PDB Short entry for 1PKH HEADER HYDROLASE 05-JUN-03 1PKH TITLE STRUCTURAL BASIS FOR RECOGNITION AND CATALYSIS BY THE BIFUNCTIONAL TITLE 2 DCTP DEAMINASE AND DUTPASE FROM METHANOCOCCUS JANNASCHII COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIFUNCTIONAL DEAMINASE/DIPHOSPHATASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: MJDCD-DUT, DCD/DUT; COMPND 5 EC: 3.5.4.13, 3.6.1.23; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII; SOURCE 3 ORGANISM_TAXID: 2190; SOURCE 4 GENE: MJ0430; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) RIL; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET17B KEYWDS DCTP DEAMINASE, DUTPASE, DCD-DUT, MJ0430, DCTP, DUTP, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.L.HUFFMAN,H.LI,R.H.WHITE,J.A.TAINER REVDAT 3 14-FEB-24 1PKH 1 REMARK REVDAT 2 24-FEB-09 1PKH 1 VERSN REVDAT 1 19-AUG-03 1PKH 0 JRNL AUTH J.L.HUFFMAN,H.LI,R.H.WHITE,J.A.TAINER JRNL TITL STRUCTURAL BASIS FOR RECOGNITION AND CATALYSIS BY THE JRNL TITL 2 BIFUNCTIONAL DCTP DEAMINASE AND DUTPASE FROM METHANOCOCCUS JRNL TITL 3 JANNASCHII JRNL REF J.MOL.BIOL. V. 331 885 2003 JRNL REFN ISSN 0022-2836 JRNL PMID 12909016 JRNL DOI 10.1016/S0022-2836(03)00789-7 REMARK 2 REMARK 2 RESOLUTION. 1.42 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.42 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.186 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.185 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 4251 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 80707 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.175 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.175 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 3839 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 72586 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2886 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 361 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 3278.8 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 2914.0 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 13127 REMARK 3 NUMBER OF RESTRAINTS : 11979 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 ANGLE DISTANCES (A) : 0.028 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.031 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.060 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.067 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.029 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.067 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1PKH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JUN-03. REMARK 100 THE DEPOSITION ID IS D_1000019391. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-DEC-02 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 : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9800 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 84993 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.420 REMARK 200 RESOLUTION RANGE LOW (A) : 45.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.700 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : 0.04800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 56.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.47 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.35800 REMARK 200 R SYM FOR SHELL (I) : 0.35800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 7.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NANOPURE WATER, PH 7, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 3 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 5555 Z,X,Y REMARK 290 6555 Z+1/2,-X+1/2,-Y REMARK 290 7555 -Z+1/2,-X,Y+1/2 REMARK 290 8555 -Z,X+1/2,-Y+1/2 REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z+1/2,-X+1/2 REMARK 290 11555 Y+1/2,-Z+1/2,-X REMARK 290 12555 -Y+1/2,-Z,X+1/2 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 55.35000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.35000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 55.35000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.35000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 55.35000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 55.35000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 55.35000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 55.35000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 55.35000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 55.35000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 55.35000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 55.35000 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 55.35000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 55.35000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 55.35000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 55.35000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 55.35000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 55.35000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 23230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 41290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -133.1 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 0.000000 0.000000 -1.000000 55.35000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 110.70000 REMARK 350 BIOMT3 2 0.000000 1.000000 0.000000 -55.35000 REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 110.70000 REMARK 350 BIOMT2 3 0.000000 0.000000 1.000000 55.35000 REMARK 350 BIOMT3 3 -1.000000 0.000000 0.000000 55.35000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 110.70000 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 -55.35000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 55.35000 REMARK 350 BIOMT1 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT2 5 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 1.000000 0.000000 -110.70000 REMARK 350 BIOMT1 6 0.000000 -1.000000 0.000000 166.05000 REMARK 350 BIOMT2 6 0.000000 0.000000 -1.000000 110.70000 REMARK 350 BIOMT3 6 1.000000 0.000000 0.000000 -55.35000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 212 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 288 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 369 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 225 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 271 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 469 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 183 REMARK 465 LYS A 184 REMARK 465 TYR A 185 REMARK 465 ALA A 186 REMARK 465 TYR A 187 REMARK 465 GLN A 188 REMARK 465 LYS A 189 REMARK 465 SER A 190 REMARK 465 VAL A 191 REMARK 465 MET A 192 REMARK 465 PRO A 193 REMARK 465 SER A 194 REMARK 465 LEU A 195 REMARK 465 ILE A 196 REMARK 465 HIS A 197 REMARK 465 LEU A 198 REMARK 465 ASP A 199 REMARK 465 ASN A 200 REMARK 465 HIS A 201 REMARK 465 LYS A 202 REMARK 465 LYS A 203 REMARK 465 ASP A 204 REMARK 465 GLY B 176 REMARK 465 TYR B 177 REMARK 465 SER B 178 REMARK 465 GLU B 179 REMARK 465 ARG B 180 REMARK 465 LYS B 181 REMARK 465 THR B 182 REMARK 465 SER B 183 REMARK 465 LYS B 184 REMARK 465 TYR B 185 REMARK 465 ALA B 186 REMARK 465 TYR B 187 REMARK 465 GLN B 188 REMARK 465 LYS B 189 REMARK 465 SER B 190 REMARK 465 VAL B 191 REMARK 465 MET B 192 REMARK 465 PRO B 193 REMARK 465 SER B 194 REMARK 465 LEU B 195 REMARK 465 ILE B 196 REMARK 465 HIS B 197 REMARK 465 LEU B 198 REMARK 465 ASP B 199 REMARK 465 ASN B 200 REMARK 465 HIS B 201 REMARK 465 LYS B 202 REMARK 465 LYS B 203 REMARK 465 ASP B 204 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 ASP A 5 CB - CG - OD2 ANGL. DEV. = 8.3 DEGREES REMARK 500 ARG A 16 NH1 - CZ - NH2 ANGL. DEV. = 7.2 DEGREES REMARK 500 ARG A 16 NE - CZ - NH2 ANGL. DEV. = -6.5 DEGREES REMARK 500 PHE A 26 CB - CG - CD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ASP A 135 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 ARG A 160 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 PHE A 166 CB - CG - CD2 ANGL. DEV. = -4.5 DEGREES REMARK 500 TYR B 32 CB - CG - CD2 ANGL. DEV. = -4.4 DEGREES REMARK 500 TYR B 32 CB - CG - CD1 ANGL. DEV. = 3.6 DEGREES REMARK 500 TYR B 43 CB - CG - CD1 ANGL. DEV. = 3.8 DEGREES REMARK 500 TYR B 43 CG - CD2 - CE2 ANGL. DEV. = 6.6 DEGREES REMARK 500 TYR B 43 CZ - CE2 - CD2 ANGL. DEV. = -6.1 DEGREES REMARK 500 TYR B 114 CD1 - CE1 - CZ ANGL. DEV. = -5.7 DEGREES REMARK 500 TYR B 156 CB - CG - CD2 ANGL. DEV. = 7.2 DEGREES REMARK 500 TYR B 156 CB - CG - CD1 ANGL. DEV. = -3.7 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 CYS A 30 40.37 -152.90 REMARK 500 ASN A 63 -36.86 -145.59 REMARK 500 ASN A 73 79.09 49.01 REMARK 500 ASP A 150 -70.94 -129.12 REMARK 500 LYS A 181 -91.45 -81.63 REMARK 500 CYS B 30 38.85 -155.65 REMARK 500 ASN B 63 -44.88 -134.34 REMARK 500 ASN B 73 72.23 46.85 REMARK 500 ASP B 150 -71.19 -129.92 REMARK 500 ASP B 174 50.49 -96.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 210 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1PKJ RELATED DB: PDB REMARK 900 BIFUNCTIONAL DEAMINASE/DIPHOSPHATASE COMPLEXED WITH DEOXYURIDINE 5'- REMARK 900 TRIPHOSPHATE REMARK 900 RELATED ID: 1PKK RELATED DB: PDB REMARK 900 BIFUNCTIONAL DEAMINASE/DIPHOSPHATASE COMPLEXED WITH 2'- REMARK 900 DEOXYCYTIDINE-5'-TRIPHOSPHATE DBREF 1PKH A 1 204 UNP Q57872 DCD_METJA 1 204 DBREF 1PKH B 1 204 UNP Q57872 DCD_METJA 1 204 SEQRES 1 A 204 MET ILE LEU SER ASP LYS ASP ILE ILE ASP TYR VAL THR SEQRES 2 A 204 SER LYS ARG ILE ILE ILE LYS PRO PHE ASN LYS ASP PHE SEQRES 3 A 204 VAL GLY PRO CYS SER TYR ASP VAL THR LEU GLY ASP GLU SEQRES 4 A 204 PHE ILE ILE TYR ASP ASP GLU VAL TYR ASP LEU SER LYS SEQRES 5 A 204 GLU LEU ASN TYR LYS ARG ILE LYS ILE LYS ASN SER ILE SEQRES 6 A 204 LEU VAL CYS PRO LEU ASN TYR ASN LEU THR GLU GLU LYS SEQRES 7 A 204 ILE ASN TYR PHE LYS GLU LYS TYR ASN VAL ASP TYR VAL SEQRES 8 A 204 VAL GLU GLY GLY VAL LEU GLY THR THR ASN GLU TYR ILE SEQRES 9 A 204 GLU LEU PRO ASN ASP ILE SER ALA GLN TYR GLN GLY ARG SEQRES 10 A 204 SER SER LEU GLY ARG VAL PHE LEU THR SER HIS GLN THR SEQRES 11 A 204 ALA GLY TRP ILE ASP ALA GLY PHE LYS GLY LYS ILE THR SEQRES 12 A 204 LEU GLU ILE VAL ALA PHE ASP LYS PRO VAL ILE LEU TYR SEQRES 13 A 204 LYS ASN GLN ARG ILE GLY GLN LEU ILE PHE SER LYS LEU SEQRES 14 A 204 LEU SER PRO ALA ASP VAL GLY TYR SER GLU ARG LYS THR SEQRES 15 A 204 SER LYS TYR ALA TYR GLN LYS SER VAL MET PRO SER LEU SEQRES 16 A 204 ILE HIS LEU ASP ASN HIS LYS LYS ASP SEQRES 1 B 204 MET ILE LEU SER ASP LYS ASP ILE ILE ASP TYR VAL THR SEQRES 2 B 204 SER LYS ARG ILE ILE ILE LYS PRO PHE ASN LYS ASP PHE SEQRES 3 B 204 VAL GLY PRO CYS SER TYR ASP VAL THR LEU GLY ASP GLU SEQRES 4 B 204 PHE ILE ILE TYR ASP ASP GLU VAL TYR ASP LEU SER LYS SEQRES 5 B 204 GLU LEU ASN TYR LYS ARG ILE LYS ILE LYS ASN SER ILE SEQRES 6 B 204 LEU VAL CYS PRO LEU ASN TYR ASN LEU THR GLU GLU LYS SEQRES 7 B 204 ILE ASN TYR PHE LYS GLU LYS TYR ASN VAL ASP TYR VAL SEQRES 8 B 204 VAL GLU GLY GLY VAL LEU GLY THR THR ASN GLU TYR ILE SEQRES 9 B 204 GLU LEU PRO ASN ASP ILE SER ALA GLN TYR GLN GLY ARG SEQRES 10 B 204 SER SER LEU GLY ARG VAL PHE LEU THR SER HIS GLN THR SEQRES 11 B 204 ALA GLY TRP ILE ASP ALA GLY PHE LYS GLY LYS ILE THR SEQRES 12 B 204 LEU GLU ILE VAL ALA PHE ASP LYS PRO VAL ILE LEU TYR SEQRES 13 B 204 LYS ASN GLN ARG ILE GLY GLN LEU ILE PHE SER LYS LEU SEQRES 14 B 204 LEU SER PRO ALA ASP VAL GLY TYR SER GLU ARG LYS THR SEQRES 15 B 204 SER LYS TYR ALA TYR GLN LYS SER VAL MET PRO SER LEU SEQRES 16 B 204 ILE HIS LEU ASP ASN HIS LYS LYS ASP HET EDO A 205 4 HET EDO A 206 4 HET EDO A 207 4 HET EDO B 205 4 HET EDO B 206 4 HET EDO B 207 4 HET EDO B 208 4 HET EDO B 209 4 HET EDO B 210 4 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 EDO 9(C2 H6 O2) FORMUL 12 HOH *361(H2 O) HELIX 1 1 SER A 4 SER A 14 1 11 HELIX 2 2 ASN A 23 VAL A 27 5 5 HELIX 3 3 THR A 75 ASN A 87 1 13 HELIX 4 4 ARG A 117 ARG A 122 1 6 HELIX 5 5 SER B 4 SER B 14 1 11 HELIX 6 6 ASN B 23 ASP B 25 5 3 HELIX 7 7 THR B 75 ASN B 87 1 13 HELIX 8 8 ARG B 117 ARG B 122 1 6 SHEET 1 A 4 ILE A 18 LYS A 20 0 SHEET 2 A 4 VAL A 96 GLU A 105 -1 O TYR A 103 N LYS A 20 SHEET 3 A 4 LYS A 139 ALA A 148 -1 O ILE A 146 N VAL A 96 SHEET 4 A 4 LEU A 125 THR A 126 -1 N THR A 126 O VAL A 147 SHEET 1 B 4 TYR A 32 THR A 35 0 SHEET 2 B 4 ARG A 160 LYS A 168 -1 O LEU A 164 N TYR A 32 SHEET 3 B 4 ILE A 110 GLY A 116 -1 N SER A 111 O SER A 167 SHEET 4 B 4 TRP A 133 ILE A 134 -1 O ILE A 134 N ALA A 112 SHEET 1 C 2 GLU A 39 TYR A 43 0 SHEET 2 C 2 TYR A 56 LYS A 60 -1 O ILE A 59 N PHE A 40 SHEET 1 D 3 TYR A 90 GLU A 93 0 SHEET 2 D 3 SER A 64 CYS A 68 1 N CYS A 68 O VAL A 92 SHEET 3 D 3 VAL A 153 TYR A 156 -1 O LEU A 155 N ILE A 65 SHEET 1 E 3 TYR A 177 ARG A 180 0 SHEET 2 E 3 TYR B 56 ILE B 61 -1 O ARG B 58 N ARG A 180 SHEET 3 E 3 GLU B 39 TYR B 43 -1 N PHE B 40 O ILE B 59 SHEET 1 F 4 ILE B 18 LYS B 20 0 SHEET 2 F 4 VAL B 96 GLU B 105 -1 O TYR B 103 N LYS B 20 SHEET 3 F 4 LYS B 139 ALA B 148 -1 O GLY B 140 N ILE B 104 SHEET 4 F 4 LEU B 125 THR B 126 -1 N THR B 126 O VAL B 147 SHEET 1 G 5 VAL B 27 GLY B 28 0 SHEET 2 G 5 SER B 31 THR B 35 -1 O SER B 31 N GLY B 28 SHEET 3 G 5 ARG B 160 LYS B 168 -1 O ILE B 161 N VAL B 34 SHEET 4 G 5 ILE B 110 GLY B 116 -1 N SER B 111 O SER B 167 SHEET 5 G 5 TRP B 133 ILE B 134 -1 O ILE B 134 N ALA B 112 SHEET 1 H 3 TYR B 90 GLU B 93 0 SHEET 2 H 3 SER B 64 CYS B 68 1 N CYS B 68 O VAL B 92 SHEET 3 H 3 VAL B 153 TYR B 156 -1 O LEU B 155 N ILE B 65 CISPEP 1 LYS A 20 PRO A 21 0 -7.99 CISPEP 2 LYS B 20 PRO B 21 0 -5.00 SITE 1 AC1 6 LYS A 139 GLU B 76 ILE B 79 ASN B 80 SITE 2 AC1 6 LYS B 83 HOH B 415 SITE 1 AC2 6 ASP B 25 PHE B 26 VAL B 27 GLY B 28 SITE 2 AC2 6 ASP B 33 ARG B 160 SITE 1 AC3 7 ASP A 25 PHE A 26 VAL A 27 ASP A 33 SITE 2 AC3 7 ARG A 160 ASN B 87 HOH B 504 SITE 1 AC4 5 GLU B 39 ILE B 41 LEU B 97 GLY B 98 SITE 2 AC4 5 THR B 99 SITE 1 AC5 7 ASP A 174 TYR A 177 SER A 178 HOH A 433 SITE 2 AC5 7 LYS B 60 LYS B 62 HOH B 338 SITE 1 AC6 6 ARG B 16 GLU B 105 LEU B 106 PRO B 107 SITE 2 AC6 6 HOH B 286 HOH B 453 SITE 1 AC7 5 PRO A 21 ASN A 23 THR A 35 GLU A 102 SITE 2 AC7 5 HOH A 404 SITE 1 AC8 5 GLY B 37 ASP B 38 ASN B 101 LYS B 157 SITE 2 AC8 5 ASN B 158 SITE 1 AC9 2 THR B 35 HOH B 501 CRYST1 110.700 110.700 110.700 90.00 90.00 90.00 P 21 3 24 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 0.009033 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009033 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009033 0.00000