HEADER HYDROLASE/HYDROLASE INHIBITOR 12-JUN-13 4L6C TITLE CRYSTAL STRUCTURE OF HUMAN MITOCHONDRIAL DEOXYRIBONUCLEOTIDASE IN TITLE 2 COMPLEX WITH THE INHIBITOR PIB-T COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'(3')-DEOXYRIBONUCLEOTIDASE, MITOCHONDRIAL; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 32-228; 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: DNT2, NT5M; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PMCSG7 KEYWDS 5'-NUCLEOTIDASE, MITOCHONDRIA, PROTEIN CONFORMATION, SEQUENCE KEYWDS 2 HOMOLOGY, HAD-LIKE, HYDROLASE, DEPHOSPHORYLATION, PHOSPHORYLATION, KEYWDS 3 HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.PACHL,J.BRYNDA,P.REZACOVA REVDAT 3 28-FEB-24 4L6C 1 REMARK SEQADV LINK REVDAT 2 08-OCT-14 4L6C 1 JRNL REVDAT 1 10-SEP-14 4L6C 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. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 27581 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) : 0.151 REMARK 3 R VALUE (WORKING SET) : 0.150 REMARK 3 FREE R VALUE : 0.172 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1382 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1718 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2160 REMARK 3 BIN FREE R VALUE SET COUNT : 98 REMARK 3 BIN FREE R VALUE : 0.2610 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1636 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 85 REMARK 3 SOLVENT ATOMS : 176 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.04 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.45000 REMARK 3 B22 (A**2) : 0.45000 REMARK 3 B33 (A**2) : -0.90000 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): 0.086 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.051 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.052 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.961 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1823 ; 0.021 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 1308 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2476 ; 2.120 ; 2.002 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3144 ; 1.098 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 218 ; 5.929 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 87 ;29.481 ;23.103 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 298 ;13.123 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;10.396 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 260 ; 0.132 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1977 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 393 ; 0.002 ; 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): 1 ; 0.000 ; 5.000 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 : 3 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 99 REMARK 3 ORIGIN FOR THE GROUP (A): -2.9970 29.3260 22.5920 REMARK 3 T TENSOR REMARK 3 T11: 0.0591 T22: 0.0209 REMARK 3 T33: 0.1753 T12: -0.0189 REMARK 3 T13: 0.0526 T23: -0.0131 REMARK 3 L TENSOR REMARK 3 L11: 1.8505 L22: 0.8468 REMARK 3 L33: 0.8937 L12: -0.3070 REMARK 3 L13: -0.3486 L23: -0.0432 REMARK 3 S TENSOR REMARK 3 S11: 0.0819 S12: -0.0190 S13: 0.3396 REMARK 3 S21: 0.0667 S22: 0.0211 S23: -0.0950 REMARK 3 S31: -0.2010 S32: 0.0792 S33: -0.1030 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 100 A 227 REMARK 3 ORIGIN FOR THE GROUP (A): -2.5810 15.4340 17.5800 REMARK 3 T TENSOR REMARK 3 T11: 0.0076 T22: 0.0413 REMARK 3 T33: 0.1379 T12: 0.0024 REMARK 3 T13: 0.0263 T23: -0.0235 REMARK 3 L TENSOR REMARK 3 L11: 1.5188 L22: 0.7953 REMARK 3 L33: 0.9926 L12: 0.2443 REMARK 3 L13: -0.2674 L23: -0.0700 REMARK 3 S TENSOR REMARK 3 S11: 0.0377 S12: 0.1430 S13: -0.0876 REMARK 3 S21: -0.0334 S22: 0.0014 S23: -0.1128 REMARK 3 S31: -0.0148 S32: 0.1039 S33: -0.0391 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 301 A 576 REMARK 3 ORIGIN FOR THE GROUP (A): -3.6240 24.7680 28.8380 REMARK 3 T TENSOR REMARK 3 T11: 0.2273 T22: 0.1974 REMARK 3 T33: 0.4513 T12: 0.0093 REMARK 3 T13: 0.0811 T23: -0.0629 REMARK 3 L TENSOR REMARK 3 L11: 21.4462 L22: 25.4938 REMARK 3 L33: 11.4867 L12: 18.9013 REMARK 3 L13: -7.3369 L23: -15.3711 REMARK 3 S TENSOR REMARK 3 S11: 0.0270 S12: 0.1899 S13: -0.5464 REMARK 3 S21: 0.2211 S22: 0.3273 S23: 0.0276 REMARK 3 S31: -0.2141 S32: -0.2208 S33: -0.3543 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 4 REMARK 4 4L6C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUN-13. REMARK 100 THE DEPOSITION ID IS D_1000080236. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91502 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27645 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 34.836 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 16.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07900 REMARK 200 FOR THE DATA SET : 23.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 16.00 REMARK 200 R MERGE FOR SHELL (I) : 0.58500 REMARK 200 R SYM FOR SHELL (I) : 0.58500 REMARK 200 FOR SHELL : 1.300 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8% PEG 8000, 20MM DIHYDROGEN POTASSIUM REMARK 280 PHOSPHATE, 10% GLYCEROL, PH 4.2, 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 52.75500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 36.90500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 36.90500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 79.13250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 36.90500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 36.90500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.37750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 36.90500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.90500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 79.13250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 36.90500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.90500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 26.37750 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 52.75500 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: 7870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 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 52.75500 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 547 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 CYS A 228 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 GLU A 148 CD GLU A 148 OE2 -0.086 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. = 5.5 DEGREES REMARK 500 ARG A 37 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 60 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 72 NE - CZ - NH2 ANGL. DEV. = -3.8 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 -73.76 -96.89 REMARK 500 VAL A 45 -54.00 -130.46 REMARK 500 PRO A 207 35.89 -97.40 REMARK 500 SER A 213 176.99 178.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 41 OD2 REMARK 620 2 ASP A 43 O 88.7 REMARK 620 3 ASP A 176 OD1 86.0 87.9 REMARK 620 4 PO4 A 302 O2 91.2 93.6 176.7 REMARK 620 5 HOH A 417 O 90.9 179.0 91.2 87.3 REMARK 620 6 HOH A 418 O 171.3 85.3 87.5 95.5 95.0 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 0BT A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL 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 EDO A 311 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 312 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4L6A RELATED DB: PDB DBREF 4L6C A 32 228 UNP Q9NPB1 NT5M_HUMAN 32 228 SEQADV 4L6C SER A 27 UNP Q9NPB1 EXPRESSION TAG SEQADV 4L6C ASN A 28 UNP Q9NPB1 EXPRESSION TAG SEQADV 4L6C ALA A 29 UNP Q9NPB1 EXPRESSION TAG SEQADV 4L6C ALA A 30 UNP Q9NPB1 EXPRESSION TAG SEQADV 4L6C SER A 31 UNP Q9NPB1 EXPRESSION TAG SEQRES 1 A 202 SER ASN ALA ALA SER GLY GLY ARG ALA LEU ARG VAL LEU SEQRES 2 A 202 VAL ASP MET ASP GLY VAL LEU ALA ASP PHE GLU GLY GLY SEQRES 3 A 202 PHE LEU ARG LYS PHE ARG ALA ARG PHE PRO ASP GLN PRO SEQRES 4 A 202 PHE ILE ALA LEU GLU ASP ARG ARG GLY PHE TRP VAL SER SEQRES 5 A 202 GLU GLN TYR GLY ARG LEU ARG PRO GLY LEU SER GLU LYS SEQRES 6 A 202 ALA ILE SER ILE TRP GLU SER LYS ASN PHE PHE PHE GLU SEQRES 7 A 202 LEU GLU PRO LEU PRO GLY ALA VAL GLU ALA VAL LYS GLU SEQRES 8 A 202 MET ALA SER LEU GLN ASN THR ASP VAL PHE ILE CYS THR SEQRES 9 A 202 SER PRO ILE LYS MET PHE LYS TYR CYS PRO TYR GLU LYS SEQRES 10 A 202 TYR ALA TRP VAL GLU LYS TYR PHE GLY PRO ASP PHE LEU SEQRES 11 A 202 GLU GLN ILE VAL LEU THR ARG ASP LYS THR VAL VAL SER SEQRES 12 A 202 ALA ASP LEU LEU ILE ASP ASP ARG PRO ASP ILE THR GLY SEQRES 13 A 202 ALA GLU PRO THR PRO SER TRP GLU HIS VAL LEU PHE THR SEQRES 14 A 202 ALA CYS HIS ASN GLN HIS LEU GLN LEU GLN PRO PRO ARG SEQRES 15 A 202 ARG ARG LEU HIS SER TRP ALA ASP ASP TRP LYS ALA ILE SEQRES 16 A 202 LEU ASP SER LYS ARG PRO CYS HET MG A 301 1 HET PO4 A 302 5 HET 0BT A 303 29 HET GOL A 304 6 HET GOL A 305 6 HET GOL A 306 6 HET GOL A 307 6 HET GOL A 308 6 HET GOL A 309 6 HET GOL A 310 6 HET EDO A 311 4 HET EDO A 312 4 HETNAM MG MAGNESIUM ION HETNAM PO4 PHOSPHATE ION HETNAM 0BT 1-{2-DEOXY-3,5-O-[(4-IODOPHENYL)(PHOSPHONO) HETNAM 2 0BT METHYLIDENE]-BETA-D-THREO-PENTOFURANOSYL}-5- HETNAM 3 0BT METHYLPYRIMIDINE-2,4(1H,3H)-DIONE HETNAM GOL GLYCEROL HETNAM EDO 1,2-ETHANEDIOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 MG MG 2+ FORMUL 3 PO4 O4 P 3- FORMUL 4 0BT C17 H18 I N2 O8 P FORMUL 5 GOL 7(C3 H8 O3) FORMUL 12 EDO 2(C2 H6 O2) FORMUL 14 HOH *176(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 SER A 120 1 11 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 164 VAL A 168 5 5 HELIX 9 9 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 1.99 LINK O ASP A 43 MG MG A 301 1555 1555 2.01 LINK OD1 ASP A 176 MG MG A 301 1555 1555 2.10 LINK MG MG A 301 O2 PO4 A 302 1555 1555 2.08 LINK MG MG A 301 O HOH A 417 1555 1555 1.99 LINK MG MG A 301 O HOH A 418 1555 1555 2.11 CISPEP 1 PRO A 206 PRO A 207 0 3.85 SITE 1 AC1 6 ASP A 41 ASP A 43 ASP A 176 PO4 A 302 SITE 2 AC1 6 HOH A 417 HOH A 418 SITE 1 AC2 10 ASP A 41 MET A 42 ASP A 43 THR A 130 SITE 2 AC2 10 SER A 131 LYS A 165 MG A 301 0BT A 303 SITE 3 AC2 10 HOH A 417 HOH A 439 SITE 1 AC3 13 PHE A 75 TRP A 76 VAL A 77 TRP A 96 SITE 2 AC3 13 ILE A 133 LYS A 134 ARG A 163 PO4 A 302 SITE 3 AC3 13 HOH A 415 HOH A 418 HOH A 447 HOH A 449 SITE 4 AC3 13 HOH A 567 SITE 1 AC4 9 ARG A 73 GLY A 74 HIS A 198 ASN A 199 SITE 2 AC4 9 GLN A 200 HIS A 201 LEU A 202 HOH A 471 SITE 3 AC4 9 HOH A 500 SITE 1 AC5 9 SER A 27 ASN A 28 ALA A 119 THR A 124 SITE 2 AC5 9 ASP A 125 VAL A 126 GLN A 158 GOL A 309 SITE 3 AC5 9 HOH A 490 SITE 1 AC6 4 TRP A 76 ARG A 177 PRO A 178 ASP A 179 SITE 1 AC7 8 TYR A 138 TRP A 214 ALA A 215 ASP A 216 SITE 2 AC7 8 ASP A 217 TRP A 218 LYS A 219 HOH A 510 SITE 1 AC8 7 ASP A 48 LEU A 108 ALA A 196 CYS A 197 SITE 2 AC8 7 HOH A 436 HOH A 484 HOH A 511 SITE 1 AC9 3 ASP A 154 GLN A 158 GOL A 305 SITE 1 BC1 6 ARG A 37 SER A 169 ALA A 170 ASP A 171 SITE 2 BC1 6 GLU A 184 HOH A 470 SITE 1 BC2 3 PRO A 65 PHE A 66 HOH A 448 SITE 1 BC3 9 ASN A 28 ALA A 29 GLY A 33 ARG A 34 SITE 2 BC3 9 ALA A 35 ASP A 125 ALA A 183 PRO A 185 SITE 3 BC3 9 HOH A 538 CRYST1 73.810 73.810 105.510 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 0.013548 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013548 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009478 0.00000