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 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,VAGIN,DODSON 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 DT C 1 OP1 REMARK 620 2 HOH A 716 O 160.3 REMARK 620 3 HOH A 717 O 97.3 77.1 REMARK 620 4 HOH A 718 O 87.3 73.8 89.4 REMARK 620 5 GLU A 161 OE2 106.2 76.7 153.6 79.9 REMARK 620 N 1 2 3 4 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 HOH B 632 O REMARK 620 2 HOH B 727 O 120.4 REMARK 620 3 HOH B 648 O 91.2 87.7 REMARK 620 4 GLU B 161 OE2 84.4 101.9 170.4 REMARK 620 5 HOH B 527 O 66.3 170.6 85.5 84.9 REMARK 620 6 HOH B 649 O 146.1 83.9 64.7 115.3 87.2 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 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 HOH A 722 O 135.3 REMARK 620 3 THR A 366 OG1 107.1 116.8 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 OP1 DT C 1 MG MG C 101 1555 1555 2.08 LINK MG MG B 401 O HOH B 632 1555 1555 2.17 LINK MG MG C 101 O HOH A 716 1555 1555 2.21 LINK MG MG B 401 O HOH B 727 1555 1555 2.28 LINK OD1 ASP B 341 NA NA B 402 1555 1555 2.28 LINK MG MG B 401 O HOH B 648 1555 1555 2.29 LINK MG MG C 101 O HOH A 717 1555 1555 2.36 LINK NA NA B 402 O HOH B 713 1555 1555 2.39 LINK OE2 GLU B 161 MG MG B 401 1555 1555 2.39 LINK OD2 ASP A 341 NA NA A 401 1555 1555 2.41 LINK NA NA A 401 O HOH A 722 1555 1555 2.43 LINK MG MG C 101 O HOH A 718 1555 1555 2.45 LINK MG MG B 401 O HOH B 527 1555 1555 2.47 LINK OG1 THR A 366 NA NA A 401 1555 1555 2.55 LINK MG MG B 401 O BHOH B 649 1555 1555 2.59 LINK NA NA B 402 O HOH B 741 1555 1555 2.64 LINK OE2 GLU A 161 MG MG C 101 1555 1555 2.85 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 MASTER 379 0 7 15 28 0 12 6 0 0 0 41 END