2PO1 - Header Asymmetric Unit

HEADER HYDROLASE/HYDROLASE/RNA 25-APR-07 2PO1

TITLE CRYSTAL STRUCTURE OF THE P. ABYSSI EXOSOME RNASE PH RING TITLE 2 COMPLEXED WITH A SINGLE STRANDED 10-MER POLY(A) RNA

COMPND MOL_ID: 1; COMPND 2 MOLECULE: 10-MER POLY(A); COMPND 3 CHAIN: C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1; COMPND 7 CHAIN: A; COMPND 8 EC: 3.1.13.-; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2; COMPND 12 CHAIN: B; COMPND 13 EC: 3.1.13.-; COMPND 14 ENGINEERED: YES

SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: PYROCOCCUS ABYSSI; SOURCE 5 ORGANISM_TAXID: 29292; SOURCE 6 GENE: RRP41; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET29; SOURCE 12 MOL_ID: 3; SOURCE 13 ORGANISM_SCIENTIFIC: PYROCOCCUS ABYSSI; SOURCE 14 ORGANISM_TAXID: 29292; SOURCE 15 GENE: RRP42; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PAE

KEYWDS RNASE PH, HYDROLASE/HYDROLASE/RNA COMPLEX

EXPDTA X-RAY DIFFRACTION

AUTHOR M.V.A.S.NAVARRO,B.G.GUIMARAES

REVDAT 3 24-FEB-09 2PO1 1 VERSN REVDAT 2 27-MAY-08 2PO1 1 JRNL REVDAT 1 18-MAR-08 2PO1 0

JRNL AUTH M.V.A.S.NAVARRO,C.C.OLIVEIRA,N.I.ZANCHIN, JRNL AUTH 2 B.G.GUIMARAES JRNL TITL INSIGHTS INTO THE MECHANISM OF PROGRESSIVE RNA JRNL TITL 2 DEGRADATION 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 1

REMARK 2 REMARK 2 RESOLUTION. 1.94 ANGSTROMS.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 44547 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) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2374 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) : 1.94 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.99 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2736 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.22 REMARK 3 BIN R VALUE (WORKING SET) : 0.2550 REMARK 3 BIN FREE R VALUE SET COUNT : 140 REMARK 3 BIN FREE R VALUE : 0.3300 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3915 REMARK 3 NUCLEIC ACID ATOMS : 154 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 348 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.41 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): 0.151 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.152 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.122 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.473 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.927 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4185 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5696 ; 2.065 ; 2.055 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 508 ; 6.547 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 166 ;38.956 ;24.759 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 756 ;17.827 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 29 ;17.121 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 668 ; 0.132 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3001 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2465 ; 0.230 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2890 ; 0.328 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 452 ; 0.195 ; 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): 149 ; 0.244 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 29 ; 0.191 ; 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): 2579 ; 1.101 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4085 ; 1.559 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1805 ; 2.621 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1608 ; 3.938 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 9 A 244 REMARK 3 ORIGIN FOR THE GROUP (A): 17.7830 -24.1781 -25.2061 REMARK 3 T TENSOR REMARK 3 T11: -0.2252 T22: 0.0132 REMARK 3 T33: -0.0229 T12: 0.0041 REMARK 3 T13: 0.0216 T23: 0.0005 REMARK 3 L TENSOR REMARK 3 L11: 1.6837 L22: 2.4940 REMARK 3 L33: 1.5898 L12: -0.4363 REMARK 3 L13: -0.1496 L23: 0.0654 REMARK 3 S TENSOR REMARK 3 S11: 0.0005 S12: -0.0080 S13: 0.0045 REMARK 3 S21: 0.0747 S22: 0.0163 S23: 0.2260 REMARK 3 S31: 0.0306 S32: -0.4854 S33: -0.0168 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): 32.5447 -51.2099 -32.2068 REMARK 3 T TENSOR REMARK 3 T11: -0.0388 T22: -0.1641 REMARK 3 T33: -0.1266 T12: -0.0946 REMARK 3 T13: -0.0009 T23: -0.0211 REMARK 3 L TENSOR REMARK 3 L11: 1.4166 L22: 1.6848 REMARK 3 L33: 2.1715 L12: 0.0179 REMARK 3 L13: 0.0782 L23: -0.2653 REMARK 3 S TENSOR REMARK 3 S11: -0.0231 S12: 0.0912 S13: -0.0876 REMARK 3 S21: -0.1336 S22: 0.0097 S23: 0.0759 REMARK 3 S31: 0.3265 S32: -0.2284 S33: 0.0134 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 395 C 395 REMARK 3 RESIDUE RANGE : C 398 C 398 REMARK 3 RESIDUE RANGE : C 400 C 404 REMARK 3 ORIGIN FOR THE GROUP (A): 36.8147 -20.3249 -33.6047 REMARK 3 T TENSOR REMARK 3 T11: 0.2000 T22: 0.0183 REMARK 3 T33: 0.1778 T12: -0.0339 REMARK 3 T13: 0.1836 T23: -0.0451 REMARK 3 L TENSOR REMARK 3 L11: 6.6670 L22: 6.8143 REMARK 3 L33: 18.6653 L12: 4.0336 REMARK 3 L13: -0.4010 L23: -1.2330 REMARK 3 S TENSOR REMARK 3 S11: 0.1942 S12: 1.4345 S13: -0.0277 REMARK 3 S21: -0.6442 S22: -0.0979 S23: -0.5556 REMARK 3 S31: 0.4949 S32: 1.6621 S33: -0.0963 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 284 C 409 REMARK 3 ORIGIN FOR THE GROUP (A): 26.8504 -40.9970 -29.3623 REMARK 3 T TENSOR REMARK 3 T11: -0.0406 T22: 0.0360 REMARK 3 T33: 0.0223 T12: -0.0895 REMARK 3 T13: -0.0146 T23: -0.0140 REMARK 3 L TENSOR REMARK 3 L11: 0.6746 L22: 1.2830 REMARK 3 L33: 0.5624 L12: -0.4447 REMARK 3 L13: -0.0471 L23: 0.0173 REMARK 3 S TENSOR REMARK 3 S11: 0.0036 S12: 0.0425 S13: -0.0317 REMARK 3 S21: -0.0371 S22: 0.0010 S23: 0.1652 REMARK 3 S31: 0.1881 S32: -0.2539 S33: -0.0045 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 REMARK 3 RIDING POSITIONS

REMARK 4 REMARK 4 2PO1 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-MAY-07. REMARK 100 THE RCSB ID CODE IS RCSB042590.

REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-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 : 46981 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.940 REMARK 200 RESOLUTION RANGE LOW (A) : 46.780 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 11.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.94 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.1 REMARK 200 DATA REDUNDANCY IN SHELL : 9.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.62700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.500 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 (%): 52.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 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, REMARK 300 Z 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: NONAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: NONAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 29630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 55550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -234.7 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, 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 46.77750 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -81.02101 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 93.55500 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 A C 396 REMARK 465 A C 397 REMARK 465 A C 399 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 O HOH A 379 O HOH A 381 1.95 REMARK 500 O PRO A 154 O HOH A 383 2.07 REMARK 500 O HOH A 384 O HOH A 385 2.16 REMARK 500 O HOH B 380 O HOH B 407 2.18 REMARK 500 O HOH A 346 O HOH A 355 2.19 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 A C 398 N3 A C 398 C4 0.074 REMARK 500 A C 398 C4 A C 398 C5 0.053 REMARK 500 A C 398 C6 A C 398 N1 0.074 REMARK 500 A C 398 C5 A C 398 N7 0.048 REMARK 500 A C 398 C8 A C 398 N9 0.071 REMARK 500 LYS A 22 CE LYS A 22 NZ 0.178 REMARK 500 GLU B 174 CD GLU B 174 OE2 0.180 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 A C 398 C4 - C5 - N7 ANGL. DEV. = 3.7 DEGREES REMARK 500 A C 398 C5 - N7 - C8 ANGL. DEV. = -3.6 DEGREES REMARK 500 A C 398 N9 - C4 - C5 ANGL. DEV. = -2.6 DEGREES REMARK 500 A C 398 N1 - C6 - N6 ANGL. DEV. = 4.7 DEGREES REMARK 500 A C 401 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 A C 402 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES REMARK 500 A C 404 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 ARG A 17 NE - CZ - NH1 ANGL. DEV. = -4.7 DEGREES REMARK 500 ARG A 17 NE - CZ - NH2 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG A 21 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 PRO A 94 C - N - CA ANGL. DEV. = -13.4 DEGREES REMARK 500 ASP A 95 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG A 96 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG B 262 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG B 262 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 GLU A 13 -107.72 -78.58 REMARK 500 ASN A 14 78.47 -154.21 REMARK 500 ASP A 133 45.76 -160.76 REMARK 500 ALA A 134 139.52 71.66 REMARK 500 ALA A 242 2.49 -63.64 REMARK 500 SER B 91 139.40 -174.24 REMARK 500 LYS B 131 -40.99 -141.14 REMARK 500 ASP B 208 70.17 51.49 REMARK 500 GLU B 238 -166.38 62.01 REMARK 500 REMARK 500 REMARK: NULL

REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 375 DISTANCE = 5.46 ANGSTROMS REMARK 525 HOH B 434 DISTANCE = 6.75 ANGSTROMS

REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 250 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 280 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 281 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 282 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 283

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 REMARK 900 COMPLEXED WITH UDP AND GMP REMARK 900 RELATED ID: 2PO0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE P. ABYSSI EXOSOME RNASE PH RING REMARK 900 COMPLEXED WITH ADP IN DOUBLE CONFORMATION REMARK 900 RELATED ID: 2PO2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE P. ABYSSI EXOSOME RNASE PH RING REMARK 900 COMPLEXED WITH CDP

DBREF 2PO1 A 1 249 UNP Q9V119 ECX1_PYRAB 1 249 DBREF 2PO1 B 1 274 UNP Q9V118 ECX2_PYRAB 1 274 DBREF 2PO1 C 395 404 PDB 2PO1 2PO1 395 404

SEQRES 1 C 10 A A A A A A A A A A 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 MPD A 250 8 HET MPD A 283 8 HET MPD B 280 8 HET MPD B 281 8 HET MPD B 282 8

HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL

FORMUL 4 MPD 5(C6 H14 O2) FORMUL 9 HOH *308(H2 O)

HELIX 1 1 PRO A 64 GLN A 68 5 5 HELIX 2 2 PRO A 83 VAL A 86 5 4 HELIX 3 3 ASP A 95 GLU A 110 1 16 HELIX 4 4 PRO A 111 LEU A 113 5 3 HELIX 5 5 ILE A 114 PHE A 118 5 5 HELIX 6 6 GLY A 135 ALA A 151 1 17 HELIX 7 7 ASN A 176 TYR A 182 1 7 HELIX 8 8 THR A 208 ALA A 242 1 35 HELIX 9 9 GLY B 9 GLU B 21 1 13 HELIX 10 10 PRO B 88 SER B 91 5 4 HELIX 11 11 ASP B 100 GLU B 116 1 17 HELIX 12 12 ASN B 121 LYS B 124 5 4 HELIX 13 13 ASN B 148 ALA B 164 1 17 HELIX 14 14 SER B 210 MET B 217 1 8 HELIX 15 15 LYS B 243 LYS B 273 1 31

SHEET 1 A 5 ILE A 29 VAL A 33 0 SHEET 2 A 5 GLY A 41 TRP A 47 -1 O TYR A 44 N GLU A 32 SHEET 3 A 5 ASN A 50 GLU A 61 -1 O ILE A 52 N ILE A 45 SHEET 4 A 5 THR A 121 GLN A 131 -1 O ASP A 124 N TYR A 57 SHEET 5 A 5 ILE A 74 MET A 81 1 N ARG A 76 O VAL A 125 SHEET 1 B 4 GLU A 170 LEU A 173 0 SHEET 2 B 4 ALA A 160 ILE A 167 -1 N GLY A 165 O VAL A 172 SHEET 3 B 4 ALA A 185 MET A 192 -1 O VAL A 187 N ALA A 164 SHEET 4 B 4 ASP A 197 LEU A 201 -1 O ASP A 197 N MET A 192 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 204 GLY A 205 -1 O ASP A 204 N ASP A 186 SHEET 1 D 5 ILE B 36 VAL B 40 0 SHEET 2 D 5 GLY B 48 LEU B 54 -1 O LEU B 51 N GLU B 39 SHEET 3 D 5 THR B 57 GLY B 68 -1 O ILE B 63 N GLY B 48 SHEET 4 D 5 ILE B 132 ASP B 144 -1 O HIS B 141 N LEU B 60 SHEET 5 D 5 VAL B 79 LEU B 86 1 N THR B 81 O ILE B 138 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 HIS B 141 N LEU B 60 SHEET 5 E 5 VAL B 126 VAL B 128 -1 N VAL B 128 O ILE B 132 SHEET 1 F 2 ARG B 165 TYR B 171 0 SHEET 2 F 2 VAL B 178 PRO B 186 -1 O GLU B 183 N LYS B 168 SHEET 1 G 4 ILE B 204 VAL B 207 0 SHEET 2 G 4 VAL B 194 ILE B 201 -1 N ILE B 201 O ILE B 204 SHEET 3 G 4 GLY B 219 THR B 225 -1 O GLY B 219 N LYS B 200 SHEET 4 G 4 ILE B 231 SER B 237 -1 O ALA B 233 N THR B 224

CISPEP 1 LYS A 9 LEU A 10 0 3.61 CISPEP 2 ASN A 14 GLY A 15 0 -6.91 CISPEP 3 TYR A 57 GLY A 58 0 -18.06 CISPEP 4 GLY A 58 PRO A 59 0 20.11 CISPEP 5 HIS A 63 PRO A 64 0 6.12 CISPEP 6 GLN A 243 GLU A 244 0 7.27

SITE 1 AC1 7 ASP A 180 GLY A 183 GLU A 184 ALA A 185 SITE 2 AC1 7 ASP A 204 HOH A 294 GLU B 116 SITE 1 AC2 5 GLU B 190 LYS B 191 GLU B 227 LEU B 266 SITE 2 AC2 5 HOH B 356 SITE 1 AC3 4 PHE B 30 LEU B 205 TYR B 249 HOH B 405 SITE 1 AC4 4 TYR A 24 LEU A 26 LYS B 256 HOH B 377 SITE 1 AC5 4 TYR A 44 LEU B 51 LYS B 53 GLN B 58

CRYST1 93.555 93.555 125.951 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 0.010689 0.006171 0.000000 0.00000

SCALE2 0.000000 0.012342 0.000000 0.00000

SCALE3 0.000000 0.000000 0.007940 0.00000