HEADER HYDROLASE 27-MAR-07 2PAU TITLE CRYSTAL STRUCTURE OF THE 5'-DEOXYNUCLEOTIDASE YFBR MUTANT E72A TITLE 2 COMPLEXED WITH CO(2+) AND DAMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-DEOXYNUCLEOTIDASE YFBR; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: NUCLEOSIDE 5'-MONOPHOSPHATE PHOSPHOHYDROLASE, 5'- COMPND 5 DEOXYRIBONUCLEOTIDASE; COMPND 6 EC: 3.1.3.5; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: YFBR, B2291, JW2288; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA2(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: MODIFIED PET-15B KEYWDS NUCLEOTIDASE, 5'-DEOXYNUCLEOTIDASE, YFBR, HD DOMAIN PHOSPHOHYDROLASE, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.D.ZIMMERMAN,M.PROUDFOOT,A.YAKUNIN,W.MINOR REVDAT 6 30-AUG-23 2PAU 1 REMARK REVDAT 5 13-APR-22 2PAU 1 AUTHOR JRNL REVDAT 4 20-OCT-21 2PAU 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 2PAU 1 VERSN REVDAT 2 06-MAY-08 2PAU 1 JRNL VERSN REVDAT 1 04-MAR-08 2PAU 0 JRNL AUTH M.D.ZIMMERMAN,M.PROUDFOOT,A.YAKUNIN,W.MINOR JRNL TITL STRUCTURAL INSIGHT INTO THE MECHANISM OF SUBSTRATE JRNL TITL 2 SPECIFICITY AND CATALYTIC ACTIVITY OF AN HD-DOMAIN JRNL TITL 3 PHOSPHOHYDROLASE: THE 5'-DEOXYRIBONUCLEOTIDASE YFBR FROM JRNL TITL 4 ESCHERICHIA COLI. JRNL REF J.MOL.BIOL. V. 378 215 2008 JRNL REFN ISSN 0022-2836 JRNL PMID 18353368 JRNL DOI 10.1016/J.JMB.2008.02.036 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.13 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 19971 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1028 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1270 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.74 REMARK 3 BIN R VALUE (WORKING SET) : 0.2500 REMARK 3 BIN FREE R VALUE SET COUNT : 72 REMARK 3 BIN FREE R VALUE : 0.3570 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2724 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 53 REMARK 3 SOLVENT ATOMS : 53 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 45.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.53 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.13000 REMARK 3 B22 (A**2) : -0.13000 REMARK 3 B33 (A**2) : 0.19000 REMARK 3 B12 (A**2) : -0.06000 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): 0.259 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.221 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.175 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.201 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.917 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2825 ; 0.022 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2577 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3830 ; 1.908 ; 1.980 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5943 ; 0.902 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 349 ; 6.341 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 130 ;36.108 ;24.231 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 464 ;15.351 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;17.821 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 438 ; 0.104 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3129 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 560 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 690 ; 0.238 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2573 ; 0.183 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1373 ; 0.190 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1686 ; 0.093 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 108 ; 0.168 ; 0.200 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): 15 ; 0.337 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 39 ; 0.330 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.145 ; 0.200 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): 1819 ; 0.983 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 706 ; 0.276 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2805 ; 1.450 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1147 ; 2.411 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1025 ; 3.615 ; 4.500 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 4 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 4 A 4 A 301 4 REMARK 3 2 B 2 B 301 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 2618 ; 0.51 ; 0.50 REMARK 3 MEDIUM THERMAL 1 A (A**2): 2618 ; 0.79 ; 2.00 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. COOT PROGRAM HAS ALSO BEEN USED IN THE REFINEMENT. REMARK 4 REMARK 4 2PAU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-MAR-07. REMARK 100 THE DEPOSITION ID IS D_1000042174. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUN-06 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97937 REMARK 200 MONOCHROMATOR : ROSENBAUM-ROCK HIGH-RESOLUTION REMARK 200 SI(111) DOUBLE-CRYSTAL REMARK 200 OPTICS : LN2 COOLED FIRST CRYSTAL, REMARK 200 SAGITAL FOCUSING 2ND CRYSTAL, REMARK 200 ROSENBAUM-ROCK VERTICAL FOCUSING REMARK 200 MIRROR, BEAM DEFINING SLITS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25437 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : 0.06600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.56300 REMARK 200 R SYM FOR SHELL (I) : 0.56300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: HKL-3000, MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1WPH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M NH4 CITRATE, 0.1 % W/V NDSB 256, REMARK 280 5 % W/V PEG 3350, PH 5.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 67.79750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 39.14290 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 18.31200 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 67.79750 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 39.14290 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 18.31200 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 67.79750 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 39.14290 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 18.31200 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 78.28581 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 36.62400 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 78.28581 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 36.62400 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 78.28581 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 36.62400 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -52.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 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 GLY A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 LYS A 2 REMARK 465 GLN A 3 REMARK 465 VAL A 82 REMARK 465 LYS A 83 REMARK 465 TYR A 84 REMARK 465 PHE A 85 REMARK 465 ASN A 86 REMARK 465 SER A 87 REMARK 465 GLN A 88 REMARK 465 HIS A 187 REMARK 465 LEU A 188 REMARK 465 SER A 189 REMARK 465 LEU A 190 REMARK 465 ASP A 191 REMARK 465 GLU A 192 REMARK 465 ILE A 193 REMARK 465 SER A 194 REMARK 465 GLN A 195 REMARK 465 ASP A 196 REMARK 465 SER A 197 REMARK 465 PRO A 198 REMARK 465 LEU A 199 REMARK 465 GLY B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 VAL B 82 REMARK 465 LYS B 83 REMARK 465 TYR B 84 REMARK 465 PHE B 85 REMARK 465 ASN B 86 REMARK 465 SER B 87 REMARK 465 GLN B 88 REMARK 465 ILE B 89 REMARK 465 HIS B 187 REMARK 465 LEU B 188 REMARK 465 SER B 189 REMARK 465 LEU B 190 REMARK 465 ASP B 191 REMARK 465 GLU B 192 REMARK 465 ILE B 193 REMARK 465 SER B 194 REMARK 465 GLN B 195 REMARK 465 ASP B 196 REMARK 465 SER B 197 REMARK 465 PRO B 198 REMARK 465 LEU B 199 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 LYS A 14 NZ REMARK 470 ILE A 89 CG1 CG2 CD1 REMARK 470 GLN A 91 CG CD OE1 NE2 REMARK 470 TYR A 93 CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 94 CG CD CE NZ REMARK 470 ILE A 96 CG1 CG2 CD1 REMARK 470 LYS A 98 CG CD CE NZ REMARK 470 LYS A 103 CD CE NZ REMARK 470 LYS A 130 CE NZ REMARK 470 ARG A 162 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 180 CG CD OE1 OE2 REMARK 470 PHE A 186 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS B 2 CG CD CE NZ REMARK 470 LYS B 14 CE NZ REMARK 470 GLN B 91 CG CD OE1 NE2 REMARK 470 GLU B 92 CG CD OE1 OE2 REMARK 470 TYR B 93 CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS B 94 CG CD CE NZ REMARK 470 ILE B 96 CG1 CG2 CD1 REMARK 470 LYS B 98 CD CE NZ REMARK 470 GLN B 102 CG CD OE1 NE2 REMARK 470 LYS B 103 CD CE NZ REMARK 470 LYS B 130 CD CE NZ REMARK 470 LEU B 158 CG CD1 CD2 REMARK 470 LYS B 160 NZ 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 ALA A 95 C ALA A 95 O 0.129 REMARK 500 GLU A 174 CB GLU A 174 CG -0.172 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 SER B 11 -18.81 -48.54 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 CO A 201 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 33 NE2 REMARK 620 2 HIS A 68 NE2 93.8 REMARK 620 3 ASP A 69 OD2 85.0 84.1 REMARK 620 4 ASP A 137 OD1 88.8 92.5 172.8 REMARK 620 5 D5M A 301 O1P 97.5 168.5 94.6 90.0 REMARK 620 6 HOH A 425 O 167.8 95.0 87.5 99.2 73.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO B 201 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 33 NE2 REMARK 620 2 HIS B 68 NE2 99.6 REMARK 620 3 ASP B 69 OD2 86.3 82.1 REMARK 620 4 ASP B 137 OD1 86.6 98.6 172.9 REMARK 620 5 D5M B 301 O1P 93.8 164.0 90.0 91.0 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE D5M A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE D5M B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2PAQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 5'-DEOXYNUCLEOTIDASE YFBR REMARK 900 RELATED ID: 2PAR RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 5'-DEOXYNUCLEOTIDASE YFBR MUTANT E72A REMARK 900 COMPLEXED WITH CO(2+) AND TMP DBREF 2PAU A 1 199 UNP P76491 YFBR_ECOLI 1 199 DBREF 2PAU B 1 199 UNP P76491 YFBR_ECOLI 1 199 SEQADV 2PAU GLY A -1 UNP P76491 EXPRESSION TAG SEQADV 2PAU HIS A 0 UNP P76491 EXPRESSION TAG SEQADV 2PAU ALA A 72 UNP P76491 GLU 72 ENGINEERED MUTATION SEQADV 2PAU GLY B -1 UNP P76491 EXPRESSION TAG SEQADV 2PAU HIS B 0 UNP P76491 EXPRESSION TAG SEQADV 2PAU ALA B 72 UNP P76491 GLU 72 ENGINEERED MUTATION SEQRES 1 A 201 GLY HIS MET LYS GLN SER HIS PHE PHE ALA HIS LEU SER SEQRES 2 A 201 ARG LEU LYS LEU ILE ASN ARG TRP PRO LEU MET ARG ASN SEQRES 3 A 201 VAL ARG THR GLU ASN VAL SER GLU HIS SER LEU GLN VAL SEQRES 4 A 201 ALA MET VAL ALA HIS ALA LEU ALA ALA ILE LYS ASN ARG SEQRES 5 A 201 LYS PHE GLY GLY ASN VAL ASN ALA GLU ARG ILE ALA LEU SEQRES 6 A 201 LEU ALA MET TYR HIS ASP ALA SER ALA VAL LEU THR GLY SEQRES 7 A 201 ASP LEU PRO THR PRO VAL LYS TYR PHE ASN SER GLN ILE SEQRES 8 A 201 ALA GLN GLU TYR LYS ALA ILE GLU LYS ILE ALA GLN GLN SEQRES 9 A 201 LYS LEU VAL ASP MET VAL PRO GLU GLU LEU ARG ASP ILE SEQRES 10 A 201 PHE ALA PRO LEU ILE ASP GLU HIS ALA TYR SER ASP GLU SEQRES 11 A 201 GLU LYS SER LEU VAL LYS GLN ALA ASP ALA LEU CYS ALA SEQRES 12 A 201 TYR LEU LYS CYS LEU GLU GLU LEU ALA ALA GLY ASN ASN SEQRES 13 A 201 GLU PHE LEU LEU ALA LYS THR ARG LEU GLU ALA THR LEU SEQRES 14 A 201 GLU ALA ARG ARG SER GLN GLU MET ASP TYR PHE MET GLU SEQRES 15 A 201 ILE PHE VAL PRO SER PHE HIS LEU SER LEU ASP GLU ILE SEQRES 16 A 201 SER GLN ASP SER PRO LEU SEQRES 1 B 201 GLY HIS MET LYS GLN SER HIS PHE PHE ALA HIS LEU SER SEQRES 2 B 201 ARG LEU LYS LEU ILE ASN ARG TRP PRO LEU MET ARG ASN SEQRES 3 B 201 VAL ARG THR GLU ASN VAL SER GLU HIS SER LEU GLN VAL SEQRES 4 B 201 ALA MET VAL ALA HIS ALA LEU ALA ALA ILE LYS ASN ARG SEQRES 5 B 201 LYS PHE GLY GLY ASN VAL ASN ALA GLU ARG ILE ALA LEU SEQRES 6 B 201 LEU ALA MET TYR HIS ASP ALA SER ALA VAL LEU THR GLY SEQRES 7 B 201 ASP LEU PRO THR PRO VAL LYS TYR PHE ASN SER GLN ILE SEQRES 8 B 201 ALA GLN GLU TYR LYS ALA ILE GLU LYS ILE ALA GLN GLN SEQRES 9 B 201 LYS LEU VAL ASP MET VAL PRO GLU GLU LEU ARG ASP ILE SEQRES 10 B 201 PHE ALA PRO LEU ILE ASP GLU HIS ALA TYR SER ASP GLU SEQRES 11 B 201 GLU LYS SER LEU VAL LYS GLN ALA ASP ALA LEU CYS ALA SEQRES 12 B 201 TYR LEU LYS CYS LEU GLU GLU LEU ALA ALA GLY ASN ASN SEQRES 13 B 201 GLU PHE LEU LEU ALA LYS THR ARG LEU GLU ALA THR LEU SEQRES 14 B 201 GLU ALA ARG ARG SER GLN GLU MET ASP TYR PHE MET GLU SEQRES 15 B 201 ILE PHE VAL PRO SER PHE HIS LEU SER LEU ASP GLU ILE SEQRES 16 B 201 SER GLN ASP SER PRO LEU HET CO A 201 1 HET D5M A 301 22 HET PEG A 401 7 HET CO B 201 1 HET D5M B 301 22 HETNAM CO COBALT (II) ION HETNAM D5M 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 3 CO 2(CO 2+) FORMUL 4 D5M 2(C10 H14 N5 O6 P) FORMUL 5 PEG C4 H10 O3 FORMUL 8 HOH *53(H2 O) HELIX 1 1 HIS A 5 SER A 11 1 7 HELIX 2 2 ARG A 12 ILE A 16 5 5 HELIX 3 3 ASN A 29 PHE A 52 1 24 HELIX 4 4 ASN A 57 HIS A 68 1 12 HELIX 5 5 SER A 71 GLY A 76 1 6 HELIX 6 6 ILE A 89 ASP A 106 1 18 HELIX 7 7 MET A 107 VAL A 108 5 2 HELIX 8 8 PRO A 109 GLU A 111 5 3 HELIX 9 9 LEU A 112 GLU A 122 1 11 HELIX 10 10 SER A 126 ALA A 151 1 26 HELIX 11 11 GLY A 152 GLU A 155 5 4 HELIX 12 12 PHE A 156 ARG A 170 1 15 HELIX 13 13 SER A 172 PHE A 182 1 11 HELIX 14 14 HIS B 5 SER B 11 1 7 HELIX 15 15 ARG B 12 ILE B 16 5 5 HELIX 16 16 ASN B 29 GLY B 53 1 25 HELIX 17 17 ASN B 57 HIS B 68 1 12 HELIX 18 18 SER B 71 GLY B 76 1 6 HELIX 19 19 ALA B 90 VAL B 108 1 19 HELIX 20 20 PRO B 109 GLU B 111 5 3 HELIX 21 21 LEU B 112 ASP B 121 1 10 HELIX 22 22 GLU B 122 TYR B 125 5 4 HELIX 23 23 SER B 126 ALA B 151 1 26 HELIX 24 24 GLY B 152 GLU B 155 5 4 HELIX 25 25 PHE B 156 ARG B 170 1 15 HELIX 26 26 SER B 172 VAL B 183 1 12 LINK NE2 HIS A 33 CO CO A 201 1555 1555 2.03 LINK NE2 HIS A 68 CO CO A 201 1555 1555 2.12 LINK OD2 ASP A 69 CO CO A 201 1555 1555 2.33 LINK OD1 ASP A 137 CO CO A 201 1555 1555 2.16 LINK CO CO A 201 O1P D5M A 301 1555 1555 2.28 LINK CO CO A 201 O HOH A 425 1555 1555 2.24 LINK NE2 HIS B 33 CO CO B 201 1555 1555 2.03 LINK NE2 HIS B 68 CO CO B 201 1555 1555 2.13 LINK OD2 ASP B 69 CO CO B 201 1555 1555 2.25 LINK OD1 ASP B 137 CO CO B 201 1555 1555 2.26 LINK CO CO B 201 O1P D5M B 301 1555 1555 2.36 SITE 1 AC1 5 HIS A 33 HIS A 68 ASP A 69 ASP A 137 SITE 2 AC1 5 HOH A 425 SITE 1 AC2 4 HIS B 33 HIS B 68 ASP B 69 ASP B 137 SITE 1 AC3 9 ARG A 18 TRP A 19 HIS A 33 ASP A 69 SITE 2 AC3 9 ASP A 77 PRO A 79 THR A 80 ASP A 137 SITE 3 AC3 9 HOH A 425 SITE 1 AC4 10 ARG B 18 TRP B 19 HIS B 33 ASP B 69 SITE 2 AC4 10 ASP B 77 LEU B 78 PRO B 79 THR B 80 SITE 3 AC4 10 PRO B 81 ASP B 137 SITE 1 AC5 4 GLU A 122 TYR A 125 LYS A 134 ASP A 137 CRYST1 135.595 135.595 54.936 90.00 90.00 120.00 H 3 18 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 0.007380 0.004260 0.000000 0.00000 SCALE2 0.000000 0.008520 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018200 0.00000