HEADER HYDROLASE 12-JUN-13 4L6A TITLE STRUCTURE OF HUMAN MITOCHONDRIAL 5'(3')-DEOXYRIBONUCLEOTIDASE 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 PROTEIN CONFORMATION, SEQUENCE HOMOLOGY, HAD-LIKE, HYDROLASE, KEYWDS 2 DEPHOSPHORYLATION, PHOSPHORYLATION EXPDTA X-RAY DIFFRACTION AUTHOR P.PACHL,J.BRYNDA,P.REZACOVA REVDAT 3 28-FEB-24 4L6A 1 REMARK SEQADV LINK REVDAT 2 18-APR-18 4L6A 1 JRNL REVDAT 1 12-FEB-14 4L6A 0 JRNL AUTH P.PACHL,M.FABRY,I.ROSENBERG,O.SIMAK,P.REZACOVA,J.BRYNDA JRNL TITL STRUCTURES OF HUMAN CYTOSOLIC AND MITOCHONDRIAL JRNL TITL 2 NUCLEOTIDASES: IMPLICATIONS FOR STRUCTURE-BASED DESIGN OF JRNL TITL 3 SELECTIVE INHIBITORS. JRNL REF ACTA CRYSTALLOGR. D BIOL. V. 70 461 2014 JRNL REF 2 CRYSTALLOGR. JRNL REFN ESSN 1399-0047 JRNL PMID 24531480 JRNL DOI 10.1107/S1399004713030502 REMARK 2 REMARK 2 RESOLUTION. 1.40 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 57598 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) : 0.141 REMARK 3 R VALUE (WORKING SET) : 0.141 REMARK 3 FREE R VALUE : 0.154 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2902 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) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3693 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2550 REMARK 3 BIN FREE R VALUE SET COUNT : 190 REMARK 3 BIN FREE R VALUE : 0.2840 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 : 80 REMARK 3 SOLVENT ATOMS : 312 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.54 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.16000 REMARK 3 B22 (A**2) : -0.16000 REMARK 3 B33 (A**2) : 0.32000 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): 0.043 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.043 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.027 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.219 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.976 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.973 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1848 ; 0.017 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 1365 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2498 ; 2.087 ; 1.993 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3277 ; 1.014 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 228 ; 6.082 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 90 ;31.385 ;23.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 313 ;12.024 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;12.098 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 264 ; 0.109 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1999 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 402 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 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 100 REMARK 3 ORIGIN FOR THE GROUP (A): -4.3360 29.3930 22.2250 REMARK 3 T TENSOR REMARK 3 T11: 0.0272 T22: 0.0222 REMARK 3 T33: 0.0516 T12: -0.0095 REMARK 3 T13: 0.0162 T23: -0.0141 REMARK 3 L TENSOR REMARK 3 L11: 1.3461 L22: 1.5880 REMARK 3 L33: 0.7658 L12: -0.7567 REMARK 3 L13: -0.5618 L23: 0.3718 REMARK 3 S TENSOR REMARK 3 S11: 0.0628 S12: -0.0934 S13: 0.2278 REMARK 3 S21: -0.0702 S22: 0.0334 S23: -0.2297 REMARK 3 S31: -0.1263 S32: 0.0364 S33: -0.0962 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 101 A 221 REMARK 3 ORIGIN FOR THE GROUP (A): -1.9940 14.6130 17.5660 REMARK 3 T TENSOR REMARK 3 T11: 0.0137 T22: 0.0157 REMARK 3 T33: 0.0289 T12: -0.0021 REMARK 3 T13: 0.0176 T23: -0.0005 REMARK 3 L TENSOR REMARK 3 L11: 0.7663 L22: 0.5064 REMARK 3 L33: 0.5475 L12: 0.1223 REMARK 3 L13: -0.2725 L23: -0.0472 REMARK 3 S TENSOR REMARK 3 S11: -0.0215 S12: 0.0057 S13: -0.0859 REMARK 3 S21: -0.0519 S22: -0.0042 S23: -0.0873 REMARK 3 S31: 0.0118 S32: 0.0324 S33: 0.0257 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 4L6A 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_1000080234. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-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 : 57600 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 25.498 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06300 REMARK 200 FOR THE DATA SET : 11.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.47200 REMARK 200 R SYM FOR SHELL (I) : 0.47200 REMARK 200 FOR SHELL : 1.600 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 (%): 60.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8% PEG 8000, 20MM POTASSIUM PHOSPHATE, REMARK 280 10% GLYCEROL, PH 4.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 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 53.17000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 36.70500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 36.70500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 79.75500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 36.70500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 36.70500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.58500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 36.70500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.70500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 79.75500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 36.70500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.70500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 26.58500 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 53.17000 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: 9750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 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 53.17000 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 695 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: 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 OD2 ASP A 63 O HOH A 477 2.10 REMARK 500 REMARK 500 REMARK: NULL 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 HIS A 212 CG HIS A 212 CD2 0.059 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. = 6.3 DEGREES REMARK 500 ARG A 37 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ASP A 63 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ASP A 179 CB - CA - C ANGL. DEV. = 13.4 DEGREES REMARK 500 ASP A 179 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ARG A 209 NE - CZ - NH1 ANGL. DEV. = 4.6 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 SER A 31 124.32 -30.87 REMARK 500 MET A 42 -74.70 -100.24 REMARK 500 VAL A 45 -50.85 -128.77 REMARK 500 ASN A 100 -2.23 75.07 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 313 REMARK 610 PEG A 314 REMARK 610 PEG A 315 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 85.5 REMARK 620 3 ASP A 176 OD1 84.0 90.9 REMARK 620 4 PO4 A 302 O2 86.7 94.1 169.0 REMARK 620 5 HOH A 430 O 90.8 176.1 89.6 84.8 REMARK 620 6 HOH A 448 O 172.9 88.0 93.3 96.6 95.8 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 GOL 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 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 K A 316 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4L6C RELATED DB: PDB DBREF 4L6A A 32 228 UNP Q9NPB1 NT5M_HUMAN 32 228 SEQADV 4L6A SER A 27 UNP Q9NPB1 EXPRESSION TAG SEQADV 4L6A ASN A 28 UNP Q9NPB1 EXPRESSION TAG SEQADV 4L6A ALA A 29 UNP Q9NPB1 EXPRESSION TAG SEQADV 4L6A ALA A 30 UNP Q9NPB1 EXPRESSION TAG SEQADV 4L6A 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 GOL A 303 6 HET GOL A 304 6 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 7 HET PEG A 313 4 HET PEG A 314 4 HET PEG A 315 4 HET K A 316 1 HETNAM MG MAGNESIUM ION HETNAM PO4 PHOSPHATE ION HETNAM GOL GLYCEROL HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM K POTASSIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 MG MG 2+ FORMUL 3 PO4 O4 P 3- FORMUL 4 GOL 9(C3 H8 O3) FORMUL 13 PEG 4(C4 H10 O3) FORMUL 17 K K 1+ FORMUL 18 HOH *312(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 VAL A 40 O PHE A 127 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 LEU A 211 N LEU A 193 LINK OD2 ASP A 41 MG MG A 301 1555 1555 2.13 LINK O ASP A 43 MG MG A 301 1555 1555 2.09 LINK OD1 ASP A 176 MG MG A 301 1555 1555 2.03 LINK O PRO A 178 K K A 316 1555 1555 3.30 LINK MG MG A 301 O2 PO4 A 302 1555 1555 2.12 LINK MG MG A 301 O HOH A 430 1555 1555 2.05 LINK MG MG A 301 O HOH A 448 1555 1555 2.02 CISPEP 1 PRO A 206 PRO A 207 0 7.66 SITE 1 AC1 6 ASP A 41 ASP A 43 ASP A 176 PO4 A 302 SITE 2 AC1 6 HOH A 430 HOH A 448 SITE 1 AC2 13 ASP A 41 MET A 42 ASP A 43 THR A 130 SITE 2 AC2 13 SER A 131 LYS A 143 LYS A 165 MG A 301 SITE 3 AC2 13 GOL A 303 GOL A 308 HOH A 403 HOH A 430 SITE 4 AC2 13 HOH A 448 SITE 1 AC3 9 PHE A 49 GLU A 50 PHE A 75 PO4 A 302 SITE 2 AC3 9 GOL A 305 GOL A 308 HOH A 448 HOH A 503 SITE 3 AC3 9 HOH A 597 SITE 1 AC4 7 TRP A 96 GLU A 97 ILE A 133 LYS A 134 SITE 2 AC4 7 MET A 135 GOL A 305 HOH A 570 SITE 1 AC5 11 PHE A 49 VAL A 77 TRP A 96 ILE A 133 SITE 2 AC5 11 GOL A 303 GOL A 304 GOL A 308 HOH A 441 SITE 3 AC5 11 HOH A 595 HOH A 644 HOH A 645 SITE 1 AC6 11 SER A 27 ASN A 28 ALA A 119 THR A 124 SITE 2 AC6 11 ASP A 125 VAL A 126 PHE A 155 GLN A 158 SITE 3 AC6 11 HOH A 495 HOH A 547 HOH A 627 SITE 1 AC7 5 ARG A 163 ARG A 177 THR A 181 HOH A 428 SITE 2 AC7 5 HOH A 687 SITE 1 AC8 14 PHE A 75 TRP A 76 SER A 131 PRO A 132 SITE 2 AC8 14 ARG A 163 PO4 A 302 GOL A 303 GOL A 305 SITE 3 AC8 14 HOH A 476 HOH A 595 HOH A 611 HOH A 639 SITE 4 AC8 14 HOH A 644 HOH A 645 SITE 1 AC9 10 ILE A 93 GLU A 97 MET A 135 HIS A 212 SITE 2 AC9 10 HOH A 482 HOH A 508 HOH A 578 HOH A 659 SITE 3 AC9 10 HOH A 673 HOH A 690 SITE 1 BC1 8 TYR A 138 ASP A 217 TRP A 218 LYS A 219 SITE 2 BC1 8 PEG A 313 PEG A 315 HOH A 418 HOH A 685 SITE 1 BC2 11 ASN A 100 PHE A 103 LYS A 137 TYR A 141 SITE 2 BC2 11 PEG A 314 HOH A 607 HOH A 629 HOH A 635 SITE 3 BC2 11 HOH A 642 HOH A 646 HOH A 656 SITE 1 BC3 13 ARG A 72 ARG A 73 GLY A 74 CYS A 197 SITE 2 BC3 13 HIS A 198 ASN A 199 GLN A 200 HIS A 201 SITE 3 BC3 13 LEU A 202 HOH A 429 HOH A 523 HOH A 624 SITE 4 BC3 13 HOH A 650 SITE 1 BC4 7 TRP A 214 ALA A 215 ASP A 216 TRP A 218 SITE 2 BC4 7 GOL A 310 HOH A 471 HOH A 538 SITE 1 BC5 10 PHE A 103 LYS A 149 PRO A 207 ARG A 208 SITE 2 BC5 10 ARG A 209 GOL A 311 HOH A 469 HOH A 631 SITE 3 BC5 10 HOH A 635 HOH A 656 SITE 1 BC6 5 LYS A 99 TYR A 138 ASP A 217 GOL A 310 SITE 2 BC6 5 HOH A 695 SITE 1 BC7 3 PRO A 178 ILE A 180 HIS A 191 CRYST1 73.410 73.410 106.340 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 0.013622 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013622 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009404 0.00000