HEADER HYDROLASE/DNA 07-MAR-16 5INP TITLE MOUSE TDP2 REACTION PRODUCT (5'-PHOSPHORYLATED DNA)-MN2+ COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSYL-DNA PHOSPHODIESTERASE 2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 118-370; COMPND 5 SYNONYM: TYR-DNA PHOSPHODIESTERASE 2,5'-TYROSYL-DNA COMPND 6 PHOSPHODIESTERASE,5'-TYR-DNA PHOSPHODIESTERASE,TRAF AND TNF RECEPTOR- COMPND 7 ASSOCIATED PROTEIN; COMPND 8 EC: 3.1.4.-; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3'); COMPND 12 CHAIN: C, D; COMPND 13 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: TDP2, TTRAP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS HYDROLASE/DNA, DNA REPAIR, ENDONUCLEASE/EXONUCLEASE/PHOSPHATASE (EEP) KEYWDS 2 DOMAIN, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.J.SCHELLENBERG,R.S.WILLIAMS REVDAT 5 27-SEP-23 5INP 1 LINK REVDAT 4 18-DEC-19 5INP 1 REMARK REVDAT 3 20-SEP-17 5INP 1 JRNL REMARK REVDAT 2 18-MAY-16 5INP 1 JRNL REVDAT 1 27-APR-16 5INP 0 JRNL AUTH M.J.SCHELLENBERG,L.PERERA,C.N.STROM,C.A.WATERS,B.MONIAN, JRNL AUTH 2 C.D.APPEL,C.K.VILAS,J.G.WILLIAMS,D.A.RAMSDEN,R.S.WILLIAMS JRNL TITL REVERSAL OF DNA DAMAGE INDUCED TOPOISOMERASE 2 DNA-PROTEIN JRNL TITL 2 CROSSLINKS BY TDP2. JRNL REF NUCLEIC ACIDS RES. V. 44 3829 2016 JRNL REFN ESSN 1362-4962 JRNL PMID 27060144 JRNL DOI 10.1093/NAR/GKW228 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 3 NUMBER OF REFLECTIONS : 82918 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.144 REMARK 3 R VALUE (WORKING SET) : 0.143 REMARK 3 FREE R VALUE : 0.170 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 4171 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 29.8453 - 6.0345 0.96 2721 112 0.1929 0.2070 REMARK 3 2 6.0345 - 4.7962 0.99 2830 118 0.1431 0.1835 REMARK 3 3 4.7962 - 4.1918 1.00 2765 149 0.1124 0.1253 REMARK 3 4 4.1918 - 3.8094 1.00 2787 145 0.1209 0.1407 REMARK 3 5 3.8094 - 3.5368 1.00 2822 156 0.1301 0.1403 REMARK 3 6 3.5368 - 3.3286 1.00 2806 162 0.1381 0.1510 REMARK 3 7 3.3286 - 3.1621 1.00 2782 158 0.1360 0.1624 REMARK 3 8 3.1621 - 3.0246 1.00 2775 141 0.1425 0.1848 REMARK 3 9 3.0246 - 2.9082 1.00 2842 139 0.1544 0.1898 REMARK 3 10 2.9082 - 2.8080 1.00 2812 127 0.1535 0.1989 REMARK 3 11 2.8080 - 2.7202 1.00 2789 169 0.1390 0.1713 REMARK 3 12 2.7202 - 2.6425 1.00 2792 152 0.1445 0.1723 REMARK 3 13 2.6425 - 2.5730 1.00 2792 145 0.1403 0.1761 REMARK 3 14 2.5730 - 2.5102 1.00 2786 169 0.1405 0.1750 REMARK 3 15 2.5102 - 2.4532 1.00 2811 149 0.1342 0.1678 REMARK 3 16 2.4532 - 2.4010 1.00 2808 150 0.1470 0.1731 REMARK 3 17 2.4010 - 2.3530 1.00 2757 155 0.1456 0.1860 REMARK 3 18 2.3530 - 2.3086 1.00 2772 164 0.1429 0.1608 REMARK 3 19 2.3086 - 2.2674 1.00 2841 130 0.1401 0.2007 REMARK 3 20 2.2674 - 2.2290 1.00 2828 147 0.1291 0.1697 REMARK 3 21 2.2290 - 2.1930 1.00 2766 132 0.1406 0.1826 REMARK 3 22 2.1930 - 2.1593 0.98 2792 153 0.1466 0.1830 REMARK 3 23 2.1593 - 2.1276 0.95 2646 150 0.1480 0.1927 REMARK 3 24 2.1276 - 2.0976 0.92 2530 149 0.1638 0.2291 REMARK 3 25 2.0976 - 2.0693 0.86 2435 134 0.1583 0.2140 REMARK 3 26 2.0693 - 2.0424 0.82 2304 115 0.1746 0.1898 REMARK 3 27 2.0424 - 2.0169 0.76 2129 110 0.1768 0.1859 REMARK 3 28 2.0169 - 1.9926 0.71 1993 107 0.1692 0.1900 REMARK 3 29 1.9926 - 1.9694 0.64 1774 98 0.1778 0.2216 REMARK 3 30 1.9694 - 1.9473 0.53 1460 86 0.2064 0.2623 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.40 REMARK 3 SHRINKAGE RADIUS : 1.20 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.75 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.44 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 4695 REMARK 3 ANGLE : 1.026 6461 REMARK 3 CHIRALITY : 0.044 720 REMARK 3 PLANARITY : 0.004 776 REMARK 3 DIHEDRAL : 15.293 1811 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): -11.2799 -15.9626 13.1070 REMARK 3 T TENSOR REMARK 3 T11: 0.1983 T22: 0.1709 REMARK 3 T33: 0.1646 T12: -0.0118 REMARK 3 T13: -0.0137 T23: -0.0246 REMARK 3 L TENSOR REMARK 3 L11: 2.0237 L22: 1.0710 REMARK 3 L33: 1.2550 L12: -0.0274 REMARK 3 L13: 0.1589 L23: 0.0249 REMARK 3 S TENSOR REMARK 3 S11: 0.0421 S12: -0.1363 S13: 0.0225 REMARK 3 S21: 0.1070 S22: -0.0179 S23: -0.0379 REMARK 3 S31: 0.0258 S32: -0.1030 S33: 0.0042 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): 10.2001 -59.4993 28.8157 REMARK 3 T TENSOR REMARK 3 T11: 0.2586 T22: 0.1659 REMARK 3 T33: 0.1729 T12: -0.0184 REMARK 3 T13: -0.0178 T23: -0.0100 REMARK 3 L TENSOR REMARK 3 L11: 1.4979 L22: 2.0688 REMARK 3 L33: 1.5304 L12: 0.0281 REMARK 3 L13: -0.0076 L23: -0.0850 REMARK 3 S TENSOR REMARK 3 S11: 0.0804 S12: 0.0141 S13: 0.0730 REMARK 3 S21: 0.1301 S22: -0.1163 S23: -0.0540 REMARK 3 S31: -0.1111 S32: 0.0174 S33: 0.0331 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN C REMARK 3 ORIGIN FOR THE GROUP (A): 8.8155 -37.7526 11.6047 REMARK 3 T TENSOR REMARK 3 T11: 0.4775 T22: 0.7152 REMARK 3 T33: 0.5825 T12: -0.0003 REMARK 3 T13: -0.0341 T23: 0.2053 REMARK 3 L TENSOR REMARK 3 L11: 3.2968 L22: 7.0978 REMARK 3 L33: 1.0079 L12: -4.7789 REMARK 3 L13: 1.6513 L23: -2.2170 REMARK 3 S TENSOR REMARK 3 S11: 0.0425 S12: 1.4487 S13: 0.4839 REMARK 3 S21: -0.2342 S22: -0.4776 S23: 0.0003 REMARK 3 S31: -0.1234 S32: 0.0810 S33: 0.1498 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN D REMARK 3 ORIGIN FOR THE GROUP (A): 5.8352 -37.5495 9.4828 REMARK 3 T TENSOR REMARK 3 T11: 0.6055 T22: 0.6198 REMARK 3 T33: 0.6272 T12: 0.2151 REMARK 3 T13: -0.1323 T23: 0.0229 REMARK 3 L TENSOR REMARK 3 L11: 2.0230 L22: 4.6561 REMARK 3 L33: 2.1211 L12: -1.2237 REMARK 3 L13: 1.1924 L23: -1.0465 REMARK 3 S TENSOR REMARK 3 S11: 0.2445 S12: 0.2067 S13: -0.8810 REMARK 3 S21: 0.2777 S22: -0.1854 S23: -0.3378 REMARK 3 S31: 0.7096 S32: 1.2268 S33: -0.0450 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5INP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000219027. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAY-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 92 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 82918 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.947 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.18100 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: PHENIX REMARK 200 STARTING MODEL: 4GZ1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES, 14-18% PEG3350, 200 MM REMARK 280 SODIUM ACETATE, 10MM MAGNESIUM ACETATE. CRYSTAL WAS SOAKED INTO REMARK 280 THE SAME CONDITION WITH 5MM MANGANESE CHLORIDE INSTEAD OF REMARK 280 MAGNESIUM ACETATE, PH 7.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 295K 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 27.29600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 83.44950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.26050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 83.44950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.29600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.26050 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: 3750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 SER A 115 REMARK 465 SER B 115 REMARK 465 LYS B 116 REMARK 465 GLY B 117 REMARK 465 LEU B 118 REMARK 465 GLU B 119 REMARK 465 ASP B 120 REMARK 465 SER B 121 REMARK 465 SER B 122 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 ALA A 175 49.51 -141.19 REMARK 500 GLU A 238 130.06 -38.44 REMARK 500 THR A 240 154.07 83.68 REMARK 500 PRO A 318 49.55 -84.09 REMARK 500 GLU A 334 68.01 37.65 REMARK 500 GLU B 238 131.99 -38.37 REMARK 500 THR B 240 153.41 84.35 REMARK 500 PRO B 318 44.89 -83.03 REMARK 500 GLU B 334 108.55 -36.15 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 733 DISTANCE = 6.52 ANGSTROMS REMARK 525 HOH B 687 DISTANCE = 6.21 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 EPE B 401 REMARK 610 EPE B 402 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 MN A 401 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 162 OE2 REMARK 620 2 HOH A 516 O 89.7 REMARK 620 3 HOH A 534 O 170.6 87.2 REMARK 620 4 HOH A 546 O 83.5 89.8 87.6 REMARK 620 5 DC D 1 OP2 92.8 176.3 90.8 93.1 REMARK 620 6 HOH D 106 O 90.6 94.9 98.5 172.4 82.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 403 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 162 OE2 REMARK 620 2 HOH B 513 O 88.2 REMARK 620 3 HOH B 528 O 168.1 83.9 REMARK 620 4 HOH B 532 O 83.9 90.2 87.2 REMARK 620 5 DC C 1 OP2 94.5 175.2 94.0 94.0 REMARK 620 6 HOH C 106 O 89.1 93.3 100.2 172.1 82.9 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 MN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPE B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPE B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4GZ1 RELATED DB: PDB REMARK 900 4GZ1 CONTAINS THE SAME PROTEIN-DNA COMPLEX, BUT WITH A MG2+ COFACTOR REMARK 900 RELATED ID: 5INP RELATED DB: PDB REMARK 900 RELATED ID: 5INM RELATED DB: PDB REMARK 900 RELATED ID: 5INL RELATED DB: PDB REMARK 900 RELATED ID: 5INK RELATED DB: PDB REMARK 900 RELATED ID: 5INO RELATED DB: PDB REMARK 900 RELATED ID: 5INN RELATED DB: PDB DBREF 5INP A 118 370 UNP Q9JJX7 TYDP2_MOUSE 118 370 DBREF 5INP B 118 370 UNP Q9JJX7 TYDP2_MOUSE 118 370 DBREF 5INP C 1 9 PDB 5INP 5INP 1 9 DBREF 5INP D 1 9 PDB 5INP 5INP 1 9 SEQADV 5INP SER A 115 UNP Q9JJX7 EXPRESSION TAG SEQADV 5INP LYS A 116 UNP Q9JJX7 EXPRESSION TAG SEQADV 5INP GLY A 117 UNP Q9JJX7 EXPRESSION TAG SEQADV 5INP SER B 115 UNP Q9JJX7 EXPRESSION TAG SEQADV 5INP LYS B 116 UNP Q9JJX7 EXPRESSION TAG SEQADV 5INP GLY B 117 UNP Q9JJX7 EXPRESSION TAG SEQRES 1 A 256 SER LYS GLY LEU GLU ASP SER SER THR ILE SER PHE ILE SEQRES 2 A 256 THR TRP ASN ILE ASP GLY LEU ASP GLY CYS ASN LEU PRO SEQRES 3 A 256 GLU ARG ALA ARG GLY VAL CYS SER CYS LEU ALA LEU TYR SEQRES 4 A 256 SER PRO ASP VAL VAL PHE LEU GLN GLU VAL ILE PRO PRO SEQRES 5 A 256 TYR CYS ALA TYR LEU LYS LYS ARG ALA ALA SER TYR THR SEQRES 6 A 256 ILE ILE THR GLY ASN GLU GLU GLY TYR PHE THR ALA ILE SEQRES 7 A 256 LEU LEU LYS LYS GLY ARG VAL LYS PHE LYS SER GLN GLU SEQRES 8 A 256 ILE ILE PRO PHE PRO ASN THR LYS MET MET ARG ASN LEU SEQRES 9 A 256 LEU CYS VAL ASN VAL SER LEU GLY GLY ASN GLU PHE CYS SEQRES 10 A 256 LEU MET THR SER HIS LEU GLU SER THR ARG GLU HIS SER SEQRES 11 A 256 ALA GLU ARG ILE ARG GLN LEU LYS THR VAL LEU GLY LYS SEQRES 12 A 256 MET GLN GLU ALA PRO ASP SER THR THR VAL ILE PHE ALA SEQRES 13 A 256 GLY ASP THR ASN LEU ARG ASP GLN GLU VAL ILE LYS CYS SEQRES 14 A 256 GLY GLY LEU PRO ASP ASN VAL PHE ASP ALA TRP GLU PHE SEQRES 15 A 256 LEU GLY LYS PRO LYS HIS CYS GLN TYR THR TRP ASP THR SEQRES 16 A 256 LYS ALA ASN ASN ASN LEU ARG ILE PRO ALA ALA TYR LYS SEQRES 17 A 256 HIS ARG PHE ASP ARG ILE PHE PHE ARG ALA GLU GLU GLY SEQRES 18 A 256 HIS LEU ILE PRO GLN SER LEU ASP LEU VAL GLY LEU GLU SEQRES 19 A 256 LYS LEU ASP CYS GLY ARG PHE PRO SER ASP HIS TRP GLY SEQRES 20 A 256 LEU LEU CYS THR LEU ASN VAL VAL LEU SEQRES 1 B 256 SER LYS GLY LEU GLU ASP SER SER THR ILE SER PHE ILE SEQRES 2 B 256 THR TRP ASN ILE ASP GLY LEU ASP GLY CYS ASN LEU PRO SEQRES 3 B 256 GLU ARG ALA ARG GLY VAL CYS SER CYS LEU ALA LEU TYR SEQRES 4 B 256 SER PRO ASP VAL VAL PHE LEU GLN GLU VAL ILE PRO PRO SEQRES 5 B 256 TYR CYS ALA TYR LEU LYS LYS ARG ALA ALA SER TYR THR SEQRES 6 B 256 ILE ILE THR GLY ASN GLU GLU GLY TYR PHE THR ALA ILE SEQRES 7 B 256 LEU LEU LYS LYS GLY ARG VAL LYS PHE LYS SER GLN GLU SEQRES 8 B 256 ILE ILE PRO PHE PRO ASN THR LYS MET MET ARG ASN LEU SEQRES 9 B 256 LEU CYS VAL ASN VAL SER LEU GLY GLY ASN GLU PHE CYS SEQRES 10 B 256 LEU MET THR SER HIS LEU GLU SER THR ARG GLU HIS SER SEQRES 11 B 256 ALA GLU ARG ILE ARG GLN LEU LYS THR VAL LEU GLY LYS SEQRES 12 B 256 MET GLN GLU ALA PRO ASP SER THR THR VAL ILE PHE ALA SEQRES 13 B 256 GLY ASP THR ASN LEU ARG ASP GLN GLU VAL ILE LYS CYS SEQRES 14 B 256 GLY GLY LEU PRO ASP ASN VAL PHE ASP ALA TRP GLU PHE SEQRES 15 B 256 LEU GLY LYS PRO LYS HIS CYS GLN TYR THR TRP ASP THR SEQRES 16 B 256 LYS ALA ASN ASN ASN LEU ARG ILE PRO ALA ALA TYR LYS SEQRES 17 B 256 HIS ARG PHE ASP ARG ILE PHE PHE ARG ALA GLU GLU GLY SEQRES 18 B 256 HIS LEU ILE PRO GLN SER LEU ASP LEU VAL GLY LEU GLU SEQRES 19 B 256 LYS LEU ASP CYS GLY ARG PHE PRO SER ASP HIS TRP GLY SEQRES 20 B 256 LEU LEU CYS THR LEU ASN VAL VAL LEU SEQRES 1 C 9 DC DC DG DA DA DT DT DC DG SEQRES 1 D 9 DC DC DG DA DA DT DT DC DG HET MN A 401 1 HET EPE B 401 7 HET EPE B 402 6 HET MN B 403 1 HETNAM MN MANGANESE (II) ION HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN EPE HEPES FORMUL 5 MN 2(MN 2+) FORMUL 6 EPE 2(C8 H18 N2 O4 S) FORMUL 9 HOH *440(H2 O) HELIX 1 AA1 ASN A 138 SER A 154 1 17 HELIX 2 AA2 ILE A 164 ALA A 175 1 12 HELIX 3 AA3 THR A 240 GLU A 242 5 3 HELIX 4 AA4 HIS A 243 ALA A 261 1 19 HELIX 5 AA5 ARG A 276 GLY A 284 1 9 HELIX 6 AA6 ALA A 293 LEU A 297 1 5 HELIX 7 AA7 PRO A 300 GLN A 304 5 5 HELIX 8 AA8 ASN B 138 SER B 154 1 17 HELIX 9 AA9 ILE B 164 ALA B 175 1 12 HELIX 10 AB1 THR B 240 GLU B 242 5 3 HELIX 11 AB2 HIS B 243 ALA B 261 1 19 HELIX 12 AB3 ARG B 276 CYS B 283 1 8 HELIX 13 AB4 ALA B 293 LEU B 297 1 5 HELIX 14 AB5 PRO B 300 GLN B 304 5 5 SHEET 1 AA1 6 TYR A 178 THR A 182 0 SHEET 2 AA1 6 PHE A 189 LYS A 195 -1 O ILE A 192 N ILE A 181 SHEET 3 AA1 6 VAL A 157 VAL A 163 -1 N VAL A 158 O LEU A 193 SHEET 4 AA1 6 THR A 123 ASN A 130 1 N ILE A 127 O PHE A 159 SHEET 5 AA1 6 GLY A 361 VAL A 368 -1 O CYS A 364 N PHE A 126 SHEET 6 AA1 6 LEU A 337 VAL A 345 -1 N GLN A 340 O THR A 365 SHEET 1 AA2 6 VAL A 199 PRO A 208 0 SHEET 2 AA2 6 ASN A 217 LEU A 225 -1 O CYS A 220 N GLU A 205 SHEET 3 AA2 6 ASN A 228 SER A 235 -1 O PHE A 230 N VAL A 223 SHEET 4 AA2 6 THR A 266 ASP A 272 1 O ILE A 268 N MET A 233 SHEET 5 AA2 6 ASP A 326 ARG A 331 -1 O PHE A 329 N PHE A 269 SHEET 6 AA2 6 VAL A 290 ASP A 292 -1 N PHE A 291 O PHE A 330 SHEET 1 AA3 2 TRP A 307 ASP A 308 0 SHEET 2 AA3 2 LYS A 322 HIS A 323 -1 O HIS A 323 N TRP A 307 SHEET 1 AA4 6 TYR B 178 THR B 182 0 SHEET 2 AA4 6 PHE B 189 LYS B 195 -1 O LEU B 194 N THR B 179 SHEET 3 AA4 6 VAL B 157 VAL B 163 -1 N VAL B 158 O LEU B 193 SHEET 4 AA4 6 ILE B 124 ASN B 130 1 N ILE B 127 O PHE B 159 SHEET 5 AA4 6 GLY B 361 VAL B 368 -1 O CYS B 364 N PHE B 126 SHEET 6 AA4 6 LEU B 337 VAL B 345 -1 N GLN B 340 O THR B 365 SHEET 1 AA5 6 LYS B 200 PRO B 208 0 SHEET 2 AA5 6 ASN B 217 LEU B 225 -1 O CYS B 220 N GLU B 205 SHEET 3 AA5 6 ASN B 228 SER B 235 -1 O PHE B 230 N VAL B 223 SHEET 4 AA5 6 THR B 266 ASP B 272 1 O ILE B 268 N MET B 233 SHEET 5 AA5 6 ASP B 326 ARG B 331 -1 O PHE B 329 N PHE B 269 SHEET 6 AA5 6 PHE B 291 ASP B 292 -1 N PHE B 291 O PHE B 330 SHEET 1 AA6 2 TRP B 307 ASP B 308 0 SHEET 2 AA6 2 LYS B 322 HIS B 323 -1 O HIS B 323 N TRP B 307 LINK OE2 GLU A 162 MN MN A 401 1555 1555 2.16 LINK MN MN A 401 O HOH A 516 1555 1555 2.19 LINK MN MN A 401 O HOH A 534 1555 1555 2.19 LINK MN MN A 401 O HOH A 546 1555 1555 2.25 LINK MN MN A 401 OP2 DC D 1 1555 1555 2.16 LINK MN MN A 401 O HOH D 106 1555 1555 2.25 LINK OE2 GLU B 162 MN MN B 403 1555 1555 2.12 LINK MN MN B 403 O HOH B 513 1555 1555 2.17 LINK MN MN B 403 O HOH B 528 1555 1555 2.20 LINK MN MN B 403 O HOH B 532 1555 1555 2.21 LINK MN MN B 403 OP2 DC C 1 1555 1555 2.10 LINK MN MN B 403 O HOH C 106 1555 1555 2.23 SITE 1 AC1 6 GLU A 162 HOH A 516 HOH A 534 HOH A 546 SITE 2 AC1 6 DC D 1 HOH D 106 SITE 1 AC2 5 HOH A 678 PHE B 201 HOH B 502 HOH B 630 SITE 2 AC2 5 HOH B 644 SITE 1 AC3 6 CYS B 149 TYR B 153 VAL B 345 GLY B 346 SITE 2 AC3 6 LEU B 347 HOH B 657 SITE 1 AC4 6 GLU B 162 HOH B 513 HOH B 528 HOH B 532 SITE 2 AC4 6 DC C 1 HOH C 106 CRYST1 54.592 68.521 166.899 90.00 90.00 90.00 P 21 21 21 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 0.018318 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014594 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005992 0.00000