HEADER HYDROLASE/HYDROLASE 25-APR-07 2PO2 TITLE CRYSTAL STRUCTURE OF THE P. ABYSSI EXOSOME RNASE PH RING COMPLEXED TITLE 2 WITH CDP 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 2PO2 1 REMARK SEQADV REVDAT 3 24-FEB-09 2PO2 1 VERSN REVDAT 2 27-MAY-08 2PO2 1 JRNL REVDAT 1 18-MAR-08 2PO2 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. 2.41 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) : 2.41 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 23727 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) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1273 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) : 2.41 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.47 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1590 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.82 REMARK 3 BIN R VALUE (WORKING SET) : 0.2300 REMARK 3 BIN FREE R VALUE SET COUNT : 91 REMARK 3 BIN FREE R VALUE : 0.3620 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 : 65 REMARK 3 SOLVENT ATOMS : 176 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02000 REMARK 3 B22 (A**2) : 0.02000 REMARK 3 B33 (A**2) : -0.02000 REMARK 3 B12 (A**2) : 0.01000 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): 0.341 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.265 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.190 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 18.254 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.899 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; 0.021 ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; 2.106 ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; 7.593 ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ;40.218 ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ;21.308 ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ;15.579 ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; 0.127 ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; 0.007 ; NULL REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; 0.242 ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; 0.324 ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; 0.192 ; 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 : 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 250 REMARK 3 ORIGIN FOR THE GROUP (A): -29.8998 3.4298 -37.5581 REMARK 3 T TENSOR REMARK 3 T11: -0.0910 T22: -0.1996 REMARK 3 T33: -0.0389 T12: 0.1036 REMARK 3 T13: 0.0241 T23: -0.0044 REMARK 3 L TENSOR REMARK 3 L11: 3.9418 L22: 1.9655 REMARK 3 L33: 2.2832 L12: 0.1468 REMARK 3 L13: 0.1262 L23: 0.6165 REMARK 3 S TENSOR REMARK 3 S11: -0.0077 S12: 0.0389 S13: -0.2543 REMARK 3 S21: 0.0145 S22: 0.0462 S23: -0.0846 REMARK 3 S31: 0.4873 S32: 0.2536 S33: -0.0385 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 283 REMARK 3 ORIGIN FOR THE GROUP (A): -60.5409 2.5841 -30.6802 REMARK 3 T TENSOR REMARK 3 T11: -0.1097 T22: -0.2133 REMARK 3 T33: -0.1529 T12: -0.0831 REMARK 3 T13: 0.0350 T23: 0.0212 REMARK 3 L TENSOR REMARK 3 L11: 2.5637 L22: 1.8893 REMARK 3 L33: 3.6805 L12: 0.0746 REMARK 3 L13: 0.8719 L23: 0.0084 REMARK 3 S TENSOR REMARK 3 S11: 0.0392 S12: -0.1300 S13: -0.1372 REMARK 3 S21: 0.1771 S22: -0.0609 S23: 0.0251 REMARK 3 S31: 0.3734 S32: -0.1616 S33: 0.0217 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 284 B 382 REMARK 3 ORIGIN FOR THE GROUP (A): -47.6192 4.6663 -33.8176 REMARK 3 T TENSOR REMARK 3 T11: -0.0381 T22: -0.1652 REMARK 3 T33: -0.0797 T12: -0.0210 REMARK 3 T13: -0.0058 T23: 0.0211 REMARK 3 L TENSOR REMARK 3 L11: 2.0040 L22: 0.5223 REMARK 3 L33: 0.4518 L12: -0.0219 REMARK 3 L13: -0.0805 L23: 0.0786 REMARK 3 S TENSOR REMARK 3 S11: -0.0557 S12: -0.0688 S13: -0.0256 REMARK 3 S21: -0.0045 S22: 0.0518 S23: -0.0494 REMARK 3 S31: 0.2498 S32: -0.0381 S33: 0.0039 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 2PO2 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_1000042591. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAY-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL 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 : 25053 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 43.630 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.12400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.60700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.800 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 (%): 55.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.75 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: 21990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 57630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -229.8 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 -46.74900 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 80.97164 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -93.49800 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 ASP A 197 O HOH A 353 2.12 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 240 CG LYS A 240 CD 0.206 REMARK 500 GLU B 174 CG GLU B 174 CD 0.236 REMARK 500 GLU B 174 CD GLU B 174 OE1 0.180 REMARK 500 GLU B 174 CD GLU B 174 OE2 0.105 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 97 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 ARG A 97 NE - CZ - NH2 ANGL. DEV. = -5.9 DEGREES REMARK 500 LEU B 89 CA - CB - CG ANGL. DEV. = 20.5 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 13 124.92 143.17 REMARK 500 GLU A 61 121.38 -34.72 REMARK 500 LYS A 65 7.69 -58.81 REMARK 500 ARG A 89 114.25 -37.86 REMARK 500 ARG A 120 9.51 84.78 REMARK 500 ASP A 133 47.15 -158.91 REMARK 500 ALA A 134 147.69 70.41 REMARK 500 CYS A 162 148.67 -170.98 REMARK 500 ASP A 174 78.89 62.07 REMARK 500 ALA A 242 54.59 -67.13 REMARK 500 LYS B 131 -45.44 -141.72 REMARK 500 ASP B 144 112.57 -171.33 REMARK 500 GLU B 173 -11.96 -49.40 REMARK 500 GLU B 238 -162.93 66.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LYS A 9 LEU A 10 -34.09 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 CDP A 250 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 251 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 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 282 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 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 COMPLEXED REMARK 900 WITH UDP AND GMP REMARK 900 RELATED ID: 2PO0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE P. ABYSSI EXOSOME RNASE PH RING COMPLEXED REMARK 900 WITH ADP IN DOUBLE CONFORMATION 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 DBREF 2PO2 A 1 249 UNP Q9V119 ECX1_PYRAB 1 249 DBREF 2PO2 B 1 274 UNP Q9V118 ECX2_PYRAB 1 274 SEQADV 2PO2 GLY B -2 UNP Q9V118 EXPRESSION TAG SEQADV 2PO2 SER B -1 UNP Q9V118 EXPRESSION TAG SEQADV 2PO2 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 CDP A 250 25 HET MPD A 251 8 HET MPD A 283 8 HET MPD B 280 8 HET MPD B 281 8 HET MPD B 282 8 HETNAM CDP CYTIDINE-5'-DIPHOSPHATE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 3 CDP C9 H15 N3 O11 P2 FORMUL 4 MPD 5(C6 H14 O2) FORMUL 9 HOH *176(H2 O) HELIX 1 1 PRO A 83 VAL A 86 5 4 HELIX 2 2 ASP A 95 GLU A 110 1 16 HELIX 3 3 PRO A 111 LEU A 113 5 3 HELIX 4 4 ILE A 114 PHE A 118 5 5 HELIX 5 5 GLY A 135 ALA A 151 1 17 HELIX 6 6 ASN A 176 GLY A 183 1 8 HELIX 7 7 THR A 208 ILE A 241 1 34 HELIX 8 8 GLY B 9 GLU B 21 1 13 HELIX 9 9 PRO B 88 SER B 91 5 4 HELIX 10 10 ASP B 100 SER B 117 1 18 HELIX 11 11 ASN B 121 LYS B 124 5 4 HELIX 12 12 ASN B 148 ALA B 164 1 17 HELIX 13 13 SER B 210 MET B 217 1 8 HELIX 14 14 LYS B 243 ALA B 272 1 30 SHEET 1 A 5 ILE A 29 VAL A 33 0 SHEET 2 A 5 GLY A 41 TRP A 47 -1 O GLU A 46 N LYS A 30 SHEET 3 A 5 ASN A 50 GLU A 61 -1 O VAL A 56 N GLY A 41 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 ILE A 74 O ILE A 123 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 ILE A 191 N ALA A 160 SHEET 4 B 4 ASP A 197 LEU A 201 -1 O LEU A 200 N ALA A 190 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 ILE A 191 N ALA A 160 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 VAL B 79 O VAL B 136 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 185 N VAL B 166 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 ILE B 221 N PHE B 198 SHEET 4 G 4 ILE B 231 SER B 237 -1 O ALA B 233 N THR B 224 CISPEP 1 GLU A 13 ASN A 14 0 9.29 CISPEP 2 ASN A 14 GLY A 15 0 1.80 CISPEP 3 TYR A 57 GLY A 58 0 -15.35 CISPEP 4 GLY A 58 PRO A 59 0 9.39 CISPEP 5 HIS A 63 PRO A 64 0 11.59 CISPEP 6 GLN A 243 GLU A 244 0 11.00 SITE 1 AC1 12 ARG A 97 ALA A 132 ASP A 133 ALA A 134 SITE 2 AC1 12 GLY A 135 THR A 136 ARG A 137 ASP A 180 SITE 3 AC1 12 ASP A 186 HOH A 285 HOH A 312 HOH A 337 SITE 1 AC2 6 ASP A 180 ASN A 181 GLY A 183 ALA A 185 SITE 2 AC2 6 GLY A 205 GLU B 116 SITE 1 AC3 5 LEU B 162 GLU B 190 LYS B 191 GLU B 227 SITE 2 AC3 5 LEU B 266 SITE 1 AC4 4 TYR A 24 LEU A 173 LYS A 221 LYS B 256 SITE 1 AC5 3 ASN B 203 LEU B 205 TYR B 249 SITE 1 AC6 5 TYR A 44 ILE A 53 LEU B 51 LYS B 53 SITE 2 AC6 5 GLN B 58 CRYST1 93.498 93.498 125.714 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 0.010695 0.006175 0.000000 0.00000 SCALE2 0.000000 0.012350 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007955 0.00000