10 20 30 40 50 60 70 80 2PO0 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE/HYDROLASE 25-APR-07 2PO0
TITLE CRYSTAL STRUCTURE OF THE P. ABYSSI EXOSOME RNASE PH RING TITLE 2 COMPLEXED 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 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, 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. 2.30 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) : 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 : 3900 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 54 REMARK 3 SOLVENT ATOMS : 175 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 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1610 ; 2.244 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1401 ; 3.208 ; 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 : 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 REMARK 3 RIDING POSITIONS
REMARK 4 REMARK 4 2PO0 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 RCSB042589.
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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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, 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: 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. = -5.7 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 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 B 351 DISTANCE = 5.27 ANGSTROMS
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 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 250 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 280 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 REMARK 900 COMPLEXED WITH UDP AND GMP REMARK 900 RELATED ID: 2PO1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE P. ABYSSI EXOSOME RNASE PH RING REMARK 900 COMPLEXED 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 REMARK 900 COMPLEXED 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