HEADER HYDROLASE/DNA 07-MAR-16 5INL TITLE MOUSE TDP2 REACTION PRODUCT (5'-PHOSPHORYLATED DNA)-MG2+ COMPLEX WITH TITLE 2 DEOXYADENOSINE 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*AP*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,C.K.VILAS,R.S.WILLIAMS REVDAT 5 27-SEP-23 5INL 1 LINK REVDAT 4 18-DEC-19 5INL 1 REMARK REVDAT 3 20-SEP-17 5INL 1 JRNL REMARK REVDAT 2 18-MAY-16 5INL 1 JRNL REVDAT 1 27-APR-16 5INL 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. 1.55 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 91871 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.131 REMARK 3 R VALUE (WORKING SET) : 0.129 REMARK 3 FREE R VALUE : 0.168 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 4604 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 34.0862 - 4.8158 0.98 3148 175 0.1752 0.1838 REMARK 3 2 4.8158 - 3.8241 1.00 3060 146 0.1239 0.1362 REMARK 3 3 3.8241 - 3.3412 1.00 3014 166 0.1252 0.1694 REMARK 3 4 3.3412 - 3.0359 1.00 2953 180 0.1334 0.1670 REMARK 3 5 3.0359 - 2.8184 1.00 3011 148 0.1436 0.1791 REMARK 3 6 2.8184 - 2.6523 1.00 2969 156 0.1323 0.1955 REMARK 3 7 2.6523 - 2.5195 1.00 2946 157 0.1267 0.1508 REMARK 3 8 2.5195 - 2.4099 1.00 2968 158 0.1259 0.1704 REMARK 3 9 2.4099 - 2.3171 1.00 2950 150 0.1205 0.1853 REMARK 3 10 2.3171 - 2.2372 1.00 2951 151 0.1171 0.1717 REMARK 3 11 2.2372 - 2.1672 1.00 2972 151 0.1104 0.1682 REMARK 3 12 2.1672 - 2.1053 1.00 2929 150 0.1077 0.1381 REMARK 3 13 2.1053 - 2.0499 1.00 2940 146 0.1068 0.1522 REMARK 3 14 2.0499 - 1.9999 1.00 2957 148 0.1025 0.1513 REMARK 3 15 1.9999 - 1.9544 1.00 2917 156 0.1030 0.1679 REMARK 3 16 1.9544 - 1.9128 1.00 2916 168 0.1153 0.1683 REMARK 3 17 1.9128 - 1.8746 1.00 2913 150 0.1084 0.1593 REMARK 3 18 1.8746 - 1.8392 1.00 2909 169 0.0998 0.1503 REMARK 3 19 1.8392 - 1.8064 1.00 2955 145 0.1006 0.1451 REMARK 3 20 1.8064 - 1.7757 1.00 2920 144 0.0999 0.1712 REMARK 3 21 1.7757 - 1.7471 1.00 2935 159 0.1043 0.1372 REMARK 3 22 1.7471 - 1.7202 1.00 2925 160 0.1059 0.1685 REMARK 3 23 1.7202 - 1.6949 1.00 2882 162 0.1181 0.1923 REMARK 3 24 1.6949 - 1.6710 1.00 2922 154 0.1347 0.1941 REMARK 3 25 1.6710 - 1.6485 1.00 2928 131 0.1437 0.2099 REMARK 3 26 1.6485 - 1.6271 1.00 2928 162 0.1472 0.1762 REMARK 3 27 1.6271 - 1.6067 0.97 2793 122 0.1570 0.2206 REMARK 3 28 1.6067 - 1.5874 0.94 2767 159 0.1685 0.2110 REMARK 3 29 1.5874 - 1.5689 0.92 2597 152 0.1986 0.2329 REMARK 3 30 1.5689 - 1.5513 0.78 2292 129 0.2199 0.2677 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 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) : 15.340 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.51 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.17 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 : 0.005 4786 REMARK 3 ANGLE : 0.848 6600 REMARK 3 CHIRALITY : 0.054 736 REMARK 3 PLANARITY : 0.006 791 REMARK 3 DIHEDRAL : 17.026 1867 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 5INL 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_1000217735. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-AUG-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 91961 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 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 (%) : 99.0 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.58800 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 (%): 51.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14% PEG3350, 100MM HEPES, 200MM NAOAC, REMARK 280 25 MM MAGNESIUM ACETATE, PH 7, 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 27.45150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 83.90250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.52550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 83.90250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.45150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.52550 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: 4010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 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 GLU A 333 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 615 O HOH A 812 1.94 REMARK 500 O HOH D 121 O HOH D 127 2.07 REMARK 500 O HOH A 593 O HOH A 677 2.14 REMARK 500 REMARK 500 REMARK: NULL 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 O HOH A 703 O HOH B 555 1465 2.06 REMARK 500 O HOH A 549 O HOH A 765 4445 2.14 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 DA C 1 O4' - C1' - N9 ANGL. DEV. = 1.9 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 240 152.02 85.07 REMARK 500 GLU B 238 130.74 -39.44 REMARK 500 THR B 240 155.88 85.05 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 856 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH A 857 DISTANCE = 6.48 ANGSTROMS REMARK 525 HOH A 858 DISTANCE = 6.78 ANGSTROMS REMARK 525 HOH B 775 DISTANCE = 6.04 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 MG A 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 162 OE2 REMARK 620 2 HOH A 519 O 88.5 REMARK 620 3 HOH A 523 O 84.9 92.9 REMARK 620 4 HOH A 550 O 173.7 89.3 89.3 REMARK 620 5 DA D 1 OP2 94.0 175.1 91.5 88.6 REMARK 620 6 HOH D 117 O 90.6 89.4 174.9 95.3 86.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 404 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 535 O REMARK 620 2 GLN B 340 OE1 84.7 REMARK 620 3 HOH B 585 O 82.4 92.9 REMARK 620 4 HOH B 704 O 74.8 94.9 155.1 REMARK 620 5 HOH B 704 O 165.4 80.7 97.8 106.8 REMARK 620 6 HOH B 754 O 81.9 166.6 85.8 81.2 112.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 162 OE2 REMARK 620 2 HOH B 527 O 89.1 REMARK 620 3 HOH B 533 O 85.2 92.4 REMARK 620 4 HOH B 556 O 175.9 90.0 90.8 REMARK 620 5 DA C 1 OP2 93.2 173.7 93.7 88.1 REMARK 620 6 HOH C 120 O 89.6 88.9 174.7 94.4 85.2 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG 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 PEG B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 404 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5INQ RELATED DB: PDB REMARK 900 RELATED ID: 5INK RELATED DB: PDB REMARK 900 RELATED ID: 5INP RELATED DB: PDB REMARK 900 RELATED ID: 5INO RELATED DB: PDB REMARK 900 RELATED ID: 5INN RELATED DB: PDB REMARK 900 RELATED ID: 5INM RELATED DB: PDB DBREF 5INL A 118 370 UNP Q9JJX7 TYDP2_MOUSE 118 370 DBREF 5INL B 118 370 UNP Q9JJX7 TYDP2_MOUSE 118 370 DBREF 5INL C 1 9 PDB 5INL 5INL 1 9 DBREF 5INL D 1 9 PDB 5INL 5INL 1 9 SEQADV 5INL SER A 115 UNP Q9JJX7 EXPRESSION TAG SEQADV 5INL LYS A 116 UNP Q9JJX7 EXPRESSION TAG SEQADV 5INL GLY A 117 UNP Q9JJX7 EXPRESSION TAG SEQADV 5INL SER B 115 UNP Q9JJX7 EXPRESSION TAG SEQADV 5INL LYS B 116 UNP Q9JJX7 EXPRESSION TAG SEQADV 5INL 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 DA DC DG DA DA DT DT DC DG SEQRES 1 D 9 DA DC DG DA DA DT DT DC DG HET MG A 401 1 HET MG B 401 1 HET EPE B 402 15 HET PEG B 403 7 HET MG B 404 1 HETNAM MG MAGNESIUM ION HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN EPE HEPES FORMUL 5 MG 3(MG 2+) FORMUL 7 EPE C8 H18 N2 O4 S FORMUL 8 PEG C4 H10 O3 FORMUL 10 HOH *700(H2 O) HELIX 1 AA1 LEU A 118 SER A 121 5 4 HELIX 2 AA2 ASN A 138 SER A 154 1 17 HELIX 3 AA3 ILE A 164 ALA A 175 1 12 HELIX 4 AA4 THR A 240 GLU A 242 5 3 HELIX 5 AA5 HIS A 243 ALA A 261 1 19 HELIX 6 AA6 ARG A 276 GLY A 284 1 9 HELIX 7 AA7 ALA A 293 LEU A 297 1 5 HELIX 8 AA8 PRO A 300 GLN A 304 5 5 HELIX 9 AA9 ASN B 138 SER B 154 1 17 HELIX 10 AB1 ILE B 164 ALA B 175 1 12 HELIX 11 AB2 THR B 240 GLU B 242 5 3 HELIX 12 AB3 HIS B 243 GLN B 259 1 17 HELIX 13 AB4 ARG B 276 GLY B 284 1 9 HELIX 14 AB5 ALA B 293 LEU B 297 1 5 HELIX 15 AB6 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 LEU A 194 N THR A 179 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 ASP A 343 O LEU A 363 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 LEU A 232 N VAL A 221 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 LEU B 160 O ALA B 191 SHEET 4 AA4 6 THR B 123 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 VAL B 199 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 LEU B 232 N VAL B 221 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 MG MG A 401 1555 1555 2.08 LINK MG MG A 401 O HOH A 519 1555 1555 2.06 LINK MG MG A 401 O HOH A 523 1555 1555 2.09 LINK MG MG A 401 O HOH A 550 1555 1555 2.09 LINK MG MG A 401 OP2 DA D 1 1555 1555 2.09 LINK MG MG A 401 O HOH D 117 1555 1555 2.15 LINK O HOH A 535 MG MG B 404 3545 1555 2.94 LINK OE2 GLU B 162 MG MG B 401 1555 1555 2.08 LINK OE1 GLN B 340 MG MG B 404 1555 1555 2.31 LINK MG MG B 401 O HOH B 527 1555 1555 2.07 LINK MG MG B 401 O HOH B 533 1555 1555 2.06 LINK MG MG B 401 O HOH B 556 1555 1555 2.07 LINK MG MG B 401 OP2 DA C 1 1555 1555 2.08 LINK MG MG B 401 O HOH C 120 1555 1555 2.16 LINK MG MG B 404 O HOH B 585 1555 1555 2.25 LINK MG MG B 404 O AHOH B 704 1555 1555 2.14 LINK MG MG B 404 O BHOH B 704 1555 1555 1.95 LINK MG MG B 404 O HOH B 754 1555 1555 2.14 SITE 1 AC1 6 GLU A 162 HOH A 519 HOH A 523 HOH A 550 SITE 2 AC1 6 DA D 1 HOH D 117 SITE 1 AC2 6 GLU B 162 HOH B 527 HOH B 533 HOH B 556 SITE 2 AC2 6 DA C 1 HOH C 120 SITE 1 AC3 8 CYS B 149 LEU B 152 TYR B 153 VAL B 345 SITE 2 AC3 8 GLY B 346 LEU B 347 GLU B 348 HOH B 687 SITE 1 AC4 3 ILE B 180 HOH B 510 HOH B 600 SITE 1 AC5 5 HOH A 535 GLN B 340 HOH B 585 HOH B 704 SITE 2 AC5 5 HOH B 754 CRYST1 54.903 69.051 167.805 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 0.018214 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014482 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005959 0.00000