HEADER HYDROLASE 05-MAY-17 5NWA TITLE CRYSTAL STRUCTURE OF THE COMPLEX OF TDP1 WITH DUPLEX DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSYL-DNA PHOSPHODIESTERASE 1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: DELTA 1-148; COMPND 5 SYNONYM: TYR-DNA PHOSPHODIESTERASE 1; COMPND 6 EC: 3.1.4.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(P*AP*AP*TP*GP*CP*GP*CP*AP*TP*TP*A)-3'); COMPND 10 CHAIN: C; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TDP1; 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: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630; SOURCE 13 OTHER_DETAILS: IDT DNA SYNTHESIS KEYWDS PROTEIN-DNA COMPLEX, DNA REPAIR, NUCLEOSIDASE, PHOSPHOTYROSINE KEYWDS 2 DIESTERASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.M.RICHARDSON,E.RUKSENAITE,E.R.MORRIS REVDAT 4 17-JAN-24 5NWA 1 REMARK REVDAT 3 16-OCT-19 5NWA 1 REMARK REVDAT 2 17-JAN-18 5NWA 1 JRNL REVDAT 1 10-JAN-18 5NWA 0 JRNL AUTH F.J.FLETT,E.RUKSENAITE,L.A.ARMSTRONG,S.BHARATI,R.CARLONI, JRNL AUTH 2 E.R.MORRIS,C.L.MACKAY,H.INTERTHAL,J.M.RICHARDSON JRNL TITL STRUCTURAL BASIS FOR DNA 3'-END PROCESSING BY HUMAN JRNL TITL 2 TYROSYL-DNA PHOSPHODIESTERASE 1. JRNL REF NAT COMMUN V. 9 24 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 29295983 JRNL DOI 10.1038/S41467-017-02530-Z REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0107 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 99.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 17951 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) : 0.253 REMARK 3 R VALUE (WORKING SET) : 0.250 REMARK 3 FREE R VALUE : 0.306 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 952 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) : 3.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.28 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1270 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.3760 REMARK 3 BIN FREE R VALUE SET COUNT : 84 REMARK 3 BIN FREE R VALUE : 0.4070 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6987 REMARK 3 NUCLEIC ACID ATOMS : 199 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 73.95 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.52000 REMARK 3 B22 (A**2) : -9.63000 REMARK 3 B33 (A**2) : 6.11000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.634 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.570 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 39.876 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.912 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.869 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7435 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6872 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10141 ; 1.372 ; 1.922 REMARK 3 BOND ANGLES OTHERS (DEGREES): 15903 ; 0.954 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 867 ; 7.110 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 303 ;38.437 ;23.663 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1190 ;18.000 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;16.411 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1062 ; 0.074 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8121 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1739 ; 0.001 ; 0.020 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 : NULL 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: MOLECULAR REPLACEMENT REMARK 4 REMARK 4 5NWA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1200004831. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUL-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92819 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19558 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 99.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER, PHASER REMARK 200 STARTING MODEL: 1JY1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M AMMONIUM SULPHATE, 0.1M HEPES, REMARK 280 25% W/V PEG 8000, PH 7.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 54.59550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 99.09600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 54.59550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 99.09600 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 APPLY THE FOLLOWING TO CHAINS: A, 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 109.19100 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 124 REMARK 465 GLY A 125 REMARK 465 SER A 126 REMARK 465 SER A 127 REMARK 465 HIS A 128 REMARK 465 HIS A 129 REMARK 465 HIS A 130 REMARK 465 HIS A 131 REMARK 465 HIS A 132 REMARK 465 HIS A 133 REMARK 465 SER A 134 REMARK 465 SER A 135 REMARK 465 GLY A 136 REMARK 465 LEU A 137 REMARK 465 VAL A 138 REMARK 465 PRO A 139 REMARK 465 ARG A 140 REMARK 465 GLY A 141 REMARK 465 SER A 142 REMARK 465 HIS A 143 REMARK 465 MET A 144 REMARK 465 LEU A 145 REMARK 465 GLU A 146 REMARK 465 ASP A 147 REMARK 465 PRO A 148 REMARK 465 GLY A 149 REMARK 465 GLU A 150 REMARK 465 GLY A 151 REMARK 465 GLN A 152 REMARK 465 ASP A 153 REMARK 465 ILE A 154 REMARK 465 TRP A 155 REMARK 465 ASP A 156 REMARK 465 MET A 157 REMARK 465 LEU A 158 REMARK 465 ASP A 159 REMARK 465 PRO A 430 REMARK 465 GLY A 431 REMARK 465 LYS A 432 REMARK 465 ALA A 561 REMARK 465 GLY A 562 REMARK 465 SER A 563 REMARK 465 GLN A 564 REMARK 465 GLU A 565 REMARK 465 MET B 124 REMARK 465 GLY B 125 REMARK 465 SER B 126 REMARK 465 SER B 127 REMARK 465 HIS B 128 REMARK 465 HIS B 129 REMARK 465 HIS B 130 REMARK 465 HIS B 131 REMARK 465 HIS B 132 REMARK 465 HIS B 133 REMARK 465 SER B 134 REMARK 465 SER B 135 REMARK 465 GLY B 136 REMARK 465 LEU B 137 REMARK 465 VAL B 138 REMARK 465 PRO B 139 REMARK 465 ARG B 140 REMARK 465 GLY B 141 REMARK 465 SER B 142 REMARK 465 HIS B 143 REMARK 465 MET B 144 REMARK 465 LEU B 145 REMARK 465 GLU B 146 REMARK 465 ASP B 147 REMARK 465 PRO B 148 REMARK 465 GLY B 149 REMARK 465 GLU B 150 REMARK 465 GLY B 151 REMARK 465 GLN B 152 REMARK 465 ASP B 153 REMARK 465 ILE B 154 REMARK 465 TRP B 155 REMARK 465 ASP B 156 REMARK 465 MET B 157 REMARK 465 LEU B 158 REMARK 465 ASP B 159 REMARK 465 GLU B 426 REMARK 465 SER B 427 REMARK 465 LYS B 428 REMARK 465 THR B 429 REMARK 465 PRO B 430 REMARK 465 GLY B 431 REMARK 465 LYS B 432 REMARK 465 LYS B 558 REMARK 465 PHE B 559 REMARK 465 PHE B 560 REMARK 465 ALA B 561 REMARK 465 GLY B 562 REMARK 465 SER B 563 REMARK 465 GLN B 564 REMARK 465 GLU B 565 REMARK 465 PRO B 566 REMARK 465 MET B 567 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 THR A 429 OG1 CG2 REMARK 470 DA C -10 N9 C8 N7 C5 C6 N6 N1 REMARK 470 DA C -10 C2 N3 C4 REMARK 470 DA C 0 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DA C 0 N9 C8 N7 C5 C6 N6 N1 REMARK 470 DA C 0 C2 N3 C4 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 ARG A 232 -108.73 62.87 REMARK 500 HIS A 290 -76.65 -89.90 REMARK 500 ASN A 331 9.60 81.66 REMARK 500 TRP A 411 -63.99 -157.65 REMARK 500 SER A 414 -83.16 -90.20 REMARK 500 PRO A 461 58.74 -90.28 REMARK 500 GLN A 470 51.98 -148.06 REMARK 500 ALA A 482 53.44 -147.86 REMARK 500 ASN A 528 70.28 57.09 REMARK 500 LEU A 539 133.02 -172.63 REMARK 500 LYS A 556 91.29 -66.29 REMARK 500 MET A 567 -66.38 -123.93 REMARK 500 PRO A 607 95.57 -69.26 REMARK 500 ARG B 232 -35.36 -36.50 REMARK 500 LEU B 284 55.74 -98.55 REMARK 500 HIS B 290 -73.94 -84.17 REMARK 500 ASP B 307 126.13 -35.01 REMARK 500 ASN B 388 40.56 38.50 REMARK 500 TRP B 411 -53.15 -143.05 REMARK 500 SER B 414 -80.90 -105.50 REMARK 500 ALA B 482 56.71 -150.46 REMARK 500 PHE B 504 19.86 57.22 REMARK 500 ASN B 591 58.55 -115.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5NW9 RELATED DB: PDB REMARK 900 SIMILAR STRUCTURE WITH DIFFERENT DNA SEQUENCE DBREF 5NWA A 149 608 UNP Q9NUW8 TYDP1_HUMAN 149 608 DBREF 5NWA C -10 0 PDB 5NWA 5NWA -10 0 DBREF 5NWA B 149 608 UNP Q9NUW8 TYDP1_HUMAN 149 608 SEQADV 5NWA MET A 124 UNP Q9NUW8 INITIATING METHIONINE SEQADV 5NWA GLY A 125 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA SER A 126 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA SER A 127 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA HIS A 128 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA HIS A 129 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA HIS A 130 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA HIS A 131 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA HIS A 132 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA HIS A 133 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA SER A 134 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA SER A 135 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA GLY A 136 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA LEU A 137 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA VAL A 138 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA PRO A 139 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA ARG A 140 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA GLY A 141 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA SER A 142 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA HIS A 143 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA MET A 144 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA LEU A 145 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA GLU A 146 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA ASP A 147 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA PRO A 148 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA ASN A 322 UNP Q9NUW8 ASP 322 CONFLICT SEQADV 5NWA THR A 328 UNP Q9NUW8 MET 328 CONFLICT SEQADV 5NWA LEU A 548 UNP Q9NUW8 PHE 548 CONFLICT SEQADV 5NWA MET B 124 UNP Q9NUW8 INITIATING METHIONINE SEQADV 5NWA GLY B 125 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA SER B 126 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA SER B 127 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA HIS B 128 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA HIS B 129 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA HIS B 130 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA HIS B 131 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA HIS B 132 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA HIS B 133 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA SER B 134 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA SER B 135 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA GLY B 136 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA LEU B 137 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA VAL B 138 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA PRO B 139 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA ARG B 140 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA GLY B 141 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA SER B 142 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA HIS B 143 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA MET B 144 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA LEU B 145 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA GLU B 146 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA ASP B 147 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA PRO B 148 UNP Q9NUW8 EXPRESSION TAG SEQADV 5NWA ASN B 322 UNP Q9NUW8 ASP 322 CONFLICT SEQADV 5NWA THR B 328 UNP Q9NUW8 MET 328 CONFLICT SEQADV 5NWA LEU B 548 UNP Q9NUW8 PHE 548 CONFLICT SEQRES 1 A 485 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 485 LEU VAL PRO ARG GLY SER HIS MET LEU GLU ASP PRO GLY SEQRES 3 A 485 GLU GLY GLN ASP ILE TRP ASP MET LEU ASP LYS GLY ASN SEQRES 4 A 485 PRO PHE GLN PHE TYR LEU THR ARG VAL SER GLY VAL LYS SEQRES 5 A 485 PRO LYS TYR ASN SER GLY ALA LEU HIS ILE LYS ASP ILE SEQRES 6 A 485 LEU SER PRO LEU PHE GLY THR LEU VAL SER SER ALA GLN SEQRES 7 A 485 PHE ASN TYR CYS PHE ASP VAL ASP TRP LEU VAL LYS GLN SEQRES 8 A 485 TYR PRO PRO GLU PHE ARG LYS LYS PRO ILE LEU LEU VAL SEQRES 9 A 485 HIS GLY ASP LYS ARG GLU ALA LYS ALA HIS LEU HIS ALA SEQRES 10 A 485 GLN ALA LYS PRO TYR GLU ASN ILE SER LEU CYS GLN ALA SEQRES 11 A 485 LYS LEU ASP ILE ALA PHE GLY THR HIS HIS THR LYS MET SEQRES 12 A 485 MET LEU LEU LEU TYR GLU GLU GLY LEU ARG VAL VAL ILE SEQRES 13 A 485 HIS THR SER ASN LEU ILE HIS ALA ASP TRP HIS GLN LYS SEQRES 14 A 485 THR GLN GLY ILE TRP LEU SER PRO LEU TYR PRO ARG ILE SEQRES 15 A 485 ALA ASP GLY THR HIS LYS SER GLY GLU SER PRO THR HIS SEQRES 16 A 485 PHE LYS ALA ASN LEU ILE SER TYR LEU THR ALA TYR ASN SEQRES 17 A 485 ALA PRO SER LEU LYS GLU TRP ILE ASP VAL ILE HIS LYS SEQRES 18 A 485 HIS ASP LEU SER GLU THR ASN VAL TYR LEU ILE GLY SER SEQRES 19 A 485 THR PRO GLY ARG PHE GLN GLY SER GLN LYS ASP ASN TRP SEQRES 20 A 485 GLY HIS PHE ARG LEU LYS LYS LEU LEU LYS ASP HIS ALA SEQRES 21 A 485 SER SER MET PRO ASN ALA GLU SER TRP PRO VAL VAL GLY SEQRES 22 A 485 GLN PHE SER SER VAL GLY SER LEU GLY ALA ASP GLU SER SEQRES 23 A 485 LYS TRP LEU CYS SER GLU PHE LYS GLU SER MET LEU THR SEQRES 24 A 485 LEU GLY LYS GLU SER LYS THR PRO GLY LYS SER SER VAL SEQRES 25 A 485 PRO LEU TYR LEU ILE TYR PRO SER VAL GLU ASN VAL ARG SEQRES 26 A 485 THR SER LEU GLU GLY TYR PRO ALA GLY GLY SER LEU PRO SEQRES 27 A 485 TYR SER ILE GLN THR ALA GLU LYS GLN ASN TRP LEU HIS SEQRES 28 A 485 SER TYR PHE HIS LYS TRP SER ALA GLU THR SER GLY ARG SEQRES 29 A 485 SER ASN ALA MET PRO HIS ILE LYS THR TYR MET ARG PRO SEQRES 30 A 485 SER PRO ASP PHE SER LYS ILE ALA TRP PHE LEU VAL THR SEQRES 31 A 485 SER ALA ASN LEU SER LYS ALA ALA TRP GLY ALA LEU GLU SEQRES 32 A 485 LYS ASN GLY THR GLN LEU MET ILE ARG SER TYR GLU LEU SEQRES 33 A 485 GLY VAL LEU PHE LEU PRO SER ALA LEU GLY LEU ASP SER SEQRES 34 A 485 PHE LYS VAL LYS GLN LYS PHE PHE ALA GLY SER GLN GLU SEQRES 35 A 485 PRO MET ALA THR PHE PRO VAL PRO TYR ASP LEU PRO PRO SEQRES 36 A 485 GLU LEU TYR GLY SER LYS ASP ARG PRO TRP ILE TRP ASN SEQRES 37 A 485 ILE PRO TYR VAL LYS ALA PRO ASP THR HIS GLY ASN MET SEQRES 38 A 485 TRP VAL PRO SER SEQRES 1 C 11 DA DA DT DG DC DG DC DA DT DT DA SEQRES 1 B 485 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 485 LEU VAL PRO ARG GLY SER HIS MET LEU GLU ASP PRO GLY SEQRES 3 B 485 GLU GLY GLN ASP ILE TRP ASP MET LEU ASP LYS GLY ASN SEQRES 4 B 485 PRO PHE GLN PHE TYR LEU THR ARG VAL SER GLY VAL LYS SEQRES 5 B 485 PRO LYS TYR ASN SER GLY ALA LEU HIS ILE LYS ASP ILE SEQRES 6 B 485 LEU SER PRO LEU PHE GLY THR LEU VAL SER SER ALA GLN SEQRES 7 B 485 PHE ASN TYR CYS PHE ASP VAL ASP TRP LEU VAL LYS GLN SEQRES 8 B 485 TYR PRO PRO GLU PHE ARG LYS LYS PRO ILE LEU LEU VAL SEQRES 9 B 485 HIS GLY ASP LYS ARG GLU ALA LYS ALA HIS LEU HIS ALA SEQRES 10 B 485 GLN ALA LYS PRO TYR GLU ASN ILE SER LEU CYS GLN ALA SEQRES 11 B 485 LYS LEU ASP ILE ALA PHE GLY THR HIS HIS THR LYS MET SEQRES 12 B 485 MET LEU LEU LEU TYR GLU GLU GLY LEU ARG VAL VAL ILE SEQRES 13 B 485 HIS THR SER ASN LEU ILE HIS ALA ASP TRP HIS GLN LYS SEQRES 14 B 485 THR GLN GLY ILE TRP LEU SER PRO LEU TYR PRO ARG ILE SEQRES 15 B 485 ALA ASP GLY THR HIS LYS SER GLY GLU SER PRO THR HIS SEQRES 16 B 485 PHE LYS ALA ASN LEU ILE SER TYR LEU THR ALA TYR ASN SEQRES 17 B 485 ALA PRO SER LEU LYS GLU TRP ILE ASP VAL ILE HIS LYS SEQRES 18 B 485 HIS ASP LEU SER GLU THR ASN VAL TYR LEU ILE GLY SER SEQRES 19 B 485 THR PRO GLY ARG PHE GLN GLY SER GLN LYS ASP ASN TRP SEQRES 20 B 485 GLY HIS PHE ARG LEU LYS LYS LEU LEU LYS ASP HIS ALA SEQRES 21 B 485 SER SER MET PRO ASN ALA GLU SER TRP PRO VAL VAL GLY SEQRES 22 B 485 GLN PHE SER SER VAL GLY SER LEU GLY ALA ASP GLU SER SEQRES 23 B 485 LYS TRP LEU CYS SER GLU PHE LYS GLU SER MET LEU THR SEQRES 24 B 485 LEU GLY LYS GLU SER LYS THR PRO GLY LYS SER SER VAL SEQRES 25 B 485 PRO LEU TYR LEU ILE TYR PRO SER VAL GLU ASN VAL ARG SEQRES 26 B 485 THR SER LEU GLU GLY TYR PRO ALA GLY GLY SER LEU PRO SEQRES 27 B 485 TYR SER ILE GLN THR ALA GLU LYS GLN ASN TRP LEU HIS SEQRES 28 B 485 SER TYR PHE HIS LYS TRP SER ALA GLU THR SER GLY ARG SEQRES 29 B 485 SER ASN ALA MET PRO HIS ILE LYS THR TYR MET ARG PRO SEQRES 30 B 485 SER PRO ASP PHE SER LYS ILE ALA TRP PHE LEU VAL THR SEQRES 31 B 485 SER ALA ASN LEU SER LYS ALA ALA TRP GLY ALA LEU GLU SEQRES 32 B 485 LYS ASN GLY THR GLN LEU MET ILE ARG SER TYR GLU LEU SEQRES 33 B 485 GLY VAL LEU PHE LEU PRO SER ALA LEU GLY LEU ASP SER SEQRES 34 B 485 PHE LYS VAL LYS GLN LYS PHE PHE ALA GLY SER GLN GLU SEQRES 35 B 485 PRO MET ALA THR PHE PRO VAL PRO TYR ASP LEU PRO PRO SEQRES 36 B 485 GLU LEU TYR GLY SER LYS ASP ARG PRO TRP ILE TRP ASN SEQRES 37 B 485 ILE PRO TYR VAL LYS ALA PRO ASP THR HIS GLY ASN MET SEQRES 38 B 485 TRP VAL PRO SER HELIX 1 AA1 LYS A 175 SER A 180 1 6 HELIX 2 AA2 HIS A 184 LEU A 189 1 6 HELIX 3 AA3 SER A 190 GLY A 194 5 5 HELIX 4 AA4 ASP A 207 TYR A 215 1 9 HELIX 5 AA5 ARG A 232 ALA A 242 1 11 HELIX 6 AA6 ILE A 285 TRP A 289 5 5 HELIX 7 AA7 HIS A 318 ALA A 329 1 12 HELIX 8 AA8 ALA A 332 LYS A 344 1 13 HELIX 9 AA9 SER A 365 ASN A 369 5 5 HELIX 10 AB1 TRP A 370 ALA A 383 1 14 HELIX 11 AB2 ASN A 388 TRP A 392 5 5 HELIX 12 AB3 ASP A 407 TRP A 411 5 5 HELIX 13 AB4 SER A 414 THR A 422 1 9 HELIX 14 AB5 SER A 443 THR A 449 1 7 HELIX 15 AB6 GLY A 453 LEU A 460 5 8 HELIX 16 AB7 SER A 463 LYS A 469 1 7 HELIX 17 AB8 GLN A 470 SER A 475 5 6 HELIX 18 AB9 ALA A 482 GLY A 486 5 5 HELIX 19 AC1 SER A 518 GLY A 523 1 6 HELIX 20 AC2 PRO A 545 GLY A 549 5 5 HELIX 21 AC3 LYS B 175 ASN B 179 5 5 HELIX 22 AC4 HIS B 184 LEU B 189 1 6 HELIX 23 AC5 SER B 190 GLY B 194 5 5 HELIX 24 AC6 ASP B 207 TYR B 215 1 9 HELIX 25 AC7 PRO B 216 LYS B 221 1 6 HELIX 26 AC8 LYS B 231 LYS B 243 1 13 HELIX 27 AC9 ILE B 285 HIS B 290 5 6 HELIX 28 AD1 HIS B 318 ASN B 331 1 14 HELIX 29 AD2 LEU B 335 LYS B 344 1 10 HELIX 30 AD3 SER B 365 TRP B 370 5 6 HELIX 31 AD4 GLY B 371 ALA B 383 1 13 HELIX 32 AD5 ASN B 388 TRP B 392 5 5 HELIX 33 AD6 ASP B 407 TRP B 411 5 5 HELIX 34 AD7 PHE B 416 THR B 422 1 7 HELIX 35 AD8 SER B 443 THR B 449 1 7 HELIX 36 AD9 GLY B 453 LEU B 460 5 8 HELIX 37 AE1 SER B 463 LYS B 469 1 7 HELIX 38 AE2 GLN B 470 ASN B 471 5 2 HELIX 39 AE3 TRP B 472 SER B 475 5 4 HELIX 40 AE4 SER B 518 GLY B 523 1 6 HELIX 41 AE5 LEU B 544 GLY B 549 5 6 SHEET 1 AA1 7 PHE A 166 TYR A 167 0 SHEET 2 AA1 7 ILE A 296 LEU A 298 -1 O ILE A 296 N TYR A 167 SHEET 3 AA1 7 LEU A 275 HIS A 280 -1 N ILE A 279 O TRP A 297 SHEET 4 AA1 7 MET A 266 TYR A 271 -1 N MET A 267 O VAL A 278 SHEET 5 AA1 7 LEU A 196 PHE A 202 -1 N PHE A 202 O MET A 266 SHEET 6 AA1 7 ILE A 224 HIS A 228 1 O LEU A 225 N GLN A 201 SHEET 7 AA1 7 ILE A 248 GLN A 252 1 O SER A 249 N ILE A 224 SHEET 1 AA2 7 TYR A 353 SER A 357 0 SHEET 2 AA2 7 GLU A 538 PHE A 543 -1 O LEU A 542 N TYR A 353 SHEET 3 AA2 7 LYS A 506 THR A 513 -1 N PHE A 510 O PHE A 543 SHEET 4 AA2 7 LYS A 495 PRO A 500 -1 N ARG A 499 O ALA A 508 SHEET 5 AA2 7 VAL A 394 GLN A 397 -1 N GLN A 397 O THR A 496 SHEET 6 AA2 7 LEU A 437 ILE A 440 1 O TYR A 438 N VAL A 394 SHEET 7 AA2 7 PHE A 477 HIS A 478 1 O HIS A 478 N LEU A 439 SHEET 1 AA3 4 TYR A 353 SER A 357 0 SHEET 2 AA3 4 GLU A 538 PHE A 543 -1 O LEU A 542 N TYR A 353 SHEET 3 AA3 4 LYS A 506 THR A 513 -1 N PHE A 510 O PHE A 543 SHEET 4 AA3 4 PHE A 553 LYS A 554 -1 O PHE A 553 N ILE A 507 SHEET 1 AA4 3 GLY A 360 GLN A 363 0 SHEET 2 AA4 3 GLN A 531 ILE A 534 -1 O ILE A 534 N GLY A 360 SHEET 3 AA4 3 ALA A 524 GLU A 526 -1 N GLU A 526 O GLN A 531 SHEET 1 AA5 7 PHE B 166 LEU B 168 0 SHEET 2 AA5 7 GLY B 295 LEU B 298 -1 O ILE B 296 N TYR B 167 SHEET 3 AA5 7 GLY B 274 HIS B 280 -1 N ILE B 279 O TRP B 297 SHEET 4 AA5 7 MET B 266 TYR B 271 -1 N LEU B 269 O ARG B 276 SHEET 5 AA5 7 LEU B 196 PHE B 202 -1 N ALA B 200 O LEU B 268 SHEET 6 AA5 7 LEU B 225 HIS B 228 1 O LEU B 225 N GLN B 201 SHEET 7 AA5 7 SER B 249 GLN B 252 1 O CYS B 251 N LEU B 226 SHEET 1 AA6 2 LYS B 292 THR B 293 0 SHEET 2 AA6 2 MET B 491 PRO B 492 1 O MET B 491 N THR B 293 SHEET 1 AA7 7 TYR B 353 SER B 357 0 SHEET 2 AA7 7 GLU B 538 PHE B 543 -1 O LEU B 542 N TYR B 353 SHEET 3 AA7 7 LYS B 506 THR B 513 -1 N VAL B 512 O VAL B 541 SHEET 4 AA7 7 LYS B 495 PRO B 500 -1 N ARG B 499 O ALA B 508 SHEET 5 AA7 7 VAL B 394 GLN B 397 -1 N GLN B 397 O THR B 496 SHEET 6 AA7 7 LEU B 437 ILE B 440 1 O ILE B 440 N GLY B 396 SHEET 7 AA7 7 PHE B 477 HIS B 478 1 O HIS B 478 N LEU B 439 SHEET 1 AA8 5 TYR B 353 SER B 357 0 SHEET 2 AA8 5 GLU B 538 PHE B 543 -1 O LEU B 542 N TYR B 353 SHEET 3 AA8 5 LYS B 506 THR B 513 -1 N VAL B 512 O VAL B 541 SHEET 4 AA8 5 PHE B 553 VAL B 555 -1 O PHE B 553 N ILE B 507 SHEET 5 AA8 5 THR B 569 PHE B 570 1 O PHE B 570 N LYS B 554 SHEET 1 AA9 3 GLY B 360 GLN B 363 0 SHEET 2 AA9 3 GLN B 531 ILE B 534 -1 O LEU B 532 N PHE B 362 SHEET 3 AA9 3 ALA B 524 GLU B 526 -1 N ALA B 524 O MET B 533 CISPEP 1 LEU A 576 PRO A 577 0 4.72 CISPEP 2 LEU B 576 PRO B 577 0 1.24 CRYST1 109.191 198.192 51.325 90.00 90.00 90.00 P 21 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.009158 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005046 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019484 0.00000