HEADER HYDROLASE/HYDROLASE 25-APR-07 2PNZ
TITLE CRYSTAL STRUCTURE OF THE P. ABYSSI EXOSOME RNASE PH RING COMPLEXED
TITLE 2 WITH UDP AND GMP
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 2PNZ 1 REMARK SEQADV
REVDAT 3 24-FEB-09 2PNZ 1 VERSN
REVDAT 2 27-MAY-08 2PNZ 1 JRNL
REVDAT 1 18-MAR-08 2PNZ 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. 2.14 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) : 2.14
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.87
REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3
REMARK 3 NUMBER OF REFLECTIONS : 33921
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) : 0.191
REMARK 3 R VALUE (WORKING SET) : 0.188
REMARK 3 FREE R VALUE : 0.255
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1783
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) : 2.14
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.20
REMARK 3 REFLECTION IN BIN (WORKING SET) : 2290
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.82
REMARK 3 BIN R VALUE (WORKING SET) : 0.2440
REMARK 3 BIN FREE R VALUE SET COUNT : 115
REMARK 3 BIN FREE R VALUE : 0.3520
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 : 89
REMARK 3 SOLVENT ATOMS : 239
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 28.00
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.86
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) : 0.03000
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): 0.205
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.197
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.157
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.558
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950
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): 4061 ; 0.023 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5507 ; 2.312 ; 2.023
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 511 ; 9.836 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 165 ;40.196 ;24.848
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 757 ;20.369 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;14.232 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 643 ; 0.164 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2940 ; 0.008 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2348 ; 0.243 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2789 ; 0.323 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 323 ; 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): 93 ; 0.252 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 24 ; 0.174 ; 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): 2593 ; 1.037 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4087 ; 1.593 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1626 ; 2.787 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1415 ; 4.074 ; 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): -30.0576 3.3672 -37.7559
REMARK 3 T TENSOR
REMARK 3 T11: -0.0638 T22: -0.1409
REMARK 3 T33: 0.0009 T12: 0.0860
REMARK 3 T13: 0.0197 T23: -0.0139
REMARK 3 L TENSOR
REMARK 3 L11: 2.7310 L22: 1.7815
REMARK 3 L33: 1.4795 L12: 0.3736
REMARK 3 L13: -0.0011 L23: 0.3009
REMARK 3 S TENSOR
REMARK 3 S11: -0.0020 S12: 0.0771 S13: -0.1777
REMARK 3 S21: -0.0366 S22: 0.0344 S23: -0.0929
REMARK 3 S31: 0.3460 S32: 0.1191 S33: -0.0324
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): -60.7187 2.8566 -30.7068
REMARK 3 T TENSOR
REMARK 3 T11: -0.0957 T22: -0.1730
REMARK 3 T33: -0.1558 T12: -0.0747
REMARK 3 T13: 0.0204 T23: 0.0128
REMARK 3 L TENSOR
REMARK 3 L11: 1.9123 L22: 1.7333
REMARK 3 L33: 2.7522 L12: 0.0948
REMARK 3 L13: 0.4814 L23: 0.1449
REMARK 3 S TENSOR
REMARK 3 S11: 0.0174 S12: -0.1352 S13: -0.0669
REMARK 3 S21: 0.1254 S22: -0.0330 S23: 0.0008
REMARK 3 S31: 0.2780 S32: -0.1017 S33: 0.0156
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 283 B 420
REMARK 3 ORIGIN FOR THE GROUP (A): -48.0555 2.6847 -33.9130
REMARK 3 T TENSOR
REMARK 3 T11: 0.0095 T22: -0.1559
REMARK 3 T33: 0.0152 T12: -0.0102
REMARK 3 T13: -0.0023 T23: 0.0070
REMARK 3 L TENSOR
REMARK 3 L11: 1.6032 L22: 0.3515
REMARK 3 L33: 0.5715 L12: -0.0042
REMARK 3 L13: -0.1417 L23: 0.0163
REMARK 3 S TENSOR
REMARK 3 S11: -0.0455 S12: -0.0457 S13: -0.0595
REMARK 3 S21: -0.0148 S22: 0.0213 S23: -0.0615
REMARK 3 S31: 0.2363 S32: -0.0012 S33: 0.0242
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 2PNZ 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_1000042588.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 01-APR-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 : 36060
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.140
REMARK 200 RESOLUTION RANGE LOW (A) : 43.980
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3
REMARK 200 DATA REDUNDANCY : 14.80
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.17200
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.3000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.14
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26
REMARK 200 COMPLETENESS FOR SHELL (%) : 96.0
REMARK 200 DATA REDUNDANCY IN SHELL : 11.80
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.63900
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.300
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 2BA0
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 55.72
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.78
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: 23400 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 57870 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -237.4 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 -46.90500
REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 81.24184
REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000
REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -93.81000
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 B 144 O HOH B 363 2.19
REMARK 500 OD2 ASP A 133 O HOH A 307 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 GLU A 244 C GLU A 244 O 0.392
REMARK 500 GLU B 174 CG GLU B 174 CD 0.120
REMARK 500 GLU B 174 CD GLU B 174 OE1 0.125
REMARK 500 GLU B 174 CD GLU B 174 OE2 0.101
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 HIS A 63 N - CA - C ANGL. DEV. = 24.8 DEGREES
REMARK 500 ARG A 78 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES
REMARK 500 PRO A 94 C - N - CA ANGL. DEV. = -9.3 DEGREES
REMARK 500 GLU A 244 CA - C - O ANGL. DEV. = -13.9 DEGREES
REMARK 500 LEU B 89 CA - CB - CG ANGL. DEV. = 15.7 DEGREES
REMARK 500 ARG B 262 NE - CZ - NH1 ANGL. DEV. = 4.1 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 13 112.55 176.01
REMARK 500 GLU A 61 104.79 -36.78
REMARK 500 HIS A 66 0.22 -62.58
REMARK 500 ASP A 133 40.78 -157.13
REMARK 500 ALA A 134 141.54 67.99
REMARK 500 CYS A 162 147.00 179.83
REMARK 500 GLU A 168 48.90 39.57
REMARK 500 ASP A 174 63.70 63.09
REMARK 500 ALA A 242 38.85 -61.11
REMARK 500 SER B 91 140.05 179.40
REMARK 500 LYS B 131 -44.03 -144.24
REMARK 500 ASP B 144 113.02 -164.17
REMARK 500 PRO B 188 70.40 -65.84
REMARK 500 ASP B 208 71.00 45.65
REMARK 500 GLU B 238 -165.68 63.50
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 -37.71
REMARK 500 GLY A 48 LYS A 49 146.69
REMARK 500 LEU A 62 HIS A 63 109.97
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 UDP A 250
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 5GP A 279
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 251
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 252
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 280
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 281
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 282
REMARK 900
REMARK 900 RELATED ENTRIES
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
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 2PNZ A 1 249 UNP Q9V119 ECX1_PYRAB 1 249
DBREF 2PNZ B 1 274 UNP Q9V118 ECX2_PYRAB 1 274
SEQADV 2PNZ GLY B -2 UNP Q9V118 EXPRESSION TAG
SEQADV 2PNZ SER B -1 UNP Q9V118 EXPRESSION TAG
SEQADV 2PNZ 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 UDP A 250 25
HET 5GP A 279 24
HET MPD A 251 8
HET MPD A 252 8
HET MPD A 282 8
HET MPD B 280 8
HET MPD B 281 8
HETNAM UDP URIDINE-5'-DIPHOSPHATE
HETNAM 5GP GUANOSINE-5'-MONOPHOSPHATE
HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL
FORMUL 3 UDP C9 H14 N2 O12 P2
FORMUL 4 5GP C10 H14 N5 O8 P
FORMUL 5 MPD 5(C6 H14 O2)
FORMUL 10 HOH *239(H2 O)
HELIX 1 1 PRO A 64 GLN A 68 5 5
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 TYR A 182 1 7
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 LEU B 215 1 6
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 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 78 O ILE A 127
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 VAL B 133 N GLY B 68
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 VAL B 133 N GLY B 68
SHEET 5 E 5 VAL B 126 VAL B 128 -1 N VAL B 128 O ILE B 132
SHEET 1 F 2 VAL B 166 TYR B 171 0
SHEET 2 F 2 VAL B 178 GLU B 185 -1 O LEU B 181 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 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 18.17
CISPEP 2 ASN A 14 GLY A 15 0 -6.14
CISPEP 3 TYR A 57 GLY A 58 0 -12.96
CISPEP 4 GLY A 58 PRO A 59 0 25.60
CISPEP 5 HIS A 63 PRO A 64 0 1.68
CISPEP 6 GLN A 243 GLU A 244 0 11.79
SITE 1 AC1 11 MET A 81 ARG A 97 ASP A 133 ALA A 134
SITE 2 AC1 11 GLY A 135 THR A 136 ARG A 137 ASP A 180
SITE 3 AC1 11 ASP A 186 HOH A 285 HOH A 346
SITE 1 AC2 7 ARG A 89 LYS A 91 HOH A 318 HOH A 377
SITE 2 AC2 7 GLU B 69 PHE B 71 THR B 81
SITE 1 AC3 6 ASP A 180 GLY A 183 ALA A 185 ASP A 204
SITE 2 AC3 6 HOH A 300 GLU B 116
SITE 1 AC4 6 TYR A 24 LEU A 173 LYS A 221 ALA A 225
SITE 2 AC4 6 HOH A 341 LYS B 256
SITE 1 AC5 4 GLU B 190 ILE B 192 GLU B 227 HOH B 388
SITE 1 AC6 5 PHE B 30 ASN B 203 LEU B 205 TYR B 249
SITE 2 AC6 5 HOH B 383
SITE 1 AC7 4 ARG A 76 ASP A 124 PHE A 126 PRO B 96
CRYST1 93.810 93.810 126.260 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 0.010660 0.006154 0.000000 0.00000
SCALE2 0.000000 0.012309 0.000000 0.00000
SCALE3 0.000000 0.000000 0.007920 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
