HEADER GENE REGULATION/DNA 28-MAY-10 3N97 TITLE RNA POLYMERASE ALPHA C-TERMINAL DOMAIN (E. COLI) AND SIGMA REGION 4 TITLE 2 (T. AQ. MUTANT) BOUND TO (UP,-35 ELEMENT) DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA POLYMERASE SIGMA FACTOR; COMPND 3 CHAIN: A, D; COMPND 4 FRAGMENT: SIGMA SUBUNIT REGION 4, RESIDUES 366-438; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA-DIRECTED RNA POLYMERASE SUBUNIT ALPHA; COMPND 9 CHAIN: B, C; COMPND 10 FRAGMENT: ALPHA SUBUNIT C-TERMINAL DOMAIN, RESIDUES 246-329; COMPND 11 SYNONYM: RNAP SUBUNIT ALPHA, TRANSCRIPTASE SUBUNIT ALPHA, RNA COMPND 12 POLYMERASE SUBUNIT ALPHA; COMPND 13 EC: 2.7.7.6; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 3; COMPND 16 MOLECULE: DNA (5'- COMPND 17 D(*TP*GP*GP*AP*AP*AP*AP*AP*AP*GP*TP*AP*CP*TP*TP*GP*AP*CP*AP*TP*GP*G)- COMPND 18 3'); COMPND 19 CHAIN: M; COMPND 20 ENGINEERED: YES; COMPND 21 MOL_ID: 4; COMPND 22 MOLECULE: DNA (5'- COMPND 23 D(*CP*CP*AP*TP*GP*TP*CP*AP*AP*GP*TP*AP*CP*TP*TP*TP*TP*TP*TP*CP*C)- COMPND 24 3'); COMPND 25 CHAIN: N; COMPND 26 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS AQUATICUS; SOURCE 3 ORGANISM_TAXID: 271; SOURCE 4 GENE: RPOS; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 DE3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 12 ORGANISM_TAXID: 83333; SOURCE 13 STRAIN: K12; SOURCE 14 GENE: B3295, JW3257, PEZ, PHS, RPOA, SEZ; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 17 EXPRESSION_SYSTEM_STRAIN: BL21 DE3; SOURCE 18 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 19 EXPRESSION_SYSTEM_PLASMID: PET; SOURCE 20 MOL_ID: 3; SOURCE 21 SYNTHETIC: YES; SOURCE 22 MOL_ID: 4; SOURCE 23 SYNTHETIC: YES KEYWDS PROTEIN-PROTEIN INTERACTIONS, PROTEIN-DNA INTERACTIONS, TRANSCRIPTION KEYWDS 2 INITIATION, GENE REGULATION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.LARA-GONZALEZ,J.J.BIRKTOFT,C.L.LAWSON REVDAT 4 06-SEP-23 3N97 1 REMARK REVDAT 3 23-DEC-20 3N97 1 JRNL REVDAT 2 25-NOV-20 3N97 1 JRNL REMARK SEQADV REVDAT 1 08-JUN-11 3N97 0 JRNL AUTH S.LARA-GONZALEZ,A.C.DANTAS MACHADO,S.RAO,A.A.NAPOLI, JRNL AUTH 2 J.BIRKTOFT,R.DI FELICE,R.ROHS,C.L.LAWSON JRNL TITL THE RNA POLYMERASE ALPHA SUBUNIT RECOGNIZES THE DNA SHAPE OF JRNL TITL 2 THE UPSTREAM PROMOTER ELEMENT. JRNL REF BIOCHEMISTRY V. 59 4523 2020 JRNL REFN ISSN 0006-2960 JRNL PMID 33205945 JRNL DOI 10.1021/ACS.BIOCHEM.0C00571 REMARK 2 REMARK 2 RESOLUTION. 3.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.130 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.7 REMARK 3 NUMBER OF REFLECTIONS : 7422 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.257 REMARK 3 R VALUE (WORKING SET) : 0.254 REMARK 3 FREE R VALUE : 0.295 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.470 REMARK 3 FREE R VALUE TEST SET COUNT : 480 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 25.4530 - 4.6840 0.86 2309 161 0.2110 0.2690 REMARK 3 2 4.6840 - 3.7210 0.90 2298 169 0.2680 0.2950 REMARK 3 3 3.7210 - 3.2520 0.90 2335 150 0.3760 0.3740 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.28 REMARK 3 B_SOL : 66.44 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.540 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 98.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 138.9 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 39.77700 REMARK 3 B22 (A**2) : -5.67600 REMARK 3 B33 (A**2) : -34.10000 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 3111 REMARK 3 ANGLE : 1.212 4237 REMARK 3 CHIRALITY : 0.057 488 REMARK 3 PLANARITY : 0.008 391 REMARK 3 DIHEDRAL : 23.614 1232 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 21.4667 -15.5546 -49.2867 REMARK 3 T TENSOR REMARK 3 T11: 0.5358 T22: 0.5278 REMARK 3 T33: 0.6650 T12: -0.0575 REMARK 3 T13: -0.0907 T23: 0.0749 REMARK 3 L TENSOR REMARK 3 L11: 1.6588 L22: 1.6605 REMARK 3 L33: 6.4742 L12: -0.6447 REMARK 3 L13: -0.5868 L23: 0.5178 REMARK 3 S TENSOR REMARK 3 S11: 0.0696 S12: -0.1180 S13: -0.2897 REMARK 3 S21: -0.0551 S22: 0.1144 S23: 0.0057 REMARK 3 S31: 0.6826 S32: 0.0664 S33: -0.0016 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 4 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN A AND (RESSEQ 375:402 ) REMARK 3 SELECTION : CHAIN D AND (RESSEQ 375:402 ) REMARK 3 ATOM PAIRS NUMBER : 219 REMARK 3 RMSD : 0.152 REMARK 3 NCS GROUP : 2 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN A AND (RESSEQ 403:424 ) REMARK 3 SELECTION : CHAIN D AND (RESSEQ 403:424 ) REMARK 3 ATOM PAIRS NUMBER : 191 REMARK 3 RMSD : 0.203 REMARK 3 NCS GROUP : 3 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN B AND (RESSEQ 251:318 ) REMARK 3 SELECTION : CHAIN C AND (RESSEQ 251:318 ) REMARK 3 ATOM PAIRS NUMBER : 526 REMARK 3 RMSD : 0.152 REMARK 3 NCS GROUP : 4 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN B AND (RESSEQ 319:322 ) REMARK 3 SELECTION : CHAIN C AND (RESSEQ 319:322 ) REMARK 3 ATOM PAIRS NUMBER : 38 REMARK 3 RMSD : 0.308 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ADDITIONAL PSEUDO-BOND RESTRAINTS REMARK 3 APPLIED TO DNA BASE-PAIRS REMARK 4 REMARK 4 3N97 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JUN-10. REMARK 100 THE DEPOSITION ID IS D_1000059538. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-OCT-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92 REMARK 200 MONOCHROMATOR : DOUBLE SILICON(111) CRYSTAL REMARK 200 MONOCHROMATOR WITH CRYOGENICALLY- REMARK 200 COOLED FIRST CRYSTAL AND REMARK 200 SAGITTALLY-BENT SECOND CRYSTAL REMARK 200 HORIZONTALLY-FOCUSING AT 3.3:1 REMARK 200 DEMAGNIFICATION REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.16 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7461 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.250 REMARK 200 RESOLUTION RANGE LOW (A) : 25.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.1 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : 0.08100 REMARK 200 FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.81600 REMARK 200 R SYM FOR SHELL (I) : 0.81600 REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRIES 3N4M, 1LB2 AND 1KU7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 28% (W/V) PEG4000, 0.2 M AMMONIUM REMARK 280 ACETATE, 0.01 M SARCOSINE, 0.1 M SODIUM CITRATE, PH 5.6, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 289.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 73.55500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 73.55500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 40.35500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 43.20500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 40.35500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 43.20500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 73.55500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 40.35500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 43.20500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 73.55500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 40.35500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 43.20500 REMARK 290 SMTRY3 8 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: HEXAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, B, C, M, N 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 SER A 366 REMARK 465 GLU A 367 REMARK 465 GLU A 368 REMARK 465 LEU A 369 REMARK 465 GLU A 370 REMARK 465 LYS A 371 REMARK 465 ALA A 372 REMARK 465 LEU A 373 REMARK 465 SER A 427 REMARK 465 ARG A 428 REMARK 465 SER A 429 REMARK 465 GLU A 430 REMARK 465 LYS A 431 REMARK 465 LEU A 432 REMARK 465 ARG A 433 REMARK 465 ASP A 434 REMARK 465 PHE A 435 REMARK 465 LEU A 436 REMARK 465 GLU A 437 REMARK 465 SER D 366 REMARK 465 GLU D 367 REMARK 465 GLU D 368 REMARK 465 LEU D 369 REMARK 465 GLU D 370 REMARK 465 LYS D 371 REMARK 465 ALA D 372 REMARK 465 LEU D 373 REMARK 465 SER D 374 REMARK 465 HIS D 425 REMARK 465 PRO D 426 REMARK 465 SER D 427 REMARK 465 ARG D 428 REMARK 465 SER D 429 REMARK 465 GLU D 430 REMARK 465 LYS D 431 REMARK 465 LEU D 432 REMARK 465 ARG D 433 REMARK 465 ASP D 434 REMARK 465 PHE D 435 REMARK 465 LEU D 436 REMARK 465 GLU D 437 REMARK 465 LYS B 246 REMARK 465 PRO B 247 REMARK 465 GLU B 248 REMARK 465 PHE B 249 REMARK 465 SER B 325 REMARK 465 ILE B 326 REMARK 465 ALA B 327 REMARK 465 ASP B 328 REMARK 465 GLU B 329 REMARK 465 LYS C 246 REMARK 465 PRO C 247 REMARK 465 GLU C 248 REMARK 465 PHE C 249 REMARK 465 ALA C 324 REMARK 465 SER C 325 REMARK 465 ILE C 326 REMARK 465 ALA C 327 REMARK 465 ASP C 328 REMARK 465 GLU C 329 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 375 CG CD CE NZ REMARK 470 LYS D 375 CG CD CE NZ 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 DG M 2 C3' - C2' - C1' ANGL. DEV. = -6.0 DEGREES REMARK 500 DA M 5 C3' - C2' - C1' ANGL. DEV. = -5.7 DEGREES REMARK 500 DG M 10 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 DT M 11 C3' - C2' - C1' ANGL. DEV. = -5.7 DEGREES REMARK 500 DT M 11 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC M 13 O4' - C4' - C3' ANGL. DEV. = -2.7 DEGREES REMARK 500 DC M 13 C1' - O4' - C4' ANGL. DEV. = -8.4 DEGREES REMARK 500 DC M 13 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG M 16 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DC N 1 C3' - C2' - C1' ANGL. DEV. = -5.6 DEGREES REMARK 500 DC N 1 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DC N 2 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DA N 9 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DA N 9 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 DG N 10 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DT N 17 O4' - C1' - N1 ANGL. DEV. = 2.2 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 LEU A 390 -1.12 -55.05 REMARK 500 ILE A 391 -61.23 -91.90 REMARK 500 HIS A 425 62.75 -116.71 REMARK 500 LEU D 390 4.32 -56.57 REMARK 500 ASN B 294 -8.07 67.15 REMARK 500 ASN B 320 57.33 35.58 REMARK 500 PRO B 322 -159.98 -98.32 REMARK 500 ARG C 265 -72.12 -42.65 REMARK 500 ASN C 294 -9.52 68.67 REMARK 500 ASN C 320 63.82 36.85 REMARK 500 PRO C 322 -75.86 -100.65 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 ACT C 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3N4M RELATED DB: PDB REMARK 900 E. COLI RNA POLYMERASE ALPHA SUBUNIT C-TERMINAL DOMAIN IN COMPLEX REMARK 900 WITH CAP AND DNA REMARK 900 RELATED ID: 3K4G RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E. COLI RNA POLYMERASE ALPHA SUBUNIT C- REMARK 900 TERMINAL DOMAIN REMARK 999 REMARK 999 SEQUENCE REMARK 999 424-429 KYHESR SEQUENCE IN T. AQUATICUS RNA POLYMERASE IS REPLACED REMARK 999 WITH RHPSR SEQUENCE FROM E. COLI RNA POLYMERASE DBREF 3N97 A 366 437 UNP Q9EZJ8 Q9EZJ8_THEAQ 366 438 DBREF 3N97 D 366 437 UNP Q9EZJ8 Q9EZJ8_THEAQ 366 438 DBREF 3N97 B 246 329 UNP P0A7Z4 RPOA_ECOLI 246 329 DBREF 3N97 C 246 329 UNP P0A7Z4 RPOA_ECOLI 246 329 DBREF 3N97 M 1 22 PDB 3N97 3N97 1 22 DBREF 3N97 N 1 21 PDB 3N97 3N97 1 21 SEQADV 3N97 MET A 386 UNP Q9EZJ8 LEU 386 ENGINEERED MUTATION SEQADV 3N97 A UNP Q9EZJ8 LYS 424 SEE REMARK 999 SEQADV 3N97 ARG A 424 UNP Q9EZJ8 TYR 425 SEE REMARK 999 SEQADV 3N97 PRO A 426 UNP Q9EZJ8 GLU 427 SEE REMARK 999 SEQADV 3N97 SER A 429 UNP Q9EZJ8 THR 430 ENGINEERED MUTATION SEQADV 3N97 GLU A 430 UNP Q9EZJ8 ARG 431 ENGINEERED MUTATION SEQADV 3N97 MET D 386 UNP Q9EZJ8 LEU 386 ENGINEERED MUTATION SEQADV 3N97 D UNP Q9EZJ8 LYS 424 SEE REMARK 999 SEQADV 3N97 ARG D 424 UNP Q9EZJ8 TYR 425 SEE REMARK 999 SEQADV 3N97 PRO D 426 UNP Q9EZJ8 GLU 427 SEE REMARK 999 SEQADV 3N97 SER D 429 UNP Q9EZJ8 THR 430 ENGINEERED MUTATION SEQADV 3N97 GLU D 430 UNP Q9EZJ8 ARG 431 ENGINEERED MUTATION SEQRES 1 A 72 SER GLU GLU LEU GLU LYS ALA LEU SER LYS LEU SER GLU SEQRES 2 A 72 ARG GLU ALA MET VAL LEU LYS MET ARG LYS GLY LEU ILE SEQRES 3 A 72 ASP GLY ARG GLU HIS THR LEU GLU GLU VAL GLY ALA TYR SEQRES 4 A 72 PHE GLY VAL THR ARG GLU ARG ILE ARG GLN ILE GLU ASN SEQRES 5 A 72 LYS ALA LEU ARG LYS LEU ARG HIS PRO SER ARG SER GLU SEQRES 6 A 72 LYS LEU ARG ASP PHE LEU GLU SEQRES 1 D 72 SER GLU GLU LEU GLU LYS ALA LEU SER LYS LEU SER GLU SEQRES 2 D 72 ARG GLU ALA MET VAL LEU LYS MET ARG LYS GLY LEU ILE SEQRES 3 D 72 ASP GLY ARG GLU HIS THR LEU GLU GLU VAL GLY ALA TYR SEQRES 4 D 72 PHE GLY VAL THR ARG GLU ARG ILE ARG GLN ILE GLU ASN SEQRES 5 D 72 LYS ALA LEU ARG LYS LEU ARG HIS PRO SER ARG SER GLU SEQRES 6 D 72 LYS LEU ARG ASP PHE LEU GLU SEQRES 1 B 84 LYS PRO GLU PHE ASP PRO ILE LEU LEU ARG PRO VAL ASP SEQRES 2 B 84 ASP LEU GLU LEU THR VAL ARG SER ALA ASN CYS LEU LYS SEQRES 3 B 84 ALA GLU ALA ILE HIS TYR ILE GLY ASP LEU VAL GLN ARG SEQRES 4 B 84 THR GLU VAL GLU LEU LEU LYS THR PRO ASN LEU GLY LYS SEQRES 5 B 84 LYS SER LEU THR GLU ILE LYS ASP VAL LEU ALA SER ARG SEQRES 6 B 84 GLY LEU SER LEU GLY MET ARG LEU GLU ASN TRP PRO PRO SEQRES 7 B 84 ALA SER ILE ALA ASP GLU SEQRES 1 C 84 LYS PRO GLU PHE ASP PRO ILE LEU LEU ARG PRO VAL ASP SEQRES 2 C 84 ASP LEU GLU LEU THR VAL ARG SER ALA ASN CYS LEU LYS SEQRES 3 C 84 ALA GLU ALA ILE HIS TYR ILE GLY ASP LEU VAL GLN ARG SEQRES 4 C 84 THR GLU VAL GLU LEU LEU LYS THR PRO ASN LEU GLY LYS SEQRES 5 C 84 LYS SER LEU THR GLU ILE LYS ASP VAL LEU ALA SER ARG SEQRES 6 C 84 GLY LEU SER LEU GLY MET ARG LEU GLU ASN TRP PRO PRO SEQRES 7 C 84 ALA SER ILE ALA ASP GLU SEQRES 1 M 22 DT DG DG DA DA DA DA DA DA DG DT DA DC SEQRES 2 M 22 DT DT DG DA DC DA DT DG DG SEQRES 1 N 21 DC DC DA DT DG DT DC DA DA DG DT DA DC SEQRES 2 N 21 DT DT DT DT DT DT DC DC HET ACT C 1 4 HETNAM ACT ACETATE ION FORMUL 7 ACT C2 H3 O2 1- FORMUL 8 HOH *(H2 O) HELIX 1 1 SER A 377 GLY A 389 1 13 HELIX 2 2 THR A 397 GLY A 406 1 10 HELIX 3 3 THR A 408 HIS A 425 1 18 HELIX 4 4 SER D 377 GLY D 389 1 13 HELIX 5 5 THR D 397 GLY D 406 1 10 HELIX 6 6 THR D 408 ARG D 424 1 17 HELIX 7 7 PRO B 256 GLU B 261 5 6 HELIX 8 8 THR B 263 ALA B 272 1 10 HELIX 9 9 TYR B 277 GLN B 283 1 7 HELIX 10 10 THR B 285 THR B 292 1 8 HELIX 11 11 GLY B 296 SER B 309 1 14 HELIX 12 12 PRO C 256 GLU C 261 5 6 HELIX 13 13 THR C 263 ALA C 272 1 10 HELIX 14 14 TYR C 277 GLN C 283 1 7 HELIX 15 15 THR C 285 THR C 292 1 8 HELIX 16 16 GLY C 296 SER C 309 1 14 CISPEP 1 TRP B 321 PRO B 322 0 -4.43 CISPEP 2 TRP C 321 PRO C 322 0 -6.79 SITE 1 AC1 5 ARG C 265 ASN C 294 DA M 6 DT N 19 SITE 2 AC1 5 DC N 20 CRYST1 80.710 86.410 147.110 90.00 90.00 90.00 C 2 2 21 16 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 0.012390 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011573 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006798 0.00000 MTRIX1 1 0.092064 0.966746 0.238591 62.99730 1 MTRIX2 1 0.973654 -0.137598 0.181837 -37.83020 1 MTRIX3 1 0.208620 0.215564 -0.953944 -144.09399 1 MTRIX1 2 0.102772 0.956100 0.274428 65.33050 1 MTRIX2 2 0.966024 -0.161708 0.201615 -36.27820 1 MTRIX3 2 0.237141 0.244383 -0.940234 -143.48100 1 MTRIX1 3 0.310109 0.706236 -0.636446 9.68058 1 MTRIX2 3 -0.644763 0.648199 0.405117 23.89670 1 MTRIX3 3 0.698651 0.284726 0.656367 -31.64760 1 MTRIX1 4 0.316748 0.668369 -0.673018 8.19682 1 MTRIX2 4 -0.707628 0.639005 0.301554 21.99580 1 MTRIX3 4 0.631612 0.380730 0.675360 -30.36740 1