HEADER HYDROLASE/HYDROLASE 25-APR-07 2PO0 TITLE CRYSTAL STRUCTURE OF THE P. ABYSSI EXOSOME RNASE PH RING COMPLEXED TITLE 2 WITH ADP IN DOUBLE CONFORMATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.13.-; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2; COMPND 8 CHAIN: B; COMPND 9 EC: 3.1.13.-; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS ABYSSI; SOURCE 3 ORGANISM_TAXID: 29292; SOURCE 4 GENE: RRP41; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET29; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: PYROCOCCUS ABYSSI; SOURCE 12 ORGANISM_TAXID: 29292; SOURCE 13 GENE: RRP42; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 15 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PAE KEYWDS RNASE PH, HYDROLASE-HYDROLASE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.V.A.S.NAVARRO,B.G.GUIMARAES REVDAT 4 30-AUG-23 2PO0 1 REMARK SEQADV REVDAT 3 24-FEB-09 2PO0 1 VERSN REVDAT 2 27-MAY-08 2PO0 1 JRNL REVDAT 1 18-MAR-08 2PO0 0 JRNL AUTH M.V.A.S.NAVARRO,C.C.OLIVEIRA,N.I.ZANCHIN,B.G.GUIMARAES JRNL TITL INSIGHTS INTO THE MECHANISM OF PROGRESSIVE RNA DEGRADATION JRNL TITL 2 BY THE ARCHAEAL EXOSOME. JRNL REF J.BIOL.CHEM. V. 283 14120 2008 JRNL REFN ISSN 0021-9258 JRNL PMID 18353775 JRNL DOI 10.1074/JBC.M801005200 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 26541 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) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1433 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1681 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.97 REMARK 3 BIN R VALUE (WORKING SET) : 0.2510 REMARK 3 BIN FREE R VALUE SET COUNT : 84 REMARK 3 BIN FREE R VALUE : 0.4010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3892 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 51 REMARK 3 SOLVENT ATOMS : 151 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : 0.01000 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): 0.291 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.228 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.177 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 16.416 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.913 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4036 ; 0.021 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5467 ; 2.156 ; 2.021 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 503 ; 7.477 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 165 ;37.861 ;24.848 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 751 ;20.148 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;21.796 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 635 ; 0.130 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2929 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2005 ; 0.241 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2673 ; 0.316 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 235 ; 0.213 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 88 ; 0.250 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 18 ; 0.222 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2591 ; 0.751 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4066 ; 1.148 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1610 ; 2.244 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1401 ; 3.208 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 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 9 A 244 REMARK 3 ORIGIN FOR THE GROUP (A): -18.1584 23.9358 38.2209 REMARK 3 T TENSOR REMARK 3 T11: -0.2750 T22: 0.0399 REMARK 3 T33: -0.0955 T12: 0.0365 REMARK 3 T13: -0.0220 T23: 0.0085 REMARK 3 L TENSOR REMARK 3 L11: 2.3792 L22: 4.6552 REMARK 3 L33: 1.8855 L12: 0.2232 REMARK 3 L13: 0.8105 L23: 0.4297 REMARK 3 S TENSOR REMARK 3 S11: 0.0141 S12: -0.0111 S13: 0.0038 REMARK 3 S21: 0.1981 S22: 0.0124 S23: -0.2067 REMARK 3 S31: -0.0132 S32: 0.6162 S33: -0.0265 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 8 B 274 REMARK 3 ORIGIN FOR THE GROUP (A): -32.4303 51.3211 31.2015 REMARK 3 T TENSOR REMARK 3 T11: -0.0970 T22: -0.2332 REMARK 3 T33: -0.1782 T12: -0.1484 REMARK 3 T13: -0.0219 T23: 0.0300 REMARK 3 L TENSOR REMARK 3 L11: 1.7241 L22: 2.0999 REMARK 3 L33: 4.2702 L12: -0.0803 REMARK 3 L13: -0.1445 L23: 1.0322 REMARK 3 S TENSOR REMARK 3 S11: -0.0228 S12: 0.0532 S13: 0.0222 REMARK 3 S21: -0.0560 S22: 0.0313 S23: -0.0706 REMARK 3 S31: -0.4536 S32: 0.2831 S33: -0.0084 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 B 373 REMARK 3 ORIGIN FOR THE GROUP (A): -27.2178 40.1739 32.6227 REMARK 3 T TENSOR REMARK 3 T11: -0.1456 T22: -0.1155 REMARK 3 T33: -0.0618 T12: -0.1369 REMARK 3 T13: -0.0197 T23: 0.0163 REMARK 3 L TENSOR REMARK 3 L11: 0.7329 L22: 1.6486 REMARK 3 L33: 0.9261 L12: -0.7160 REMARK 3 L13: -0.1241 L23: 0.0771 REMARK 3 S TENSOR REMARK 3 S11: 0.0068 S12: 0.0766 S13: -0.0073 REMARK 3 S21: 0.0086 S22: -0.0126 S23: -0.1018 REMARK 3 S31: -0.1254 S32: 0.3403 S33: 0.0058 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 2PO0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-MAY-07. REMARK 100 THE DEPOSITION ID IS D_1000042589. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAY-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LNLS REMARK 200 BEAMLINE : D03B-MX1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.427 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28933 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 44.230 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 9.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09300 REMARK 200 FOR THE DATA SET : 16.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.6 REMARK 200 DATA REDUNDANCY IN SHELL : 8.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.45100 REMARK 200 FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2PNZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS, 45% MPD AND 0.1 M REMARK 280 LICL, PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A HEXAMER GENERATED FROM THE REMARK 300 HETERODIMER IN THE ASYMMETRIC UNIT BY THE OPERATIONS: -Y, X-Y+1, Z REMARK 300 AND -X+Y-1, -X, Z 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 20750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 58700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -166.4 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 -47.10000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 81.57959 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -94.20000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 MET A 2 REMARK 465 GLU A 3 REMARK 465 LYS A 4 REMARK 465 PRO A 5 REMARK 465 GLU A 6 REMARK 465 GLY A 7 REMARK 465 LEU A 8 REMARK 465 VAL A 245 REMARK 465 GLU A 246 REMARK 465 GLY A 247 REMARK 465 SER A 248 REMARK 465 GLU A 249 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 ASP B 3 REMARK 465 ASN B 4 REMARK 465 GLU B 5 REMARK 465 ILE B 6 REMARK 465 VAL B 7 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 OD1 ASN A 38 O HOH A 321 1.89 REMARK 500 OD2 ASP A 180 O3B ADP A 300 2.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NH2 ARG B 170 OE1 GLU B 183 6555 2.16 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 LYS A 217 CE LYS A 217 NZ 0.232 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 78 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ASP A 95 CB - CG - OD2 ANGL. DEV. = 6.1 DEGREES REMARK 500 ARG B 34 NE - CZ - NH1 ANGL. DEV. = -4.2 DEGREES REMARK 500 LEU B 89 CA - CB - CG ANGL. DEV. = 19.6 DEGREES REMARK 500 ARG B 108 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG B 112 NE - CZ - NH1 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG B 115 NE - CZ - NH1 ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG B 115 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 ASN A 14 68.69 62.35 REMARK 500 ASP A 133 19.93 -157.88 REMARK 500 ALA A 134 140.33 87.86 REMARK 500 GLU A 168 50.31 38.94 REMARK 500 ASP A 174 76.97 62.66 REMARK 500 ALA A 242 35.91 -73.78 REMARK 500 PRO B 88 -17.09 -44.89 REMARK 500 LYS B 131 -50.49 -132.52 REMARK 500 GLU B 238 -159.35 61.70 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 250 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 280 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 281 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2PNZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE P. ABYSSI EXOSOME RNASE PH RING COMPLEXED REMARK 900 WITH UDP AND GMP REMARK 900 RELATED ID: 2PO1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE P. ABYSSI EXOSOME RNASE PH RING COMPLEXED REMARK 900 WITH A SINGLE STRANDED 10-MER POLY(A) RNA REMARK 900 RELATED ID: 2PO2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE P. ABYSSI EXOSOME RNASE PH RING COMPLEXED REMARK 900 WITH CDP DBREF 2PO0 A 1 249 UNP Q9V119 ECX1_PYRAB 1 249 DBREF 2PO0 B 1 274 UNP Q9V118 ECX2_PYRAB 1 274 SEQADV 2PO0 GLY B -2 UNP Q9V118 EXPRESSION TAG SEQADV 2PO0 SER B -1 UNP Q9V118 EXPRESSION TAG SEQADV 2PO0 HIS B 0 UNP Q9V118 EXPRESSION TAG SEQRES 1 A 249 MET MET GLU LYS PRO GLU GLY LEU LYS LEU ILE ASP GLU SEQRES 2 A 249 ASN GLY ARG ARG ILE ASP GLY ARG LYS LYS TYR GLU LEU SEQRES 3 A 249 ARG PRO ILE LYS MET GLU VAL GLY VAL LEU LYS ASN ALA SEQRES 4 A 249 ASN GLY SER ALA TYR ILE GLU TRP GLY LYS ASN LYS ILE SEQRES 5 A 249 ILE ALA ALA VAL TYR GLY PRO ARG GLU LEU HIS PRO LYS SEQRES 6 A 249 HIS LEU GLN ARG PRO ASP ARG ALA ILE LEU ARG VAL ARG SEQRES 7 A 249 TYR ASN MET ALA PRO PHE SER VAL GLU GLU ARG LYS LYS SEQRES 8 A 249 PRO GLY PRO ASP ARG ARG SER ILE GLU ILE SER LYS VAL SEQRES 9 A 249 ILE LYS GLY ALA LEU GLU PRO ALA LEU ILE LEU GLU MET SEQRES 10 A 249 PHE PRO ARG THR ALA ILE ASP VAL PHE ILE GLU VAL LEU SEQRES 11 A 249 GLN ALA ASP ALA GLY THR ARG VAL ALA GLY ILE THR ALA SEQRES 12 A 249 ALA SER LEU ALA LEU ALA ASP ALA GLY ILE PRO MET ARG SEQRES 13 A 249 ASP LEU VAL ALA ALA CYS ALA ALA GLY LYS ILE GLU GLY SEQRES 14 A 249 GLU ILE VAL LEU ASP LEU ASN LYS GLU GLU ASP ASN TYR SEQRES 15 A 249 GLY GLU ALA ASP VAL PRO VAL ALA ILE MET PRO LEU LYS SEQRES 16 A 249 ASN ASP ILE THR LEU LEU GLN MET ASP GLY TYR LEU THR SEQRES 17 A 249 LYS ASP GLU PHE ILE GLU ALA VAL LYS LEU ALA ILE LYS SEQRES 18 A 249 GLY ALA LYS ALA VAL TYR GLN LYS GLN ARG GLU ALA LEU SEQRES 19 A 249 LYS GLU LYS TYR LEU LYS ILE ALA GLN GLU VAL GLU GLY SEQRES 20 A 249 SER GLU SEQRES 1 B 277 GLY SER HIS MET SER ASP ASN GLU ILE VAL ALA GLY ILE SEQRES 2 B 277 MET ARG ASP HIS ILE ILE ASN LEU LEU LYS GLU GLY LYS SEQRES 3 B 277 ARG ILE ASP ASP ARG GLY PHE GLU ASP TYR ARG PRO ILE SEQRES 4 B 277 GLU ILE GLU VAL GLY VAL ILE GLU LYS ALA GLU GLY SER SEQRES 5 B 277 ALA LEU VAL LYS LEU GLY SER THR GLN VAL LEU VAL GLY SEQRES 6 B 277 ILE LYS THR SER LEU GLY GLU PRO PHE PRO ASP THR PRO SEQRES 7 B 277 ASN MET GLY VAL MET THR THR ASN VAL GLU LEU VAL PRO SEQRES 8 B 277 LEU ALA SER PRO THR PHE GLU PRO GLY PRO PRO ASP GLU SEQRES 9 B 277 ARG ALA ILE GLU LEU ALA ARG VAL ILE ASP ARG GLY ILE SEQRES 10 B 277 ARG GLU SER LYS ALA LEU ASN LEU GLU LYS MET VAL ILE SEQRES 11 B 277 VAL PRO GLY LYS ILE VAL ARG VAL VAL PHE ILE ASP VAL SEQRES 12 B 277 HIS VAL LEU ASP HIS ASP GLY ASN LEU MET ASP ALA ILE SEQRES 13 B 277 GLY ILE ALA ALA ILE ALA ALA LEU LEU ASN ALA ARG VAL SEQRES 14 B 277 PRO LYS VAL ARG TYR ASN GLU GLU THR GLY GLU VAL GLU SEQRES 15 B 277 THR LEU ASP GLU THR GLU PRO LEU PRO VAL GLU LYS ILE SEQRES 16 B 277 PRO VAL PRO VAL THR PHE ALA LYS ILE GLY ASN ILE LEU SEQRES 17 B 277 VAL VAL ASP PRO SER LEU ASP GLU GLU LEU VAL MET ASP SEQRES 18 B 277 GLY LYS ILE THR ILE THR THR ASP GLU THR GLY HIS ILE SEQRES 19 B 277 SER ALA VAL GLN LYS SER GLU GLY GLY ALA PHE LYS LEU SEQRES 20 B 277 GLU GLU VAL MET TYR ALA VAL GLU THR ALA PHE LYS LYS SEQRES 21 B 277 ALA GLU GLU ILE ARG LYS LEU ILE LEU GLU ALA VAL GLU SEQRES 22 B 277 LYS ALA LYS GLN HET ADP A 300 54 HET MPD A 250 8 HET MPD B 280 8 HET MPD B 281 8 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 3 ADP C10 H15 N5 O10 P2 FORMUL 4 MPD 3(C6 H14 O2) FORMUL 7 HOH *151(H2 O) HELIX 1 1 ASP A 95 GLU A 110 1 16 HELIX 2 2 PRO A 111 LEU A 113 5 3 HELIX 3 3 ILE A 114 PHE A 118 5 5 HELIX 4 4 GLY A 135 ALA A 151 1 17 HELIX 5 5 ASN A 176 GLY A 183 1 8 HELIX 6 6 PRO A 193 ASN A 196 5 4 HELIX 7 7 THR A 208 ALA A 242 1 35 HELIX 8 8 GLY B 9 GLU B 21 1 13 HELIX 9 9 ASP B 100 LYS B 118 1 19 HELIX 10 10 ASN B 121 LYS B 124 5 4 HELIX 11 11 ASN B 148 ALA B 164 1 17 HELIX 12 12 SER B 210 MET B 217 1 8 HELIX 13 13 LYS B 243 ALA B 272 1 30 SHEET 1 A 2 ASP A 12 GLU A 13 0 SHEET 2 A 2 ARG A 16 ARG A 17 -1 O ARG A 16 N GLU A 13 SHEET 1 B 5 ILE A 29 VAL A 33 0 SHEET 2 B 5 GLY A 41 TRP A 47 -1 O GLU A 46 N LYS A 30 SHEET 3 B 5 ASN A 50 GLU A 61 -1 O ILE A 52 N ILE A 45 SHEET 4 B 5 THR A 121 GLN A 131 -1 O ASP A 124 N TYR A 57 SHEET 5 B 5 ILE A 74 MET A 81 1 N ASN A 80 O VAL A 129 SHEET 1 C 4 GLU A 170 LEU A 173 0 SHEET 2 C 4 ALA A 160 ILE A 167 -1 N GLY A 165 O VAL A 172 SHEET 3 C 4 ALA A 185 MET A 192 -1 O VAL A 187 N ALA A 164 SHEET 4 C 4 ASP A 197 LEU A 201 -1 O THR A 199 N ALA A 190 SHEET 1 D 4 GLU A 170 LEU A 173 0 SHEET 2 D 4 ALA A 160 ILE A 167 -1 N GLY A 165 O VAL A 172 SHEET 3 D 4 ALA A 185 MET A 192 -1 O VAL A 187 N ALA A 164 SHEET 4 D 4 ASP A 204 GLY A 205 -1 O ASP A 204 N ASP A 186 SHEET 1 E 5 ILE B 36 VAL B 40 0 SHEET 2 E 5 GLY B 48 LEU B 54 -1 O LEU B 51 N GLU B 39 SHEET 3 E 5 THR B 57 GLY B 68 -1 O ILE B 63 N GLY B 48 SHEET 4 E 5 ILE B 132 ASP B 144 -1 O VAL B 133 N GLY B 68 SHEET 5 E 5 VAL B 79 LEU B 86 1 N THR B 81 O ILE B 138 SHEET 1 F 5 ILE B 36 VAL B 40 0 SHEET 2 F 5 GLY B 48 LEU B 54 -1 O LEU B 51 N GLU B 39 SHEET 3 F 5 THR B 57 GLY B 68 -1 O ILE B 63 N GLY B 48 SHEET 4 F 5 ILE B 132 ASP B 144 -1 O VAL B 133 N GLY B 68 SHEET 5 F 5 VAL B 126 VAL B 128 -1 N ILE B 127 O ILE B 132 SHEET 1 G 2 ARG B 165 TYR B 171 0 SHEET 2 G 2 VAL B 178 PRO B 186 -1 O GLU B 183 N LYS B 168 SHEET 1 H 4 ILE B 204 VAL B 207 0 SHEET 2 H 4 VAL B 194 ILE B 201 -1 N ALA B 199 O VAL B 206 SHEET 3 H 4 GLY B 219 THR B 225 -1 O GLY B 219 N LYS B 200 SHEET 4 H 4 ILE B 231 SER B 237 -1 O ALA B 233 N THR B 224 CISPEP 1 ASN A 14 GLY A 15 0 -9.74 CISPEP 2 TYR A 57 GLY A 58 0 -3.95 CISPEP 3 GLY A 58 PRO A 59 0 20.39 CISPEP 4 HIS A 63 PRO A 64 0 -12.55 CISPEP 5 GLN A 243 GLU A 244 0 -12.94 SITE 1 AC1 14 MET A 81 ARG A 97 ASP A 133 ALA A 134 SITE 2 AC1 14 GLY A 135 THR A 136 ARG A 137 ASP A 180 SITE 3 AC1 14 ASP A 186 ASP A 204 HOH A 301 HOH A 302 SITE 4 AC1 14 HOH A 303 HOH A 339 SITE 1 AC2 5 ASN A 181 ALA A 185 ASP A 204 GLY A 205 SITE 2 AC2 5 GLU B 116 SITE 1 AC3 4 ASN B 203 LEU B 205 GLU B 246 TYR B 249 SITE 1 AC4 3 LEU B 162 LYS B 191 GLU B 227 CRYST1 94.200 94.200 127.700 90.00 90.00 120.00 P 3 2 1 6 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 0.010616 0.006129 0.000000 0.00000 SCALE2 0.000000 0.012258 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007831 0.00000