HEADER TRANSFERASE / PROTEIN BINDING 13-MAR-09 3GME TITLE CRYSTAL STRUCTURE OF POLYNUCLEOTIDE PHOSPHORYLASE IN COMPLEX WITH TITLE 2 RNASE E AND MANGANESE COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: POLYNUCLEOTIDE PHOSPHORYLASE, RESIDUES 1-549; COMPND 5 SYNONYM: POLYNUCLEOTIDE PHOSPHORYLASE, PNPASE; COMPND 6 EC: 2.7.7.8; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RIBONUCLEASE E; COMPND 9 CHAIN: D; COMPND 10 FRAGMENT: RNASE E RECOGNITION MICRODOMAIN, RESIDUES 1021-1061; COMPND 11 EC: 3.1.4.-; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI E24377A; SOURCE 3 ORGANISM_TAXID: 331111; SOURCE 4 STRAIN: BL21 DE3; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_COMMON: ESCHERICHIA COLI; SOURCE 8 ORGANISM_TAXID: 562; SOURCE 9 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN E. COLI KEYWDS PROTEIN-RNA COMPLEX, CYTOPLASM, NUCLEOTIDYLTRANSFERASE, RNA-BINDING, KEYWDS 2 TRANSFERASE, HYDROLASE, TRANSFERASE - PROTEIN BINDING COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.NURMOHAMED,B.L.LUISI REVDAT 2 21-FEB-24 3GME 1 REMARK REVDAT 1 09-JUN-09 3GME 0 JRNL AUTH S.NURMOHAMED,B.VAIDIALINGAM,A.J.CALLAGHAN,B.F.LUISI JRNL TITL CRYSTAL STRUCTURE OF ESCHERICHIA COLI POLYNUCLEOTIDE JRNL TITL 2 PHOSPHORYLASE CORE BOUND TO RNASE E, RNA AND MANGANESE: JRNL TITL 3 IMPLICATIONS FOR CATALYTIC MECHANISM AND RNA DEGRADOSOME JRNL TITL 4 ASSEMBLY. JRNL REF J.MOL.BIOL. V. 389 17 2009 JRNL REFN ISSN 0022-2836 JRNL PMID 19327365 JRNL DOI 10.1016/J.JMB.2009.03.051 REMARK 2 REMARK 2 RESOLUTION. 2.40 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.91 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 27938 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) : 0.286 REMARK 3 R VALUE (WORKING SET) : 0.286 REMARK 3 FREE R VALUE : 0.298 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1490 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1976 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.82 REMARK 3 BIN R VALUE (WORKING SET) : 0.3630 REMARK 3 BIN FREE R VALUE SET COUNT : 117 REMARK 3 BIN FREE R VALUE : 0.3760 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3694 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 158 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.59 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) : 0.02000 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): 0.390 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.271 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.903 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.892 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3757 ; 0.005 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5103 ; 0.765 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 497 ; 3.575 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 151 ;35.144 ;24.702 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 596 ;12.752 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;12.138 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 597 ; 0.045 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2838 ; 0.001 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1632 ; 0.136 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2565 ; 0.284 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 132 ; 0.096 ; 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): 81 ; 0.118 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 11 ; 0.106 ; 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): 2490 ; 1.533 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3980 ; 2.700 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1267 ; 3.819 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1123 ; 5.980 ; 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 3GME COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000052041. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-AUG-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.07 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27938 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 25.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : 0.12500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL 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) : 2.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.43200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.5 M NACL, 9 % W/V PEG 6000, 20 MM NA REMARK 280 - CITRATE, 20 MM MANGANESE ACETATE , VAPOR DIFFUSION REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 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 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 SMTRY1 7 1.000000 0.000000 0.000000 79.28700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 45.77637 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 52.03933 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 79.28700 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 45.77637 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 52.03933 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 79.28700 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 45.77637 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 52.03933 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 79.28700 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 45.77637 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 52.03933 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 79.28700 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 45.77637 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 52.03933 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 79.28700 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 45.77637 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 52.03933 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 91.55274 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 104.07867 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 91.55274 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 104.07867 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 91.55274 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 104.07867 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 91.55274 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 104.07867 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 91.55274 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 104.07867 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 91.55274 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 104.07867 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: ONE RNASE E RECOGNITION MICRODOMAIN BINDS TO ONE MONOMER OF REMARK 300 PNPASE 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: 15840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 59420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -100.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D 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 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 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 PHE A 78 REMARK 465 ARG A 79 REMARK 465 ARG A 80 REMARK 465 GLU A 81 REMARK 465 GLY A 82 REMARK 465 ALA A 247 REMARK 465 ALA A 248 REMARK 465 LEU A 249 REMARK 465 ALA A 250 REMARK 465 GLU A 251 REMARK 465 ALA A 252 REMARK 465 ARG A 253 REMARK 465 LEU A 254 REMARK 465 SER A 255 REMARK 465 ASP A 256 REMARK 465 ALA A 257 REMARK 465 TYR A 258 REMARK 465 ARG A 259 REMARK 465 ILE A 260 REMARK 465 ALA A 268 REMARK 465 GLN A 269 REMARK 465 VAL A 270 REMARK 465 ASP A 271 REMARK 465 VAL A 272 REMARK 465 ILE A 273 REMARK 465 LYS A 274 REMARK 465 SER A 275 REMARK 465 GLU A 276 REMARK 465 THR A 277 REMARK 465 ILE A 278 REMARK 465 ALA A 279 REMARK 465 THR A 280 REMARK 465 LEU A 281 REMARK 465 LEU A 282 REMARK 465 ALA A 283 REMARK 465 GLU A 284 REMARK 465 ASP A 285 REMARK 465 GLU A 286 REMARK 465 THR A 287 REMARK 465 LEU A 288 REMARK 465 ASP A 289 REMARK 465 GLU A 290 REMARK 465 ASN A 291 REMARK 465 GLU A 292 REMARK 465 LEU A 293 REMARK 465 GLY A 294 REMARK 465 GLU A 295 REMARK 465 ILE A 296 REMARK 465 ALA A 359 REMARK 465 ARG A 360 REMARK 465 ASP A 361 REMARK 465 ALA A 362 REMARK 465 GLN A 363 REMARK 465 VAL A 364 REMARK 465 LEU A 365 REMARK 465 ASP A 366 REMARK 465 GLU A 367 REMARK 465 LEU A 368 REMARK 465 MET A 369 REMARK 465 GLY A 370 REMARK 465 GLU A 371 REMARK 465 ARG A 372 REMARK 465 THR A 373 REMARK 465 GLY A 546 REMARK 465 ASP A 547 REMARK 465 ILE A 548 REMARK 465 SER A 549 REMARK 465 GLU D 1021 REMARK 465 ALA D 1022 REMARK 465 PRO D 1023 REMARK 465 ARG D 1024 REMARK 465 HIS D 1025 REMARK 465 SER D 1026 REMARK 465 ASP D 1027 REMARK 465 TRP D 1028 REMARK 465 GLN D 1029 REMARK 465 ARG D 1030 REMARK 465 PRO D 1031 REMARK 465 THR D 1032 REMARK 465 PHE D 1033 REMARK 465 ALA D 1034 REMARK 465 PHE D 1035 REMARK 465 GLU D 1036 REMARK 465 GLY D 1037 REMARK 465 LYS D 1038 REMARK 465 VAL D 1060 REMARK 465 GLU D 1061 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 51 CD CE NZ REMARK 470 PHE A 77 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG A 83 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 174 CD CE NZ REMARK 470 ARG A 230 CD NE CZ NH1 NH2 REMARK 470 GLU A 240 CG CD OE1 OE2 REMARK 470 ARG A 245 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 246 CG1 CG2 REMARK 470 THR A 261 OG1 CG2 REMARK 470 ASP A 262 CG OD1 OD2 REMARK 470 LYS A 263 CG CD CE NZ REMARK 470 GLN A 264 CG CD OE1 NE2 REMARK 470 GLU A 265 CG CD OE1 OE2 REMARK 470 ARG A 266 CG CD NE CZ NH1 NH2 REMARK 470 TYR A 267 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LEU A 297 CG CD1 CD2 REMARK 470 ILE A 300 CG1 CG2 CD1 REMARK 470 GLU A 301 CG CD OE1 OE2 REMARK 470 LYS A 302 CG CD CE NZ REMARK 470 LYS A 397 CG CD CE NZ REMARK 470 ARG A 398 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 399 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 471 CG CD OE1 OE2 REMARK 470 ARG A 545 CG CD NE CZ NH1 NH2 REMARK 470 GLN D1058 CG CD OE1 NE2 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 MET A 22 -54.95 -139.10 REMARK 500 ALA A 30 119.30 -161.25 REMARK 500 ASP A 36 -116.96 56.13 REMARK 500 PRO A 52 -71.02 -46.93 REMARK 500 PRO A 144 109.17 -52.09 REMARK 500 ASN A 146 44.42 -81.18 REMARK 500 HIS A 298 50.97 -93.41 REMARK 500 PRO A 396 90.81 -63.85 REMARK 500 LYS A 397 78.60 -66.49 REMARK 500 ARG A 399 -65.13 -144.14 REMARK 500 ASN A 435 49.30 -156.85 REMARK 500 SER A 437 74.40 58.81 REMARK 500 ASP A 480 72.51 50.35 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 MN A 550 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 551 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3GCM RELATED DB: PDB REMARK 900 POLYNUCLEOTIDE PHOSPHORYLASE IN COMPLEX WITH RNASE E AND RNA REMARK 900 RELATED ID: 3GLL RELATED DB: PDB REMARK 900 POLYNUCLEOTIDE PHOSPHORYLASE DBREF 3GME A 1 549 UNP A7ZS61 PNP_ECO24 1 549 DBREF 3GME D 1021 1061 UNP A7ZKI9 A7ZKI9_ECO24 1021 1061 SEQRES 1 A 549 MET LEU ASN PRO ILE VAL ARG LYS PHE GLN TYR GLY GLN SEQRES 2 A 549 HIS THR VAL THR LEU GLU THR GLY MET MET ALA ARG GLN SEQRES 3 A 549 ALA THR ALA ALA VAL MET VAL SER MET ASP ASP THR ALA SEQRES 4 A 549 VAL PHE VAL THR VAL VAL GLY GLN LYS LYS ALA LYS PRO SEQRES 5 A 549 GLY GLN ASP PHE PHE PRO LEU THR VAL ASN TYR GLN GLU SEQRES 6 A 549 ARG THR TYR ALA ALA GLY ARG ILE PRO GLY SER PHE PHE SEQRES 7 A 549 ARG ARG GLU GLY ARG PRO SER GLU GLY GLU THR LEU ILE SEQRES 8 A 549 ALA ARG LEU ILE ASP ARG PRO ILE ARG PRO LEU PHE PRO SEQRES 9 A 549 GLU GLY PHE VAL ASN GLU VAL GLN VAL ILE ALA THR VAL SEQRES 10 A 549 VAL SER VAL ASN PRO GLN VAL ASN PRO ASP ILE VAL ALA SEQRES 11 A 549 MET ILE GLY ALA SER ALA ALA LEU SER LEU SER GLY ILE SEQRES 12 A 549 PRO PHE ASN GLY PRO ILE GLY ALA ALA ARG VAL GLY TYR SEQRES 13 A 549 ILE ASN ASP GLN TYR VAL LEU ASN PRO THR GLN ASP GLU SEQRES 14 A 549 LEU LYS GLU SER LYS LEU ASP LEU VAL VAL ALA GLY THR SEQRES 15 A 549 GLU ALA ALA VAL LEU MET VAL GLU SER GLU ALA GLU LEU SEQRES 16 A 549 LEU SER GLU ASP GLN MET LEU GLY ALA VAL VAL PHE GLY SEQRES 17 A 549 HIS GLU GLN GLN GLN VAL VAL ILE GLN ASN ILE ASN GLU SEQRES 18 A 549 LEU VAL LYS GLU ALA GLY LYS PRO ARG TRP ASP TRP GLN SEQRES 19 A 549 PRO GLU PRO VAL ASN GLU ALA LEU ASN ALA ARG VAL ALA SEQRES 20 A 549 ALA LEU ALA GLU ALA ARG LEU SER ASP ALA TYR ARG ILE SEQRES 21 A 549 THR ASP LYS GLN GLU ARG TYR ALA GLN VAL ASP VAL ILE SEQRES 22 A 549 LYS SER GLU THR ILE ALA THR LEU LEU ALA GLU ASP GLU SEQRES 23 A 549 THR LEU ASP GLU ASN GLU LEU GLY GLU ILE LEU HIS ALA SEQRES 24 A 549 ILE GLU LYS ASN VAL VAL ARG SER ARG VAL LEU ALA GLY SEQRES 25 A 549 GLU PRO ARG ILE ASP GLY ARG GLU LYS ASP MET ILE ARG SEQRES 26 A 549 GLY LEU ASP VAL ARG THR GLY VAL LEU PRO ARG THR HIS SEQRES 27 A 549 GLY SER ALA LEU PHE THR ARG GLY GLU THR GLN ALA LEU SEQRES 28 A 549 VAL THR ALA THR LEU GLY THR ALA ARG ASP ALA GLN VAL SEQRES 29 A 549 LEU ASP GLU LEU MET GLY GLU ARG THR ASP THR PHE LEU SEQRES 30 A 549 PHE HIS TYR ASN PHE PRO PRO TYR SER VAL GLY GLU THR SEQRES 31 A 549 GLY MET VAL GLY SER PRO LYS ARG ARG GLU ILE GLY HIS SEQRES 32 A 549 GLY ARG LEU ALA LYS ARG GLY VAL LEU ALA VAL MET PRO SEQRES 33 A 549 ASP MET ASP LYS PHE PRO TYR THR VAL ARG VAL VAL SER SEQRES 34 A 549 GLU ILE THR GLU SER ASN GLY SER SER SER MET ALA SER SEQRES 35 A 549 VAL CYS GLY ALA SER LEU ALA LEU MET ASP ALA GLY VAL SEQRES 36 A 549 PRO ILE LYS ALA ALA VAL ALA GLY ILE ALA MET GLY LEU SEQRES 37 A 549 VAL LYS GLU GLY ASP ASN TYR VAL VAL LEU SER ASP ILE SEQRES 38 A 549 LEU GLY ASP GLU ASP HIS LEU GLY ASP MET ASP PHE LYS SEQRES 39 A 549 VAL ALA GLY SER ARG ASP GLY ILE SER ALA LEU GLN MET SEQRES 40 A 549 ASP ILE LYS ILE GLU GLY ILE THR LYS GLU ILE MET GLN SEQRES 41 A 549 VAL ALA LEU ASN GLN ALA LYS GLY ALA ARG LEU HIS ILE SEQRES 42 A 549 LEU GLY VAL MET GLU GLN ALA ILE ASN ALA PRO ARG GLY SEQRES 43 A 549 ASP ILE SER SEQRES 1 D 41 GLU ALA PRO ARG HIS SER ASP TRP GLN ARG PRO THR PHE SEQRES 2 D 41 ALA PHE GLU GLY LYS GLY ALA ALA GLY GLY HIS THR ALA SEQRES 3 D 41 THR HIS HIS ALA SER ALA ALA PRO ALA ARG PRO GLN PRO SEQRES 4 D 41 VAL GLU HET MN A 550 1 HET MN A 551 1 HETNAM MN MANGANESE (II) ION FORMUL 3 MN 2(MN 2+) FORMUL 5 HOH *158(H2 O) HELIX 1 1 THR A 67 ALA A 70 5 4 HELIX 2 2 SER A 85 ARG A 100 1 16 HELIX 3 3 PRO A 101 PHE A 103 5 3 HELIX 4 4 ASN A 125 GLY A 142 1 18 HELIX 5 5 SER A 197 GLN A 212 1 16 HELIX 6 6 GLN A 212 GLY A 227 1 16 HELIX 7 7 ASN A 239 ALA A 244 1 6 HELIX 8 8 ASP A 262 TYR A 267 1 6 HELIX 9 9 HIS A 298 GLY A 312 1 15 HELIX 10 10 PRO A 383 VAL A 387 5 5 HELIX 11 11 ARG A 399 LEU A 412 1 14 HELIX 12 12 SER A 437 GLY A 454 1 18 HELIX 13 13 LEU A 482 GLY A 489 1 8 HELIX 14 14 THR A 515 ILE A 541 1 27 SHEET 1 A 6 ILE A 5 TYR A 11 0 SHEET 2 A 6 HIS A 14 THR A 20 -1 O HIS A 14 N TYR A 11 SHEET 3 A 6 ALA A 29 MET A 35 -1 O SER A 34 N THR A 17 SHEET 4 A 6 THR A 38 GLY A 46 -1 O VAL A 42 N VAL A 31 SHEET 5 A 6 VAL A 111 SER A 119 -1 O THR A 116 N PHE A 41 SHEET 6 A 6 LEU A 59 GLU A 65 1 N ASN A 62 O VAL A 113 SHEET 1 B 8 GLN A 160 LEU A 163 0 SHEET 2 B 8 GLY A 150 ILE A 157 -1 N GLY A 155 O VAL A 162 SHEET 3 B 8 LEU A 177 GLY A 181 -1 O LEU A 177 N VAL A 154 SHEET 4 B 8 VAL A 186 LEU A 196 -1 O GLU A 190 N VAL A 178 SHEET 5 B 8 ILE A 502 ILE A 509 -1 O SER A 503 N ALA A 193 SHEET 6 B 8 MET A 491 GLY A 497 -1 N ALA A 496 O ALA A 504 SHEET 7 B 8 ALA A 462 GLU A 471 -1 N MET A 466 O PHE A 493 SHEET 8 B 8 ASN A 474 SER A 479 -1 O LEU A 478 N GLY A 467 SHEET 1 C 6 PHE A 376 ASN A 381 0 SHEET 2 C 6 THR A 424 GLU A 433 1 O VAL A 427 N HIS A 379 SHEET 3 C 6 THR A 348 GLY A 357 -1 N LEU A 351 O GLU A 430 SHEET 4 C 6 GLY A 339 ARG A 345 -1 N ARG A 345 O THR A 348 SHEET 5 C 6 LEU A 327 THR A 331 -1 N ASP A 328 O THR A 344 SHEET 6 C 6 HIS D1048 ALA D1052 -1 O ALA D1050 N VAL A 329 LINK O PHE A 41 MN MN A 551 1555 1555 2.26 CISPEP 1 GLY A 147 PRO A 148 0 -2.51 SITE 1 AC1 2 ASP A 486 ASP A 492 SITE 1 AC2 5 PHE A 41 VAL A 42 THR A 43 ILE A 114 SITE 2 AC2 5 THR A 116 CRYST1 158.574 158.574 156.118 90.00 90.00 120.00 H 3 2 18 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 0.006306 0.003641 0.000000 0.00000 SCALE2 0.000000 0.007282 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006405 0.00000