 LEU VAL MET CYS PRO TYR ASP ARG ARG ALA PHE ALA LEU SEQRES 27 A 401 LEU GLY TRP THR GLY SER ARG GLN PHE GLU ARG ASP LEU SEQRES 28 A 401 ARG ARG TYR ALA THR HIS GLU ARG LYS MET MET LEU ASP SEQRES 29 A 401 ASN HIS ALA LEU TYR ASP ARG THR LYS ARG VAL PHE LEU SEQRES 30 A 401 GLU ALA GLU SER GLU GLU GLU ILE PHE ALA HIS LEU GLY SEQRES 31 A 401 LEU ASP TYR ILE GLU PRO TRP GLU ARG ASN ALA SEQRES 1 G 8 DT DT DT DT DT DG DG DC SEQRES 1 F 8 DT DT DT DT DT DG DG DC SEQRES 1 E 6 DA DA DA DA DA DC HET NA A 601 1 HET MG A 602 1 HET DCT A 603 27 HETNAM NA SODIUM ION HETNAM MG MAGNESIUM ION HETNAM DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE FORMUL 5 NA NA 1+ FORMUL 6 MG MG 2+ FORMUL 7 DCT C9 H16 N3 O12 P3 FORMUL 8 HOH *329(H2 O) HELIX 1 AA1 TYR A 153 ARG A 157 5 5 HELIX 2 AA2 ASN A 165 ARG A 182 1 18 HELIX 3 AA3 ASN A 184 SER A 200 1 17 HELIX 4 AA4 SER A 207 GLU A 212 5 6 HELIX 5 AA5 GLY A 218 GLY A 232 1 15 HELIX 6 AA6 SER A 234 ASP A 243 1 10 HELIX 7 AA7 ASP A 243 THR A 253 1 11 HELIX 8 AA8 GLY A 259 MET A 269 1 11 HELIX 9 AA9 THR A 273 SER A 279 1 7 HELIX 10 AB1 THR A 286 TYR A 295 1 10 HELIX 11 AB2 TYR A 295 SER A 301 1 7 HELIX 12 AB3 ARG A 305 LEU A 323 1 19 HELIX 13 AB4 THR A 331 ARG A 336 1 6 HELIX 14 AB5 THR A 354 GLN A 372 1 19 HELIX 15 AB6 ARG A 382 HIS A 384 5 3 HELIX 16 AB7 ASP A 387 ASN A 391 5 5 HELIX 17 AB8 ARG A 395 VAL A 401 1 7 HELIX 18 AB9 GLY A 414 VAL A 416 5 3 HELIX 19 AC1 PRO A 440 ASP A 442 5 3 HELIX 20 AC2 ARG A 443 GLY A 453 1 11 HELIX 21 AC3 SER A 454 LYS A 470 1 17 HELIX 22 AC4 SER A 491 LEU A 499 1 9 HELIX 23 AC5 GLU A 505 ARG A 509 5 5 SHEET 1 AA1 2 VAL A 303 ASN A 304 0 SHEET 2 AA1 2 THR A 340 GLY A 341 -1 O GLY A 341 N VAL A 303 SHEET 1 AA2 5 LEU A 327 MET A 330 0 SHEET 2 AA2 5 VAL A 344 THR A 349 -1 O THR A 349 N LEU A 327 SHEET 3 AA2 5 TRP A 429 MET A 438 1 O VAL A 437 N ILE A 348 SHEET 4 AA2 5 GLU A 403 ASP A 412 -1 N SER A 405 O LEU A 436 SHEET 5 AA2 5 LEU A 375 TYR A 380 -1 N LEU A 376 O ILE A 408 SHEET 1 AA3 3 MET A 471 LEU A 473 0 SHEET 2 AA3 3 LEU A 478 ASP A 480 -1 O TYR A 479 N MET A 472 SHEET 3 AA3 3 VAL A 485 LEU A 487 -1 O LEU A 487 N LEU A 478 LINK O THR A 253 NA NA A 601 1555 1555 2.61 LINK O VAL A 258 NA NA A 601 1555 1555 2.90 LINK OD1 ASP A 343 MG MG A 602 1555 1555 2.01 LINK OD2 ASP A 345 MG MG A 602 1555 1555 2.19 LINK NA NA A 601 O HOH A 841 1555 1555 2.58 LINK NA NA A 601 O HOH A 912 1555 1555 3.02 LINK MG MG A 602 O1B DCT A 603 1555 1555 2.22 LINK MG MG A 602 O2A DCT A 603 1555 1555 2.31 LINK MG MG A 602 O1G DCT A 603 1555 1555 2.07 LINK MG MG A 602 O HOH A 779 1555 1555 2.07 CISPEP 1 GLY A 453 SER A 454 0 -1.23 SITE 1 AC1 5 THR A 253 VAL A 255 VAL A 258 HOH A 841 SITE 2 AC1 5 HOH A 912 SITE 1 AC2 4 ASP A 343 ASP A 345 DCT A 603 HOH A 779 SITE 1 AC3 22 GLY A 332 GLY A 333 ARG A 336 LYS A 338 SITE 2 AC3 22 GLY A 341 HIS A 342 ASP A 343 ASP A 345 SITE 3 AC3 22 ALA A 389 ASN A 391 LEU A 392 TRP A 451 SITE 4 AC3 22 GLY A 453 ARG A 455 GLU A 458 MG A 602 SITE 5 AC3 22 HOH A 705 HOH A 708 HOH A 762 HOH A 772 SITE 6 AC3 22 HOH A 779 DG F 6 CRYST1 86.420 189.830 46.480 90.00 90.00 90.00 P 21 21 2 8 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 0.011571 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005268 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021515 0.00000