HEADER HYDROLASE 02-OCT-15 5FIS TITLE EXONUCLEASE DOMAIN-CONTAINING 1 (EXD1) IN THE GD BOUND CONFORMATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: EXD1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: EXONUCLEASE DOMAIN, RESIDUES 73-315; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: EXD1; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: EXONUCLEASE DOMAIN, RESIDUES 73-315; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOMBYX MORI; SOURCE 3 ORGANISM_COMMON: DOMESTIC SILKWORM; SOURCE 4 ORGANISM_TAXID: 7091; SOURCE 5 CELL_LINE: BMN4; SOURCE 6 ORGAN: OVARIES; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_VECTOR: PETM-22; SOURCE 12 MOL_ID: 2; SOURCE 13 ORGANISM_SCIENTIFIC: BOMBYX MORI; SOURCE 14 ORGANISM_COMMON: DOMESTIC SILKWORM; SOURCE 15 ORGANISM_TAXID: 7091; SOURCE 16 CELL_LINE: BMN4; SOURCE 17 ORGAN: OVARIES; SOURCE 18 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 20 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 21 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 22 EXPRESSION_SYSTEM_VECTOR: PETM-22 KEYWDS HYDROLASE, EXONUCLEASE, PIRNA BIOGENESIS, DIMER, RNA BINDING EXPDTA X-RAY DIFFRACTION AUTHOR Z.YANG,K.M.CHEN,R.R.PANDEY,D.HOMOLKA,M.REUTER,B.K.RODINO JANEIRO, AUTHOR 2 R.SACHIDANANDAM,M.O.FAUVARQUE,A.A.MCCARTHY,R.S.PILLAI REVDAT 3 20-JAN-16 5FIS 1 JRNL REVDAT 2 13-JAN-16 5FIS 1 JRNL REVDAT 1 23-DEC-15 5FIS 0 JRNL AUTH Z.YANG,K.M.CHEN,R.R.PANDEY,D.HOMOLKA,M.REUTER, JRNL AUTH 2 B.K.RODINO JANEIRO,R.SACHIDANANDAM,M.O.FAUVARQUE, JRNL AUTH 3 A.A.MCCARTHY,R.S.PILLAI JRNL TITL PIWI SLICING AND EXD1 DRIVE BIOGENESIS OF NUCLEAR PIRNAS JRNL TITL 2 FROM CYTOSOLIC TARGETS OF THE MOUSE PIRNA PATHWAY JRNL REF MOL.CELL V. 61 138 2016 JRNL REFN ISSN 1097-2765 JRNL PMID 26669262 JRNL DOI 10.1016/J.MOLCEL.2015.11.009 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0131 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU, REMARK 3 STEINER,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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 99.20 REMARK 3 NUMBER OF REFLECTIONS : 72884 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) : 0.15818 REMARK 3 R VALUE (WORKING SET) : 0.15690 REMARK 3 FREE R VALUE : 0.18245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.1 REMARK 3 FREE R VALUE TEST SET COUNT : 3895 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) : 1.600 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.642 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5249 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.19 REMARK 3 BIN R VALUE (WORKING SET) : 0.225 REMARK 3 BIN FREE R VALUE SET COUNT : 273 REMARK 3 BIN FREE R VALUE : 0.241 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3914 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 17 REMARK 3 SOLVENT ATOMS : 411 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.586 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.79 REMARK 3 B22 (A**2) : -0.00 REMARK 3 B33 (A**2) : -1.78 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.072 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.073 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.047 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.257 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.962 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4001 ; 0.029 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3923 ; 0.011 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5380 ; 2.473 ; 1.960 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9065 ; 1.705 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 486 ; 5.848 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 193 ;34.389 ;25.440 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 786 ;13.495 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ; 6.185 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 601 ; 0.151 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4453 ; 0.014 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 898 ; 0.006 ; 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): 1932 ; 1.993 ; 1.921 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1931 ; 1.975 ; 1.919 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2413 ; 2.880 ; 2.873 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2069 ; 4.039 ; 2.454 REMARK 3 SIDE-CHAIN ANGLE REFINED 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 75 315 B 75 315 30078 0.08 0.05 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 75 A 315 REMARK 3 ORIGIN FOR THE GROUP (A): 26.0428 24.5103 9.9090 REMARK 3 T TENSOR REMARK 3 T11: 0.0038 T22: 0.0207 REMARK 3 T33: 0.0182 T12: -0.0068 REMARK 3 T13: 0.0006 T23: 0.0004 REMARK 3 L TENSOR REMARK 3 L11: 0.2541 L22: 0.4633 REMARK 3 L33: 0.0338 L12: 0.2654 REMARK 3 L13: -0.0804 L23: -0.0724 REMARK 3 S TENSOR REMARK 3 S11: -0.0145 S12: -0.0003 S13: -0.0377 REMARK 3 S21: -0.0067 S22: 0.0113 S23: -0.0451 REMARK 3 S31: 0.0029 S32: 0.0079 S33: 0.0032 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 : B 75 B 315 REMARK 3 ORIGIN FOR THE GROUP (A): 25.4460 44.9457 7.9991 REMARK 3 T TENSOR REMARK 3 T11: 0.0046 T22: 0.0097 REMARK 3 T33: 0.0132 T12: -0.0045 REMARK 3 T13: -0.0022 T23: -0.0053 REMARK 3 L TENSOR REMARK 3 L11: 0.3218 L22: 0.6641 REMARK 3 L33: 0.0501 L12: 0.3324 REMARK 3 L13: 0.1250 L23: 0.1182 REMARK 3 S TENSOR REMARK 3 S11: -0.0221 S12: -0.0097 S13: 0.0514 REMARK 3 S21: -0.0288 S22: -0.0006 S23: 0.0462 REMARK 3 S31: -0.0074 S32: -0.0067 S33: 0.0228 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 REMARK 3 RIDING POSITIONS. REMARK 4 REMARK 4 5FIS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-OCT-15. REMARK 100 THE PDBE ID CODE IS EBI-65186. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-OCT-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976 REMARK 200 MONOCHROMATOR : SI111 REMARK 200 OPTICS : TOROIDAL MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL (PILATUS 6M-F) REMARK 200 DETECTOR MANUFACTURER : DECTRIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 143744 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.60 REMARK 200 RESOLUTION RANGE LOW (A) : 50.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 2.8 REMARK 200 R MERGE (I) : 0.07 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.00 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.6 REMARK 200 R MERGE FOR SHELL (I) : 0.82 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.90 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELX, SHARP, BUCCANEER REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: OSCILLATION DATA WERE COLLECTED USING MXCUBEV2 REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.4 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% (W/V) PEG 2K, 200 MM KCL, REMARK 280 50 MM NA CACODYLATE (PH=6) 2 MM GDCL3, REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 41.43000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 67.85000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 41.43000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 67.85000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 6310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.5 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 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 LYS A 73 REMARK 465 VAL A 74 REMARK 465 LYS B 73 REMARK 465 VAL B 74 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 TYR B 315 CG CD1 CD2 CE1 CE2 CZ OH 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 163 CD GLU A 163 OE1 0.067 REMARK 500 GLU A 270 CG GLU A 270 CD 0.095 REMARK 500 GLU A 271 CD GLU A 271 OE2 0.148 REMARK 500 GLU B 163 CD GLU B 163 OE1 0.072 REMARK 500 GLU B 308 CD GLU B 308 OE1 0.104 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 ASP A 113 CB - CG - OD2 ANGL. DEV. = -6.6 DEGREES REMARK 500 PHE A 132 CB - CG - CD2 ANGL. DEV. = -4.9 DEGREES REMARK 500 ASP A 138 CB - CG - OD1 ANGL. DEV. = 10.4 DEGREES REMARK 500 PHE A 193 CB - CG - CD1 ANGL. DEV. = -4.9 DEGREES REMARK 500 ARG A 244 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ASP A 252 CB - CG - OD1 ANGL. DEV. = 6.6 DEGREES REMARK 500 TYR A 277 CE1 - CZ - CE2 ANGL. DEV. = 8.0 DEGREES REMARK 500 TYR A 277 CE1 - CZ - OH ANGL. DEV. = -17.1 DEGREES REMARK 500 ARG A 288 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ASP A 291 CB - CG - OD1 ANGL. DEV. = 10.1 DEGREES REMARK 500 ASP A 292 CB - CG - OD1 ANGL. DEV. = 8.0 DEGREES REMARK 500 ASP B 138 CB - CG - OD1 ANGL. DEV. = 7.7 DEGREES REMARK 500 ASP B 233 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP B 252 CB - CG - OD1 ANGL. DEV. = 6.4 DEGREES REMARK 500 TYR B 277 CB - CG - CD1 ANGL. DEV. = -4.3 DEGREES REMARK 500 ASP B 291 CB - CG - OD1 ANGL. DEV. = 6.9 DEGREES REMARK 500 ARG B 310 NE - CZ - NH2 ANGL. DEV. = -5.3 DEGREES REMARK 500 ASP B 314 CB - CG - OD1 ANGL. DEV. = 5.8 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 GLN A 150 -143.56 52.04 REMARK 500 ASP A 173 74.49 60.49 REMARK 500 SER A 191 75.57 70.63 REMARK 500 VAL A 208 -48.99 65.89 REMARK 500 LYS A 301 34.07 -142.06 REMARK 500 GLN B 150 -149.63 50.76 REMARK 500 ASP B 173 75.32 58.62 REMARK 500 SER B 191 73.26 73.38 REMARK 500 VAL B 208 -50.26 65.90 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 GD A1316 GD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 138 OD1 REMARK 620 2 GLU A 266 OE1 124.5 REMARK 620 3 ASP B 113 OD2 123.5 73.3 REMARK 620 4 HOH A2093 O 71.4 62.0 76.1 REMARK 620 5 ASP A 138 OD2 52.7 136.8 77.5 80.6 REMARK 620 6 ASP B 113 OD1 121.2 110.2 52.4 125.8 73.7 REMARK 620 7 HOH A2094 O 72.0 79.9 153.2 90.8 124.0 142.9 REMARK 620 8 HOH A2005 O 140.2 72.4 95.0 134.3 142.0 72.5 77.3 REMARK 620 9 HOH A2006 O 74.3 142.5 126.9 145.6 80.7 75.2 76.3 74.4 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 GD B1316 GD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 266 OE1 REMARK 620 2 HOH A2064 O 72.3 REMARK 620 3 HOH A2065 O 143.0 75.3 REMARK 620 4 HOH B2068 O 79.5 79.4 77.3 REMARK 620 5 ASP A 113 OD2 75.1 95.1 125.7 154.5 REMARK 620 6 HOH A2066 O 63.3 135.6 144.8 90.9 75.5 REMARK 620 7 ASP A 113 OD1 111.0 71.0 73.9 142.9 52.9 125.9 REMARK 620 8 ASP B 138 OD1 125.5 141.3 73.3 72.2 121.6 71.5 119.8 REMARK 620 9 ASP B 138 OD2 137.8 141.2 79.3 122.8 76.6 79.7 74.0 51.2 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 GD A1317 GD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 104 OE2 REMARK 620 2 TYR B 315 O 56.3 REMARK 620 3 GLU A 104 OE1 49.2 95.3 REMARK 620 4 ASP B 314 OD1 90.1 73.4 132.8 REMARK 620 5 HOH A2039 O 76.5 119.9 75.7 71.7 REMARK 620 6 HOH A2040 O 117.3 123.8 71.2 152.3 109.2 REMARK 620 7 HOH B2178 O 128.1 71.9 149.8 71.0 134.5 92.8 REMARK 620 8 HOH A2038 O 73.2 60.6 64.9 132.9 140.0 64.6 85.2 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GD A1316 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GD B1316 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GD A1317 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5FIQ RELATED DB: PDB REMARK 900 EXONUCLEASE DOMAIN-CONTAINING 1 (EXD1) IN THE NATIVE REMARK 900 CONFORMATION REMARK 999 REMARK 999 SEQUENCE REMARK 999 PROTEIN SEQUENCE CORRESPONDS TO MRNA SEQUENCE: GENBANK ID AK383154 DBREF 5FIS A 73 315 PDB 5FIS 5FIS 73 315 DBREF 5FIS B 73 315 PDB 5FIS 5FIS 73 315 SEQRES 1 A 243 LYS VAL LEU LYS ILE SER GLN THR LYS TYR GLU GLU ILE SEQRES 2 A 243 LEU LYS ILE SER LYS LYS TYR ILE PHE ILE ASN GLN VAL SEQRES 3 A 243 ASP LYS SER PHE HIS GLU ALA VAL ASP ASP LEU ASN GLN SEQRES 4 A 243 GLN ASP PHE ILE ALA VAL SER GLY ASP GLY ALA ASN MET SEQRES 5 A 243 GLY ARG LYS CSO LYS MET PRO PHE LEU VAL LEU SER THR SEQRES 6 A 243 ASP HIS GLN ILE TYR ILE PHE ASP ILE GLN VAL MET GLN SEQRES 7 A 243 TYR HIS ALA PHE GLU SER GLY LEU LYS LYS ILE LEU GLU SEQRES 8 A 243 GLY ASP SER PRO LYS LYS ILE ALA HIS ASP CYS ARG LYS SEQRES 9 A 243 LEU SER ASP CYS LEU TYR HIS LYS HIS ASN VAL LYS LEU SEQRES 10 A 243 LYS SER VAL PHE ASP THR GLN VAL GLY ASP LEU ILE ILE SEQRES 11 A 243 THR LYS ASN LYS LYS VAL THR LEU PRO ASN LYS VAL LYS SEQRES 12 A 243 SER LEU GLY GLU CYS LEU THR ASN TYR LEU GLY LEU GLN SEQRES 13 A 243 GLN ASN THR ILE ASP GLU LYS LEU ASP ILE VAL GLN SER SEQRES 14 A 243 THR GLU ARG PRO LEU SER VAL LYS ILE LYS ASP SER LEU SEQRES 15 A 243 ALA ARG ASN ILE ALA PHE LEU HIS HIS LEU SER GLU VAL SEQRES 16 A 243 ILE ASN GLU GLU MET GLN LEU PRO PHE TYR ARG GLY VAL SEQRES 17 A 243 GLU CYS TYR ILE GLU ASN ILE ARG SER SER ASP ASP PHE SEQRES 18 A 243 LYS ALA TRP GLU LEU CYS GLY LYS LEU ASN GLN ILE PRO SEQRES 19 A 243 LYS GLU PHE ARG ASN ALA ILE ASP TYR SEQRES 1 B 243 LYS VAL LEU LYS ILE SER GLN THR LYS TYR GLU GLU ILE SEQRES 2 B 243 LEU LYS ILE SER LYS LYS TYR ILE PHE ILE ASN GLN VAL SEQRES 3 B 243 ASP LYS SER PHE HIS GLU ALA VAL ASP ASP LEU ASN GLN SEQRES 4 B 243 GLN ASP PHE ILE ALA VAL SER GLY ASP GLY ALA ASN MET SEQRES 5 B 243 GLY ARG LYS CSO LYS MET PRO PHE LEU VAL LEU SER THR SEQRES 6 B 243 ASP HIS GLN ILE TYR ILE PHE ASP ILE GLN VAL MET GLN SEQRES 7 B 243 TYR HIS ALA PHE GLU SER GLY LEU LYS LYS ILE LEU GLU SEQRES 8 B 243 GLY ASP SER PRO ARG LYS ILE ALA HIS ASP CYS ARG LYS SEQRES 9 B 243 LEU SER ASP CYS LEU TYR HIS LYS HIS ASN VAL LYS LEU SEQRES 10 B 243 LYS SER VAL PHE ASP THR GLN VAL GLY ASP LEU ILE ILE SEQRES 11 B 243 THR LYS ASN LYS LYS VAL THR LEU PRO ASN LYS VAL LYS SEQRES 12 B 243 SER LEU GLY GLU CYS LEU THR ASN TYR LEU GLY LEU GLN SEQRES 13 B 243 GLN ASN THR ILE ASP GLU LYS LEU ASP ILE VAL GLN SER SEQRES 14 B 243 THR GLU ARG PRO LEU SER VAL LYS ILE LYS ASP SER LEU SEQRES 15 B 243 ALA ARG ASN ILE ALA PHE LEU HIS HIS LEU SER GLU VAL SEQRES 16 B 243 ILE ASN GLU GLU MET GLN LEU PRO PHE TYR ARG GLY VAL SEQRES 17 B 243 GLU CYS TYR ILE GLU ASN ILE ARG SER SER ASP ASP PHE SEQRES 18 B 243 LYS ALA TRP GLU LEU CYS GLY LYS LEU ASN GLN ILE PRO SEQRES 19 B 243 LYS GLU PHE ARG ASN ALA ILE ASP TYR MODRES 5FIS CSO A 128 CYS S-HYDROXYCYSTEINE MODRES 5FIS CSO B 128 CYS S-HYDROXYCYSTEINE HET CSO A 128 7 HET CSO B 128 7 HET GD A1316 1 HET GD A1317 1 HET GD B1316 1 HETNAM CSO S-HYDROXYCYSTEINE HETNAM GD GADOLINIUM ATOM FORMUL 1 CSO 2(C3 H7 N O3 S) FORMUL 3 GD 3(GD) FORMUL 6 HOH *411(H2 O) HELIX 1 1 SER A 78 LYS A 91 1 14 HELIX 2 2 ASP A 99 GLN A 111 1 13 HELIX 3 3 MET A 124 CSO A 128 5 5 HELIX 4 4 ASP A 145 GLN A 150 1 6 HELIX 5 5 GLN A 150 SER A 156 1 7 HELIX 6 6 GLY A 157 GLY A 164 1 8 HELIX 7 7 CYS A 174 ASN A 186 1 13 HELIX 8 8 THR A 195 VAL A 208 1 14 HELIX 9 9 SER A 216 GLY A 226 1 11 HELIX 10 10 ASP A 237 GLU A 243 1 7 HELIX 11 11 SER A 247 PHE A 260 1 14 HELIX 12 12 PHE A 260 MET A 272 1 13 HELIX 13 13 GLN A 273 SER A 289 1 17 HELIX 14 14 ASP A 291 GLY A 300 1 10 HELIX 15 15 GLU A 308 ASP A 314 1 7 HELIX 16 16 SER B 78 LYS B 91 1 14 HELIX 17 17 ASP B 99 GLN B 111 1 13 HELIX 18 18 MET B 124 CSO B 128 5 5 HELIX 19 19 ASP B 145 GLN B 150 1 6 HELIX 20 20 GLN B 150 SER B 156 1 7 HELIX 21 21 GLY B 157 GLY B 164 1 8 HELIX 22 22 CYS B 174 ASN B 186 1 13 HELIX 23 23 THR B 195 VAL B 208 1 14 HELIX 24 24 SER B 216 GLY B 226 1 11 HELIX 25 25 ASP B 237 GLU B 243 1 7 HELIX 26 26 SER B 247 PHE B 260 1 14 HELIX 27 27 PHE B 260 MET B 272 1 13 HELIX 28 28 GLN B 273 SER B 289 1 17 HELIX 29 29 ASP B 291 GLY B 300 1 10 HELIX 30 30 GLU B 308 ASP B 314 1 7 SHEET 1 AA 6 ILE A 93 ILE A 95 0 SHEET 2 AA 6 ILE A 141 PHE A 144 1 O ILE A 141 N ILE A 93 SHEET 3 AA 6 LEU A 133 SER A 136 -1 O LEU A 133 N PHE A 144 SHEET 4 AA 6 PHE A 114 VAL A 117 -1 O ALA A 116 N SER A 136 SHEET 5 AA 6 LYS A 168 ALA A 171 1 O LYS A 168 N ILE A 115 SHEET 6 AA 6 VAL A 192 ASP A 194 1 O PHE A 193 N ALA A 171 SHEET 1 BA 6 ILE B 93 ILE B 95 0 SHEET 2 BA 6 ILE B 141 PHE B 144 1 O ILE B 141 N ILE B 93 SHEET 3 BA 6 LEU B 133 SER B 136 -1 O LEU B 133 N PHE B 144 SHEET 4 BA 6 PHE B 114 VAL B 117 -1 O ALA B 116 N SER B 136 SHEET 5 BA 6 ARG B 168 ALA B 171 1 O ARG B 168 N ILE B 115 SHEET 6 BA 6 VAL B 192 ASP B 194 1 O PHE B 193 N ALA B 171 LINK C LYS A 127 N CSO A 128 1555 1555 1.34 LINK C CSO A 128 N LYS A 129 1555 1555 1.30 LINK GD GD A1316 OD2 ASP B 113 1555 1555 2.48 LINK GD GD A1316 O HOH A2093 1555 1555 2.40 LINK GD GD A1316 OD2 ASP A 138 1555 1555 2.44 LINK GD GD A1316 OD1 ASP B 113 1555 1555 2.43 LINK GD GD A1316 O HOH A2094 1555 1555 2.42 LINK GD GD A1316 O HOH A2005 1555 1555 2.40 LINK GD GD A1316 O HOH A2006 1555 1555 2.42 LINK GD GD A1316 OE1 GLU A 266 1555 1555 2.39 LINK GD GD A1316 OD1 ASP A 138 1555 1555 2.46 LINK GD GD A1317 OE1 GLU A 104 1555 1555 2.86 LINK GD GD A1317 O TYR B 315 1555 1556 3.14 LINK GD GD A1317 O HOH A2038 1555 1555 2.56 LINK GD GD A1317 O HOH B2178 1555 1556 2.20 LINK GD GD A1317 O HOH A2040 1555 1555 2.19 LINK GD GD A1317 O HOH A2039 1555 1555 2.45 LINK GD GD A1317 OD1 ASP B 314 1555 1556 2.18 LINK GD GD A1317 OE2 GLU A 104 1555 1555 2.25 LINK C LYS B 127 N CSO B 128 1555 1555 1.34 LINK C CSO B 128 N LYS B 129 1555 1555 1.33 LINK GD GD B1316 OD2 ASP B 138 1555 1555 2.46 LINK GD GD B1316 OD1 ASP B 138 1555 1555 2.49 LINK GD GD B1316 OD1 ASP A 113 1555 1555 2.45 LINK GD GD B1316 O HOH A2066 1555 1555 2.42 LINK GD GD B1316 OD2 ASP A 113 1555 1555 2.52 LINK GD GD B1316 O HOH B2068 1555 1555 2.39 LINK GD GD B1316 O HOH A2065 1555 1555 2.54 LINK GD GD B1316 O HOH A2064 1555 1555 2.37 LINK GD GD B1316 OE1 GLU B 266 1555 1555 2.41 CISPEP 1 SER A 166 PRO A 167 0 -2.62 CISPEP 2 ARG A 244 PRO A 245 0 -0.77 CISPEP 3 SER B 166 PRO B 167 0 -2.06 CISPEP 4 ARG B 244 PRO B 245 0 1.70 SITE 1 AC1 7 ASP A 138 GLU A 266 HOH A2005 HOH A2006 SITE 2 AC1 7 HOH A2093 HOH A2094 ASP B 113 SITE 1 AC2 7 ASP A 113 HOH A2064 HOH A2065 HOH A2066 SITE 2 AC2 7 ASP B 138 GLU B 266 HOH B2068 SITE 1 AC3 7 GLU A 104 HOH A2038 HOH A2039 HOH A2040 SITE 2 AC3 7 ASP B 314 TYR B 315 HOH B2178 CRYST1 82.860 135.700 51.460 90.00 90.00 90.00 P 21 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 0.012069 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007369 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019433 0.00000 MTRIX1 1 -0.998160 -0.003710 -0.060550 52.07223 1 MTRIX2 1 -0.007700 -0.982290 0.187200 67.34358 1 MTRIX3 1 -0.060170 0.187320 0.980450 -4.76237 1