HEADER HYDROLASE/HYDROLASE INHIBITOR 31-OCT-13 4NFL TITLE CRYSTAL STRUCTURE OF HUMAN MITOCHONDRIAL 5'(3')-DEOXYRIBONUCLEOTIDASE TITLE 2 IN COMPLEX WITH THE INHIBITOR NPB-T COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'(3')-DEOXYRIBONUCLEOTIDASE, MITOCHONDRIAL; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 32-227; COMPND 5 SYNONYM: 5',3'-NUCLEOTIDASE, MITOCHONDRIAL, DEOXY-5'-NUCLEOTIDASE 2, COMPND 6 DNT-2; COMPND 7 EC: 3.1.3.-; COMPND 8 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: NT5M, DNT2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HAD-LIKE, NUCLEOTIDASE, MITOCHONDRIA, HYDROLASE-HYDROLASE INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.PACHL,P.REZACOVA,J.BRYNDA REVDAT 3 20-SEP-23 4NFL 1 REMARK SEQADV LINK REVDAT 2 08-OCT-14 4NFL 1 JRNL REVDAT 1 10-SEP-14 4NFL 0 JRNL AUTH O.SIMAK,P.PACHL,M.FABRY,M.BUDESINSKY,T.JANDUSIK,A.HNIZDA, JRNL AUTH 2 R.SKLENICKOVA,M.PETROVA,V.VEVERKA,P.REZACOVA,J.BRYNDA, JRNL AUTH 3 I.ROSENBERG JRNL TITL CONFORMATIONALLY CONSTRAINED NUCLEOSIDE PHOSPHONIC ACIDS - JRNL TITL 2 POTENT INHIBITORS OF HUMAN MITOCHONDRIAL AND CYTOSOLIC JRNL TITL 3 5'(3')-NUCLEOTIDASES. JRNL REF ORG.BIOMOL.CHEM. V. 12 7971 2014 JRNL REFN ISSN 1477-0520 JRNL PMID 25178098 JRNL DOI 10.1039/C4OB01332H REMARK 2 REMARK 2 RESOLUTION. 1.38 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.73 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 3 NUMBER OF REFLECTIONS : 56839 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) : 0.154 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.176 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2886 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) : 1.38 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.41 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2516 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 60.02 REMARK 3 BIN R VALUE (WORKING SET) : 0.2610 REMARK 3 BIN FREE R VALUE SET COUNT : 146 REMARK 3 BIN FREE R VALUE : 0.2730 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1633 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 123 REMARK 3 SOLVENT ATOMS : 292 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.35 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.11000 REMARK 3 B22 (A**2) : -0.11000 REMARK 3 B33 (A**2) : 0.22000 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): 0.047 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.050 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.033 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.570 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.973 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.966 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1876 ; 0.016 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 1776 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2538 ; 2.044 ; 2.015 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4108 ; 0.955 ; 3.004 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 224 ; 6.006 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 88 ;28.933 ;23.182 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 302 ;11.733 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;12.020 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 266 ; 0.106 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2030 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 435 ; 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): 831 ; 1.627 ; 1.495 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 832 ; 1.626 ; 1.496 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1044 ; 2.602 ; 2.232 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 27 A 39 REMARK 3 ORIGIN FOR THE GROUP (A): -4.1839 -0.2950 14.1889 REMARK 3 T TENSOR REMARK 3 T11: 0.0916 T22: 0.0624 REMARK 3 T33: 0.0896 T12: -0.0028 REMARK 3 T13: 0.0358 T23: -0.0140 REMARK 3 L TENSOR REMARK 3 L11: 0.6208 L22: 0.2080 REMARK 3 L33: 4.0555 L12: -0.3493 REMARK 3 L13: 1.5858 L23: -0.8983 REMARK 3 S TENSOR REMARK 3 S11: 0.1410 S12: -0.0954 S13: -0.0545 REMARK 3 S21: -0.1003 S22: 0.0213 S23: 0.0339 REMARK 3 S31: 0.3859 S32: -0.2296 S33: -0.1623 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 40 A 159 REMARK 3 ORIGIN FOR THE GROUP (A): -7.2552 26.0317 20.0036 REMARK 3 T TENSOR REMARK 3 T11: 0.0215 T22: 0.0239 REMARK 3 T33: 0.0301 T12: 0.0019 REMARK 3 T13: 0.0203 T23: -0.0041 REMARK 3 L TENSOR REMARK 3 L11: 0.4871 L22: 0.5501 REMARK 3 L33: 0.1100 L12: -0.1222 REMARK 3 L13: -0.1515 L23: 0.2110 REMARK 3 S TENSOR REMARK 3 S11: 0.0217 S12: -0.0014 S13: 0.0552 REMARK 3 S21: -0.0298 S22: 0.0119 S23: -0.0693 REMARK 3 S31: -0.0158 S32: -0.0069 S33: -0.0335 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 160 A 227 REMARK 3 ORIGIN FOR THE GROUP (A): 4.7278 13.7517 18.7940 REMARK 3 T TENSOR REMARK 3 T11: 0.0079 T22: 0.0226 REMARK 3 T33: 0.0687 T12: 0.0043 REMARK 3 T13: 0.0198 T23: 0.0101 REMARK 3 L TENSOR REMARK 3 L11: 0.6105 L22: 0.2382 REMARK 3 L33: 0.3883 L12: 0.2814 REMARK 3 L13: -0.2557 L23: 0.0504 REMARK 3 S TENSOR REMARK 3 S11: -0.0011 S12: -0.0286 S13: -0.1076 REMARK 3 S21: -0.0169 S22: 0.0027 S23: -0.0957 REMARK 3 S31: -0.0143 S32: 0.0462 S33: -0.0016 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 303 A 303 REMARK 3 ORIGIN FOR THE GROUP (A): -3.8346 24.8374 28.6956 REMARK 3 T TENSOR REMARK 3 T11: 0.0459 T22: 0.0563 REMARK 3 T33: 0.2384 T12: 0.0043 REMARK 3 T13: 0.0428 T23: -0.0151 REMARK 3 L TENSOR REMARK 3 L11: 2.2766 L22: 7.6565 REMARK 3 L33: 0.7978 L12: 4.1703 REMARK 3 L13: 1.3191 L23: 2.4348 REMARK 3 S TENSOR REMARK 3 S11: 0.0792 S12: -0.0372 S13: -0.1724 REMARK 3 S21: 0.1369 S22: -0.0632 S23: -0.2787 REMARK 3 S31: 0.0554 S32: -0.0298 S33: -0.0161 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 REMARK 4 REMARK 4 4NFL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-NOV-13. REMARK 100 THE DEPOSITION ID IS D_1000083140. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JAN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97826 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE, XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 56940 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.375 REMARK 200 RESOLUTION RANGE LOW (A) : 52.078 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.04100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.1100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.38 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 61.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.67400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.910 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 4L6A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM POTASSIUM PHOSPHATE MONOBASIC, REMARK 280 8% PEG8000, 10% GLYCEROL, PH 4, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.95500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 36.82500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 36.82500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 79.43250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 36.82500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 36.82500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.47750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 36.82500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.82500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 79.43250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 36.82500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.82500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 26.47750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 52.95500 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 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: 10580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 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 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 52.95500 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 484 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 575 LIES ON A SPECIAL POSITION. 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 GLN A 205 CG CD OE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O LEU A 204 C2 PEG A 317 2.11 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 37 NE - CZ - NH1 ANGL. DEV. = 3.6 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 MET A 42 -73.24 -100.67 REMARK 500 VAL A 45 -52.32 -132.25 REMARK 500 ASN A 100 -2.32 75.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PEG A 312 REMARK 610 PEG A 313 REMARK 610 PEG A 316 REMARK 610 PEG A 317 REMARK 610 PEG A 318 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 A 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 41 OD2 REMARK 620 2 ASP A 43 O 88.1 REMARK 620 3 ASP A 176 OD1 84.1 90.8 REMARK 620 4 PO4 A 302 O2 87.9 95.1 169.9 REMARK 620 5 HOH A 401 O 90.8 178.8 88.6 85.3 REMARK 620 6 HOH A 402 O 173.3 86.4 92.2 96.3 94.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2JW A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 310 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 311 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 312 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 313 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 314 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 315 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 316 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 317 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 318 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4L6C RELATED DB: PDB REMARK 900 HUMAN MITOCHONDRIAL 5'(3')-DEOXYRIBONUCLEOTIDASE WITH INHIBITOR IPB- REMARK 900 T REMARK 900 RELATED ID: 4MWO RELATED DB: PDB REMARK 900 HUMAN MITOCHONDRIAL 5'(3')-DEOXYRIBONUCLEOTIDASE WITH INHIBITOR CPB- REMARK 900 T DBREF 4NFL A 32 227 UNP Q9NPB1 NT5M_HUMAN 32 227 SEQADV 4NFL SER A 27 UNP Q9NPB1 EXPRESSION TAG SEQADV 4NFL ASN A 28 UNP Q9NPB1 EXPRESSION TAG SEQADV 4NFL ALA A 29 UNP Q9NPB1 EXPRESSION TAG SEQADV 4NFL ALA A 30 UNP Q9NPB1 EXPRESSION TAG SEQADV 4NFL SER A 31 UNP Q9NPB1 EXPRESSION TAG SEQRES 1 A 201 SER ASN ALA ALA SER GLY GLY ARG ALA LEU ARG VAL LEU SEQRES 2 A 201 VAL ASP MET ASP GLY VAL LEU ALA ASP PHE GLU GLY GLY SEQRES 3 A 201 PHE LEU ARG LYS PHE ARG ALA ARG PHE PRO ASP GLN PRO SEQRES 4 A 201 PHE ILE ALA LEU GLU ASP ARG ARG GLY PHE TRP VAL SER SEQRES 5 A 201 GLU GLN TYR GLY ARG LEU ARG PRO GLY LEU SER GLU LYS SEQRES 6 A 201 ALA ILE SER ILE TRP GLU SER LYS ASN PHE PHE PHE GLU SEQRES 7 A 201 LEU GLU PRO LEU PRO GLY ALA VAL GLU ALA VAL LYS GLU SEQRES 8 A 201 MET ALA SER LEU GLN ASN THR ASP VAL PHE ILE CYS THR SEQRES 9 A 201 SER PRO ILE LYS MET PHE LYS TYR CYS PRO TYR GLU LYS SEQRES 10 A 201 TYR ALA TRP VAL GLU LYS TYR PHE GLY PRO ASP PHE LEU SEQRES 11 A 201 GLU GLN ILE VAL LEU THR ARG ASP LYS THR VAL VAL SER SEQRES 12 A 201 ALA ASP LEU LEU ILE ASP ASP ARG PRO ASP ILE THR GLY SEQRES 13 A 201 ALA GLU PRO THR PRO SER TRP GLU HIS VAL LEU PHE THR SEQRES 14 A 201 ALA CYS HIS ASN GLN HIS LEU GLN LEU GLN PRO PRO ARG SEQRES 15 A 201 ARG ARG LEU HIS SER TRP ALA ASP ASP TRP LYS ALA ILE SEQRES 16 A 201 LEU ASP SER LYS ARG PRO HET MG A 301 1 HET PO4 A 302 5 HET 2JW A 303 31 HET TRS A 304 8 HET GOL A 305 6 HET GOL A 306 12 HET GOL A 307 6 HET GOL A 308 6 HET GOL A 309 6 HET GOL A 310 6 HET GOL A 311 6 HET PEG A 312 5 HET PEG A 313 3 HET PEG A 314 7 HET PEG A 315 7 HET PEG A 316 4 HET PEG A 317 5 HET PEG A 318 5 HETNAM MG MAGNESIUM ION HETNAM PO4 PHOSPHATE ION HETNAM 2JW 1-{2-DEOXY-3,5-O-[(4-NITROPHENYL)(PHOSPHONO) HETNAM 2 2JW METHYLIDENE]-BETA-D-THREO-PENTOFURANOSYL}-5- HETNAM 3 2JW METHYLPYRIMIDINE-2,4(1H,3H)-DIONE HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM GOL GLYCEROL HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN TRS TRIS BUFFER HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 MG MG 2+ FORMUL 3 PO4 O4 P 3- FORMUL 4 2JW C17 H18 N3 O10 P FORMUL 5 TRS C4 H12 N O3 1+ FORMUL 6 GOL 7(C3 H8 O3) FORMUL 13 PEG 7(C4 H10 O3) FORMUL 20 HOH *292(H2 O) HELIX 1 1 ASP A 48 PHE A 61 1 14 HELIX 2 2 ALA A 68 ARG A 72 5 5 HELIX 3 3 TRP A 76 ARG A 85 1 10 HELIX 4 4 GLY A 87 GLU A 97 1 11 HELIX 5 5 GLY A 110 LEU A 121 1 12 HELIX 6 6 TYR A 138 GLY A 152 1 15 HELIX 7 7 PRO A 153 GLU A 157 5 5 HELIX 8 8 ASP A 217 SER A 224 1 8 SHEET 1 A 6 ILE A 159 LEU A 161 0 SHEET 2 A 6 THR A 124 THR A 130 1 N ILE A 128 O VAL A 160 SHEET 3 A 6 LEU A 36 VAL A 40 1 N LEU A 36 O ASP A 125 SHEET 4 A 6 LEU A 172 ASP A 175 1 O LEU A 172 N LEU A 39 SHEET 5 A 6 GLU A 190 PHE A 194 1 O VAL A 192 N LEU A 173 SHEET 6 A 6 ARG A 209 LEU A 211 1 O ARG A 209 N LEU A 193 LINK OD2 ASP A 41 MG MG A 301 1555 1555 2.10 LINK O ASP A 43 MG MG A 301 1555 1555 2.02 LINK OD1 ASP A 176 MG MG A 301 1555 1555 2.05 LINK MG MG A 301 O2 PO4 A 302 1555 1555 2.09 LINK MG MG A 301 O HOH A 401 1555 1555 2.10 LINK MG MG A 301 O HOH A 402 1555 1555 2.00 CISPEP 1 PRO A 206 PRO A 207 0 3.76 SITE 1 AC1 6 ASP A 41 ASP A 43 ASP A 176 PO4 A 302 SITE 2 AC1 6 HOH A 401 HOH A 402 SITE 1 AC2 15 ASP A 41 MET A 42 ASP A 43 THR A 130 SITE 2 AC2 15 SER A 131 LYS A 143 LYS A 165 MG A 301 SITE 3 AC2 15 2JW A 303 GOL A 310 GOL A 311 HOH A 401 SITE 4 AC2 15 HOH A 402 HOH A 418 HOH A 680 SITE 1 AC3 19 PHE A 75 TRP A 76 VAL A 77 TRP A 96 SITE 2 AC3 19 SER A 131 ILE A 133 LYS A 134 ARG A 163 SITE 3 AC3 19 ARG A 177 PO4 A 302 HOH A 402 HOH A 429 SITE 4 AC3 19 HOH A 455 HOH A 542 HOH A 600 HOH A 678 SITE 5 AC3 19 HOH A 679 HOH A 681 HOH A 683 SITE 1 AC4 11 TYR A 138 TRP A 214 ALA A 215 ASP A 216 SITE 2 AC4 11 ASP A 217 TRP A 218 LYS A 219 GOL A 309 SITE 3 AC4 11 HOH A 578 HOH A 638 HOH A 689 SITE 1 AC5 5 ASP A 48 GLY A 51 ARG A 55 PRO A 86 SITE 2 AC5 5 HOH A 408 SITE 1 AC6 9 SER A 27 ASN A 28 ALA A 119 THR A 124 SITE 2 AC6 9 ASP A 125 VAL A 126 GLN A 158 HOH A 541 SITE 3 AC6 9 HOH A 653 SITE 1 AC7 10 ASN A 100 PHE A 103 TYR A 141 PEG A 312 SITE 2 AC7 10 HOH A 420 HOH A 506 HOH A 592 HOH A 642 SITE 3 AC7 10 HOH A 655 HOH A 687 SITE 1 AC8 8 PHE A 75 TRP A 76 ARG A 177 PRO A 178 SITE 2 AC8 8 ASP A 179 HOH A 480 HOH A 572 HOH A 588 SITE 1 AC9 10 GLY A 110 GLU A 113 ALA A 114 TRP A 214 SITE 2 AC9 10 ALA A 215 TRP A 218 TRS A 304 HOH A 447 SITE 3 AC9 10 HOH A 496 HOH A 571 SITE 1 BC1 8 ASP A 43 GLU A 50 PHE A 75 PO4 A 302 SITE 2 BC1 8 GOL A 311 HOH A 402 HOH A 523 HOH A 678 SITE 1 BC2 11 PHE A 75 TRP A 76 SER A 131 PRO A 132 SITE 2 BC2 11 ARG A 163 PO4 A 302 GOL A 310 HOH A 461 SITE 3 BC2 11 HOH A 515 HOH A 542 HOH A 680 SITE 1 BC3 11 PHE A 103 LYS A 149 PRO A 207 ARG A 208 SITE 2 BC3 11 ARG A 209 GOL A 307 PEG A 317 HOH A 473 SITE 3 BC3 11 HOH A 644 HOH A 655 HOH A 687 SITE 1 BC4 7 ASN A 28 ALA A 29 GLY A 33 ALA A 35 SITE 2 BC4 7 ASP A 125 ALA A 183 HOH A 568 SITE 1 BC5 6 LYS A 56 ASN A 100 GLU A 104 HOH A 424 SITE 2 BC5 6 HOH A 471 HOH A 684 SITE 1 BC6 12 ARG A 72 ARG A 73 GLY A 74 CYS A 197 SITE 2 BC6 12 HIS A 198 ASN A 199 GLN A 200 HIS A 201 SITE 3 BC6 12 LEU A 202 HOH A 433 HOH A 589 HOH A 623 SITE 1 BC7 5 PRO A 178 ASP A 179 ILE A 180 HIS A 191 SITE 2 BC7 5 HOH A 682 SITE 1 BC8 8 GLU A 148 LYS A 149 LEU A 204 PRO A 206 SITE 2 BC8 8 ARG A 208 PEG A 312 HOH A 446 HOH A 470 SITE 1 BC9 6 ASP A 48 GLY A 51 LEU A 69 GLU A 90 SITE 2 BC9 6 HOH A 422 HOH A 615 CRYST1 73.650 73.650 105.910 90.00 90.00 90.00 P 43 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 0.013578 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013578 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009442 0.00000