HEADER HYDROLASE/DNA 22-JUN-12 4FPV TITLE CRYSTAL STRUCTURE OF D. RERIO TDP2 COMPLEXED WITH SINGLE STRAND DNA TITLE 2 PRODUCT COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSYL-DNA PHOSPHODIESTERASE 2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 113-369; COMPND 5 SYNONYM: TYR-DNA PHOSPHODIESTERASE 2, 5'-TYROSYL-DNA COMPND 6 PHOSPHODIESTERASE, 5'-TYR-DNA PHOSPHODIESTERASE, TRAF AND TNF COMPND 7 RECEPTOR-ASSOCIATED PROTEIN HOMOLOG; COMPND 8 EC: 3.1.4.-; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: DNA (5'-D(P*TP*GP*CP*AP*G)-3'); COMPND 12 CHAIN: C; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: LEOPARD DANIO,ZEBRA DANIO,ZEBRA FISH; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 GENE: TDP2, TTRAP, TTRAPL, SI:CH211-81E5.5, SI:DKEY-218N20.5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 10 ORGANISM_TAXID: 7955; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS 5'-PHOSPHOTYROSYL-DNA DIESTERASE, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.SHI,K.KURAHASHI,H.AIHARA REVDAT 5 13-MAR-24 4FPV 1 COMPND SOURCE REVDAT 4 28-FEB-24 4FPV 1 REMARK LINK REVDAT 3 15-NOV-17 4FPV 1 REMARK REVDAT 2 02-JAN-13 4FPV 1 JRNL REVDAT 1 31-OCT-12 4FPV 0 JRNL AUTH K.SHI,K.KURAHASHI,R.GAO,S.E.TSUTAKAWA,J.A.TAINER,Y.POMMIER, JRNL AUTH 2 H.AIHARA JRNL TITL STRUCTURAL BASIS FOR RECOGNITION OF 5'-PHOSPHOTYROSINE JRNL TITL 2 ADDUCTS BY TDP2. JRNL REF NAT.STRUCT.MOL.BIOL. V. 19 1372 2012 JRNL REFN ISSN 1545-9993 JRNL PMID 23104058 JRNL DOI 10.1038/NSMB.2423 REMARK 2 REMARK 2 RESOLUTION. 1.73 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.73 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.15 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 56104 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) : 0.159 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2979 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.73 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.78 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3587 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.81 REMARK 3 BIN R VALUE (WORKING SET) : 0.2980 REMARK 3 BIN FREE R VALUE SET COUNT : 184 REMARK 3 BIN FREE R VALUE : 0.3130 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4047 REMARK 3 NUCLEIC ACID ATOMS : 105 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 496 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.55 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.105 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.107 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.067 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.047 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.954 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4424 ; 0.024 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6036 ; 2.271 ; 1.937 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 544 ; 6.775 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 195 ;34.315 ;23.128 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 772 ;14.662 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 35 ;21.540 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 659 ; 0.183 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3343 ; 0.013 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4FPV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JUN-12. REMARK 100 THE DEPOSITION ID IS D_1000073205. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-DEC-11 REMARK 200 TEMPERATURE (KELVIN) : 96 REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60160 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.730 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.73 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NONE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 3,350 AND 0.2M SODIUM REMARK 280 TARTRATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, PH 5 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 29.03500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.25300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.51050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.25300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.03500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.51050 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 300 REMARK: AS IN THE ASYMMETRIC UNIT 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 THR A 113 REMARK 465 ALA A 114 REMARK 465 LYS A 115 REMARK 465 SER A 116 REMARK 465 GLU A 117 REMARK 465 VAL A 118 REMARK 465 GLU A 119 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DT C 1 P DT C 1 OP3 -0.117 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 153 56.29 33.80 REMARK 500 SER A 225 53.02 37.73 REMARK 500 GLU A 237 129.18 -39.24 REMARK 500 CYS A 239 138.20 94.39 REMARK 500 ASN A 273 18.71 54.41 REMARK 500 ASP A 276 -75.91 -38.36 REMARK 500 ALA A 277 -13.02 73.16 REMARK 500 ASN A 281 6.00 -67.60 REMARK 500 ARG A 323 72.62 -103.38 REMARK 500 MET A 348 46.92 -92.75 REMARK 500 THR B 153 59.10 31.96 REMARK 500 CYS B 239 141.82 84.96 REMARK 500 PRO B 261 129.23 -39.09 REMARK 500 ASN B 273 18.96 54.10 REMARK 500 ALA B 277 -1.70 76.18 REMARK 500 ASP B 341 -60.04 -106.04 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 MG C 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 161 OE2 REMARK 620 2 HOH A 716 O 76.7 REMARK 620 3 HOH A 717 O 153.6 77.1 REMARK 620 4 HOH A 718 O 79.9 73.8 89.4 REMARK 620 5 DT C 1 OP1 106.2 160.3 97.3 87.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 401 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 341 OD2 REMARK 620 2 THR A 366 OG1 107.1 REMARK 620 3 HOH A 722 O 135.3 116.8 REMARK 620 N 1 2 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 161 OE2 REMARK 620 2 HOH B 527 O 84.9 REMARK 620 3 HOH B 632 O 84.4 66.3 REMARK 620 4 HOH B 648 O 170.4 85.5 91.2 REMARK 620 5 HOH B 649 O 115.3 87.2 146.1 64.7 REMARK 620 6 HOH B 727 O 101.9 170.6 120.4 87.7 83.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 402 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 341 OD1 REMARK 620 2 HOH B 713 O 90.4 REMARK 620 3 HOH B 741 O 103.7 134.0 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 NA A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4F1H RELATED DB: PDB REMARK 900 RELATED ID: 4F1I RELATED DB: PDB REMARK 900 RELATED ID: 4FVA RELATED DB: PDB REMARK 900 RELATED ID: 4GEW RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 A LARGE PORTION OF THE N-TERMINAL WAS NOT OBSERVED IN THE ELECTRON REMARK 999 DENSITY DBREF 4FPV A 113 369 UNP Q5XJA0 TYDP2_DANRE 113 369 DBREF 4FPV B 113 369 UNP Q5XJA0 TYDP2_DANRE 113 369 DBREF 4FPV C 1 5 PDB 4FPV 4FPV 1 5 SEQRES 1 A 257 THR ALA LYS SER GLU VAL GLU ASP SER LYS LEU SER ILE SEQRES 2 A 257 ILE SER TRP ASN VAL ASP GLY LEU ASP THR LEU ASN LEU SEQRES 3 A 257 ALA ASP ARG ALA ARG GLY LEU CYS SER TYR LEU ALA LEU SEQRES 4 A 257 TYR THR PRO ASP VAL VAL PHE LEU GLN GLU LEU ILE PRO SEQRES 5 A 257 ALA TYR VAL GLN TYR LEU LYS LYS ARG ALA VAL SER TYR SEQRES 6 A 257 LEU PHE PHE GLU GLY SER ASP ASP GLY TYR PHE THR GLY SEQRES 7 A 257 ILE MET LEU ARG LYS SER ARG VAL LYS PHE LEU GLU SER SEQRES 8 A 257 GLU ILE ILE CYS PHE PRO THR THR GLN MET MET ARG ASN SEQRES 9 A 257 LEU LEU ILE ALA GLN VAL THR PHE SER GLY GLN LYS LEU SEQRES 10 A 257 TYR LEU MET THR SER HIS LEU GLU SER CYS LYS ASN GLN SEQRES 11 A 257 SER GLN GLU ARG THR LYS GLN LEU ARG VAL VAL LEU GLN SEQRES 12 A 257 LYS ILE LYS GLU ALA PRO GLU ASP ALA ILE VAL ILE PHE SEQRES 13 A 257 ALA GLY ASP THR ASN LEU ARG ASP ALA GLU VAL ALA ASN SEQRES 14 A 257 VAL GLY GLY LEU PRO ALA GLY VAL CYS ASP VAL TRP GLU SEQRES 15 A 257 GLN LEU GLY LYS GLN GLU HIS CYS ARG TYR THR TRP ASP SEQRES 16 A 257 THR LYS ALA ASN SER ASN LYS THR VAL PRO TYR VAL SER SEQRES 17 A 257 ARG CYS ARG PHE ASP ARG ILE PHE LEU ARG SER ALA LYS SEQRES 18 A 257 THR ALA PRO PRO VAL THR PRO ASP HIS MET ALA LEU ILE SEQRES 19 A 257 GLY MET GLU LYS LEU ASP CYS GLY ARG TYR THR SER ASP SEQRES 20 A 257 HIS TRP GLY ILE TYR CYS THR PHE ASN THR SEQRES 1 B 257 THR ALA LYS SER GLU VAL GLU ASP SER LYS LEU SER ILE SEQRES 2 B 257 ILE SER TRP ASN VAL ASP GLY LEU ASP THR LEU ASN LEU SEQRES 3 B 257 ALA ASP ARG ALA ARG GLY LEU CYS SER TYR LEU ALA LEU SEQRES 4 B 257 TYR THR PRO ASP VAL VAL PHE LEU GLN GLU LEU ILE PRO SEQRES 5 B 257 ALA TYR VAL GLN TYR LEU LYS LYS ARG ALA VAL SER TYR SEQRES 6 B 257 LEU PHE PHE GLU GLY SER ASP ASP GLY TYR PHE THR GLY SEQRES 7 B 257 ILE MET LEU ARG LYS SER ARG VAL LYS PHE LEU GLU SER SEQRES 8 B 257 GLU ILE ILE CYS PHE PRO THR THR GLN MET MET ARG ASN SEQRES 9 B 257 LEU LEU ILE ALA GLN VAL THR PHE SER GLY GLN LYS LEU SEQRES 10 B 257 TYR LEU MET THR SER HIS LEU GLU SER CYS LYS ASN GLN SEQRES 11 B 257 SER GLN GLU ARG THR LYS GLN LEU ARG VAL VAL LEU GLN SEQRES 12 B 257 LYS ILE LYS GLU ALA PRO GLU ASP ALA ILE VAL ILE PHE SEQRES 13 B 257 ALA GLY ASP THR ASN LEU ARG ASP ALA GLU VAL ALA ASN SEQRES 14 B 257 VAL GLY GLY LEU PRO ALA GLY VAL CYS ASP VAL TRP GLU SEQRES 15 B 257 GLN LEU GLY LYS GLN GLU HIS CYS ARG TYR THR TRP ASP SEQRES 16 B 257 THR LYS ALA ASN SER ASN LYS THR VAL PRO TYR VAL SER SEQRES 17 B 257 ARG CYS ARG PHE ASP ARG ILE PHE LEU ARG SER ALA LYS SEQRES 18 B 257 THR ALA PRO PRO VAL THR PRO ASP HIS MET ALA LEU ILE SEQRES 19 B 257 GLY MET GLU LYS LEU ASP CYS GLY ARG TYR THR SER ASP SEQRES 20 B 257 HIS TRP GLY ILE TYR CYS THR PHE ASN THR SEQRES 1 C 5 DT DG DC DA DG HET NA A 401 1 HET GOL A 402 6 HET MG B 401 1 HET NA B 402 1 HET GOL B 403 6 HET GOL B 404 6 HET MG C 101 1 HETNAM NA SODIUM ION HETNAM GOL GLYCEROL HETNAM MG MAGNESIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 NA 2(NA 1+) FORMUL 5 GOL 3(C3 H8 O3) FORMUL 6 MG 2(MG 2+) FORMUL 11 HOH *496(H2 O) HELIX 1 1 ASN A 137 THR A 153 1 17 HELIX 2 2 ILE A 163 ALA A 174 1 12 HELIX 3 3 CYS A 239 ASN A 241 5 3 HELIX 4 4 GLN A 242 ALA A 260 1 19 HELIX 5 5 VAL A 279 GLY A 283 5 5 HELIX 6 6 VAL A 292 LEU A 296 1 5 HELIX 7 7 GLN A 299 ARG A 303 5 5 HELIX 8 8 ALA B 114 SER B 121 1 8 HELIX 9 9 ASN B 137 THR B 153 1 17 HELIX 10 10 ILE B 163 ALA B 174 1 12 HELIX 11 11 CYS B 239 ASN B 241 5 3 HELIX 12 12 GLN B 242 ALA B 260 1 19 HELIX 13 13 VAL B 279 GLY B 283 5 5 HELIX 14 14 VAL B 292 LEU B 296 1 5 HELIX 15 15 GLN B 299 ARG B 303 5 5 SHEET 1 A 6 TYR A 177 GLU A 181 0 SHEET 2 A 6 PHE A 188 ARG A 194 -1 O LEU A 193 N LEU A 178 SHEET 3 A 6 VAL A 156 LEU A 162 -1 N LEU A 162 O PHE A 188 SHEET 4 A 6 LEU A 123 ASN A 129 1 N ILE A 126 O PHE A 158 SHEET 5 A 6 GLY A 362 ASN A 368 -1 O ILE A 363 N SER A 127 SHEET 6 A 6 THR A 339 ILE A 346 -1 N THR A 339 O ASN A 368 SHEET 1 B 6 VAL A 198 CYS A 207 0 SHEET 2 B 6 ASN A 216 PHE A 224 -1 O GLN A 221 N GLU A 202 SHEET 3 B 6 GLN A 227 THR A 233 -1 O LEU A 231 N ALA A 220 SHEET 4 B 6 ALA A 264 ASP A 271 1 O ILE A 265 N TYR A 230 SHEET 5 B 6 ASP A 325 ARG A 330 -1 O PHE A 328 N PHE A 268 SHEET 6 B 6 VAL A 289 ASP A 291 -1 N CYS A 290 O LEU A 329 SHEET 1 C 2 TRP A 306 ASP A 307 0 SHEET 2 C 2 ARG A 321 CYS A 322 -1 O CYS A 322 N TRP A 306 SHEET 1 D 6 TYR B 177 GLU B 181 0 SHEET 2 D 6 PHE B 188 ARG B 194 -1 O LEU B 193 N LEU B 178 SHEET 3 D 6 VAL B 156 LEU B 162 -1 N LEU B 159 O GLY B 190 SHEET 4 D 6 LEU B 123 ASN B 129 1 N ILE B 126 O PHE B 158 SHEET 5 D 6 GLY B 362 PHE B 367 -1 O ILE B 363 N SER B 127 SHEET 6 D 6 PRO B 340 ILE B 346 -1 N ASP B 341 O THR B 366 SHEET 1 E 6 LYS B 199 CYS B 207 0 SHEET 2 E 6 ASN B 216 PHE B 224 -1 O GLN B 221 N GLU B 202 SHEET 3 E 6 GLN B 227 THR B 233 -1 O LEU B 231 N ALA B 220 SHEET 4 E 6 ALA B 264 ASP B 271 1 O ILE B 265 N TYR B 230 SHEET 5 E 6 ASP B 325 ARG B 330 -1 O ARG B 330 N VAL B 266 SHEET 6 E 6 VAL B 289 ASP B 291 -1 N CYS B 290 O LEU B 329 SHEET 1 F 2 TRP B 306 ASP B 307 0 SHEET 2 F 2 ARG B 321 CYS B 322 -1 O CYS B 322 N TRP B 306 LINK OE2 GLU A 161 MG MG C 101 1555 1555 2.85 LINK OD2 ASP A 341 NA NA A 401 1555 1555 2.41 LINK OG1 THR A 366 NA NA A 401 1555 1555 2.55 LINK NA NA A 401 O HOH A 722 1555 1555 2.43 LINK O HOH A 716 MG MG C 101 1555 1555 2.21 LINK O HOH A 717 MG MG C 101 1555 1555 2.36 LINK O HOH A 718 MG MG C 101 1555 1555 2.45 LINK OE2 GLU B 161 MG MG B 401 1555 1555 2.39 LINK OD1 ASP B 341 NA NA B 402 1555 1555 2.28 LINK MG MG B 401 O HOH B 527 1555 1555 2.47 LINK MG MG B 401 O HOH B 632 1555 1555 2.17 LINK MG MG B 401 O HOH B 648 1555 1555 2.29 LINK MG MG B 401 O BHOH B 649 1555 1555 2.59 LINK MG MG B 401 O HOH B 727 1555 1555 2.28 LINK NA NA B 402 O HOH B 713 1555 1555 2.39 LINK NA NA B 402 O HOH B 741 1555 1555 2.64 LINK OP1 DT C 1 MG MG C 101 1555 1555 2.08 SITE 1 AC1 4 LYS A 122 ASP A 341 THR A 366 HOH A 722 SITE 1 AC2 7 ASP A 276 ALA A 277 ARG A 323 ARG A 326 SITE 2 AC2 7 HOH A 542 HOH A 672 HOH A 673 SITE 1 AC3 6 GLU B 161 HOH B 527 HOH B 632 HOH B 648 SITE 2 AC3 6 HOH B 649 HOH B 727 SITE 1 AC4 4 ASP B 341 ASN B 368 HOH B 713 HOH B 741 SITE 1 AC5 7 ARG B 275 ASP B 276 ARG B 303 ARG B 323 SITE 2 AC5 7 ARG B 326 HOH B 661 HOH B 689 SITE 1 AC6 5 GLU B 181 SER B 203 GLU B 204 HOH B 566 SITE 2 AC6 5 HOH B 567 SITE 1 AC7 5 GLU A 161 HOH A 716 HOH A 717 HOH A 718 SITE 2 AC7 5 DT C 1 CRYST1 58.070 95.021 104.506 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 0.017221 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010524 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009569 0.00000