PDB Short entry for 2AUJ HEADER TRANSFERASE 27-AUG-05 2AUJ TITLE STRUCTURE OF THERMUS AQUATICUS RNA POLYMERASE BETA'-SUBUNIT INSERT COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-DIRECTED RNA POLYMERASE BETA' CHAIN; COMPND 3 CHAIN: D; COMPND 4 FRAGMENT: RESIDUES 151-455; COMPND 5 SYNONYM: RNAP BETA' SUBUNIT, TRANSCRIPTASE BETA' CHAIN, RNA COMPND 6 POLYMERASE BETA' SUBUNIT; COMPND 7 EC: 2.7.7.6; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS AQUATICUS; SOURCE 3 ORGANISM_TAXID: 271; SOURCE 4 GENE: RPOC; 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: PET15B KEYWDS SANDWICH-BARREL HYBRID MOTIF, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.CHLENOV,S.MASUDA,K.S.MURAKAMI,V.NIKIFOROV,S.A.DARST,A.MUSTAEV REVDAT 4 14-FEB-24 2AUJ 1 SEQADV SHEET REVDAT 3 24-FEB-09 2AUJ 1 VERSN REVDAT 2 18-OCT-05 2AUJ 1 JRNL REVDAT 1 04-OCT-05 2AUJ 0 JRNL AUTH M.CHLENOV,S.MASUDA,K.S.MURAKAMI,V.NIKIFOROV,S.A.DARST, JRNL AUTH 2 A.MUSTAEV JRNL TITL STRUCTURE AND FUNCTION OF LINEAGE-SPECIFIC SEQUENCE JRNL TITL 2 INSERTIONS IN THE BACTERIAL RNA POLYMERASE BETA' SUBUNIT JRNL REF J.MOL.BIOL. V. 353 138 2005 JRNL REFN ISSN 0022-2836 JRNL PMID 16154587 JRNL DOI 10.1016/J.JMB.2005.07.073 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 10715 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.236 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 560 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2328 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2AUJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-AUG-05. REMARK 100 THE DEPOSITION ID IS D_1000034328. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-AUG-00 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92511 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10739 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: COMBINATION OF MOLECULAR REMARK 200 REPLACEMENT AND SAD REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CACODYLATE/MAGNESIUM REMARK 280 ACETATE/POLYETHYLENE GLYCOL 8000, PH 6.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 26.82450 REMARK 290 SMTRY3 2 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 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 GLY D 147 REMARK 465 SER D 148 REMARK 465 HIS D 149 REMARK 465 MET D 150 REMARK 465 GLN D 151 REMARK 465 LEU D 152 REMARK 465 ASP D 451 REMARK 465 ILE D 452 REMARK 465 ASP D 453 REMARK 465 ALA D 454 REMARK 465 ARG D 455 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 LEU D 153 CG CD1 CD2 REMARK 470 GLU D 408 CG CD OE1 OE2 REMARK 470 LYS D 426 CG CD CE NZ REMARK 470 LYS D 428 CG CD CE NZ 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 ALA D 173 149.94 -30.46 REMARK 500 PHE D 207 91.34 35.13 REMARK 500 VAL D 231 60.42 -117.82 REMARK 500 GLU D 232 111.20 -30.64 REMARK 500 ALA D 235 137.43 -172.78 REMARK 500 PRO D 248 150.41 -46.11 REMARK 500 ALA D 265 -129.17 62.86 REMARK 500 GLU D 275 -129.30 61.02 REMARK 500 ALA D 305 -158.33 -134.67 REMARK 500 GLU D 306 129.28 -174.53 REMARK 500 GLU D 327 87.25 -155.72 REMARK 500 PRO D 349 -44.15 -22.31 REMARK 500 HIS D 350 31.83 -71.11 REMARK 500 GLU D 376 159.64 -48.12 REMARK 500 ALA D 398 160.01 178.57 REMARK 500 ASP D 406 126.16 1.20 REMARK 500 ASP D 419 122.67 -30.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2AUK RELATED DB: PDB REMARK 900 STRUCTURE OF E. COLI RNA POLYMERASE BETA' G/G' INSERT DBREF 2AUJ D 151 455 UNP Q9KWU6 RPOC_THEAQ 151 455 SEQADV 2AUJ GLY D 147 UNP Q9KWU6 CLONING ARTIFACT SEQADV 2AUJ SER D 148 UNP Q9KWU6 CLONING ARTIFACT SEQADV 2AUJ HIS D 149 UNP Q9KWU6 CLONING ARTIFACT SEQADV 2AUJ MET D 150 UNP Q9KWU6 CLONING ARTIFACT SEQRES 1 D 309 GLY SER HIS MET GLN LEU LEU THR ASP GLU GLU TYR ARG SEQRES 2 D 309 GLU LEU ARG TYR GLY LYS GLN GLU THR TYR PRO LEU PRO SEQRES 3 D 309 ALA GLY VAL ASP ALA LEU VAL LYS ASP GLY GLU GLU VAL SEQRES 4 D 309 VAL LYS GLY GLN GLU LEU ALA PRO GLY VAL VAL SER ARG SEQRES 5 D 309 MET ASP GLY VAL ALA LEU TYR ARG PHE PRO ARG ARG VAL SEQRES 6 D 309 ARG VAL ASP TYR LEU ARG LYS GLU ARG ALA ALA LEU ARG SEQRES 7 D 309 ILE PRO LEU SER ALA TRP VAL GLU LYS GLU ALA TYR ARG SEQRES 8 D 309 PRO GLY GLU VAL LEU ALA GLU LEU SER GLU PRO TYR LEU SEQRES 9 D 309 PHE ARG ALA GLU GLU SER GLY VAL VAL GLU LEU LYS ASP SEQRES 10 D 309 LEU ALA GLU GLY HIS LEU ILE TYR LEU ARG GLN GLU GLU SEQRES 11 D 309 GLU VAL VAL ALA ARG TYR PHE LEU PRO ALA GLY MET THR SEQRES 12 D 309 PRO LEU VAL VAL GLU GLY GLU ILE VAL GLU VAL GLY GLN SEQRES 13 D 309 PRO LEU ALA GLU GLY LYS GLY LEU LEU ARG LEU PRO ARG SEQRES 14 D 309 HIS MET THR ALA LYS GLU VAL GLU ALA GLU GLU GLU GLY SEQRES 15 D 309 ASP SER VAL HIS LEU THR LEU PHE LEU GLU TRP THR GLU SEQRES 16 D 309 PRO LYS ASP TYR LYS VAL ALA PRO HIS MET ASN VAL ILE SEQRES 17 D 309 VAL PRO GLU GLY ALA LYS VAL GLN ALA GLY GLU LYS ILE SEQRES 18 D 309 VAL ALA ALA ILE ASP PRO GLU GLU GLU VAL ILE ALA GLU SEQRES 19 D 309 ALA GLU GLY VAL VAL HIS LEU HIS GLU PRO ALA SER ILE SEQRES 20 D 309 LEU VAL VAL LYS ALA ARG VAL TYR PRO PHE GLU ASP ASP SEQRES 21 D 309 VAL GLU VAL THR THR GLY ASP ARG VAL ALA PRO GLY ASP SEQRES 22 D 309 VAL LEU ALA ASP GLY GLY LYS VAL LYS SER GLU ILE TYR SEQRES 23 D 309 GLY ARG VAL GLU VAL ASP LEU VAL ARG ASN VAL VAL ARG SEQRES 24 D 309 VAL VAL GLU SER TYR ASP ILE ASP ALA ARG HELIX 1 1 THR D 154 TYR D 163 1 10 HELIX 2 2 ASP D 372 GLU D 376 5 5 SHEET 1 A 6 GLN D 166 PRO D 170 0 SHEET 2 A 6 GLY D 383 VAL D 396 -1 O ILE D 393 N TYR D 169 SHEET 3 A 6 GLY D 201 PRO D 226 -1 N ARG D 210 O HIS D 388 SHEET 4 A 6 SER D 330 LYS D 346 -1 O LEU D 333 N LEU D 223 SHEET 5 A 6 MET D 317 GLU D 327 -1 N THR D 318 O GLU D 338 SHEET 6 A 6 ALA D 235 TYR D 236 -1 N TYR D 236 O ALA D 319 SHEET 1 B 4 GLU D 184 VAL D 185 0 SHEET 2 B 4 GLY D 201 PRO D 226 -1 O GLY D 201 N VAL D 185 SHEET 3 B 4 GLY D 383 VAL D 396 -1 O HIS D 388 N ARG D 210 SHEET 4 B 4 LYS D 360 VAL D 361 -1 N VAL D 361 O GLY D 383 SHEET 1 C 3 VAL D 241 GLU D 244 0 SHEET 2 C 3 GLY D 307 ARG D 312 -1 O LEU D 311 N LEU D 242 SHEET 3 C 3 ALA D 286 MET D 288 -1 N ALA D 286 O ARG D 312 SHEET 1 D 4 GLU D 277 LEU D 284 0 SHEET 2 D 4 GLY D 267 GLN D 274 -1 N ILE D 270 O TYR D 282 SHEET 3 D 4 GLY D 257 LEU D 264 -1 N VAL D 258 O ARG D 273 SHEET 4 D 4 ILE D 297 VAL D 298 -1 O VAL D 298 N GLY D 257 SHEET 1 E 3 ASN D 352 VAL D 353 0 SHEET 2 E 3 LYS D 366 ALA D 369 -1 O ALA D 369 N ASN D 352 SHEET 3 E 3 VAL D 377 ILE D 378 -1 O VAL D 377 N ILE D 367 SHEET 1 F 3 ALA D 398 PRO D 402 0 SHEET 2 F 3 VAL D 443 GLU D 448 -1 O VAL D 444 N TYR D 401 SHEET 3 F 3 GLY D 433 ASP D 438 -1 N ASP D 438 O VAL D 443 SHEET 1 G 1 VAL D 420 ALA D 422 0 CRYST1 59.724 53.649 69.693 90.00 107.09 90.00 P 1 21 1 2 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 0.016744 0.000000 0.005148 0.00000 SCALE2 0.000000 0.018640 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015011 0.00000