HEADER GENE REGULATION/DNA 21-MAY-10 3N4M TITLE E. COLI RNA POLYMERASE ALPHA SUBUNIT C-TERMINAL DOMAIN IN COMPLEX WITH TITLE 2 CAP AND DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATABOLITE GENE ACTIVATOR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CAMP RECEPTOR PROTEIN, CAMP REGULATORY PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA-DIRECTED RNA POLYMERASE SUBUNIT ALPHA; COMPND 8 CHAIN: B, C; COMPND 9 FRAGMENT: ALPHA SUBUNIT C-TERMINAL DOMAIN, RESIDUES 246-329; COMPND 10 SYNONYM: RNAP SUBUNIT ALPHA, TRANSCRIPTASE SUBUNIT ALPHA, RNA COMPND 11 POLYMERASE SUBUNIT ALPHA; COMPND 12 EC: 2.7.7.6; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: DNA (5'- COMPND 16 D(*CP*TP*TP*TP*TP*TP*TP*CP*CP*TP*AP*AP*AP*AP*TP*GP*TP*GP*AP*T)-3'); COMPND 17 CHAIN: D; COMPND 18 ENGINEERED: YES; COMPND 19 MOL_ID: 4; COMPND 20 MOLECULE: DNA (5'- COMPND 21 D(*CP*TP*AP*GP*AP*TP*CP*AP*CP*AP*TP*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP* COMPND 22 AP*G)-3'); COMPND 23 CHAIN: E; COMPND 24 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: B3357, CAP, CRP, CSM, JW5702; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 DE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 13 ORGANISM_TAXID: 83333; SOURCE 14 STRAIN: K12; SOURCE 15 GENE: B3295, JW3257, PEZ, PHS, RPOA, SEZ; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21 DE3; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PET; SOURCE 21 MOL_ID: 3; SOURCE 22 SYNTHETIC: YES; SOURCE 23 MOL_ID: 4; SOURCE 24 SYNTHETIC: YES KEYWDS PROTEIN-PROTEIN INTERACTIONS, PROTEIN-DNA INTERACTIONS, GENE KEYWDS 2 REGULATION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.LARA-GONZALEZ,J.J.BIRKTOFT,C.L.LAWSON REVDAT 4 06-SEP-23 3N4M 1 REMARK REVDAT 3 26-JUL-23 3N4M 1 JRNL REVDAT 2 25-NOV-20 3N4M 1 JRNL REMARK REVDAT 1 25-MAY-11 3N4M 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 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH B.BENOFF,H.YANG,C.L.LAWSON,G.PARKINSON,J.LIU,E.BLATTER, REMARK 1 AUTH 2 Y.W.EBRIGHT,H.M.BERMAN,R.H.EBRIGHT REMARK 1 TITL STRUCTURAL BASIS OF TRANSCRIPTION ACTIVATION: THE CAP-ALPHA REMARK 1 TITL 2 CTD-DNA COMPLEX REMARK 1 REF SCIENCE V. 297 1562 2002 REMARK 1 REFN ISSN 0036-8075 REMARK 2 REMARK 2 RESOLUTION. 2.99 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) : 2.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.51 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.170 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 29042 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1481 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 38.5170 - 6.6340 0.95 2680 125 0.1650 0.1940 REMARK 3 2 6.6340 - 5.2700 0.97 2606 122 0.1700 0.1740 REMARK 3 3 5.2700 - 4.6050 0.98 2569 129 0.1540 0.1770 REMARK 3 4 4.6050 - 4.1840 0.98 2539 133 0.1660 0.1950 REMARK 3 5 4.1840 - 3.8850 0.98 2529 150 0.1770 0.2080 REMARK 3 6 3.8850 - 3.6560 0.99 2527 139 0.2150 0.2310 REMARK 3 7 3.6560 - 3.4730 0.99 2525 153 0.2320 0.2630 REMARK 3 8 3.4730 - 3.3220 0.99 2518 133 0.2610 0.2500 REMARK 3 9 3.3220 - 3.1940 0.99 2513 154 0.2820 0.2910 REMARK 3 10 3.1940 - 3.0840 0.99 2516 135 0.3190 0.3480 REMARK 3 11 3.0840 - 2.9870 0.80 2039 108 0.3560 0.4010 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 : 0.30 REMARK 3 B_SOL : 70.57 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.610 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 99.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 110.3 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 10.92000 REMARK 3 B22 (A**2) : 10.92000 REMARK 3 B33 (A**2) : -21.84000 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 : 0.004 3852 REMARK 3 ANGLE : 0.946 5391 REMARK 3 CHIRALITY : 0.051 622 REMARK 3 PLANARITY : 0.003 526 REMARK 3 DIHEDRAL : 21.362 1517 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): 112.1779 -51.2756 149.0329 REMARK 3 T TENSOR REMARK 3 T11: 0.4991 T22: 0.3004 REMARK 3 T33: 0.2578 T12: -0.0083 REMARK 3 T13: -0.0811 T23: -0.0273 REMARK 3 L TENSOR REMARK 3 L11: 1.2914 L22: 0.5189 REMARK 3 L33: 0.3702 L12: -0.2319 REMARK 3 L13: -0.2558 L23: -0.1921 REMARK 3 S TENSOR REMARK 3 S11: 0.0181 S12: -0.0200 S13: 0.1337 REMARK 3 S21: 0.4331 S22: 0.0013 S23: -0.0819 REMARK 3 S31: -0.0045 S32: 0.1066 S33: -0.0232 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN B AND (RESSEQ 250:322 ) REMARK 3 SELECTION : CHAIN C AND (RESSEQ 250:322 ) REMARK 3 ATOM PAIRS NUMBER : 572 REMARK 3 RMSD : 0.009 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3N4M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUN-10. REMARK 100 THE DEPOSITION ID IS D_1000059373. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAY-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.10 REMARK 200 MONOCHROMATOR : HORIZONTALLY FOCUSING REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : VERTICAL MIRROR, HORIZONTAL REMARK 200 MONOCHROMATOR 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 : 29113 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.987 REMARK 200 RESOLUTION RANGE LOW (A) : 38.510 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : 0.08500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.02 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 1.10600 REMARK 200 R SYM FOR SHELL (I) : 1.10600 REMARK 200 <I/SIGMA(I)> 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: AMORE REMARK 200 STARTING MODEL: 1LB2, 3K4G REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 80.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 6.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM ACETATE (PH 4.5), 625 MM REMARK 280 NACL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.2K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+2/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+1/3 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 106.73333 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 53.36667 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 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 106.73333 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 53.36667 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 106.73333 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 53.36667 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 106.73333 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 53.36667 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: DECAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E 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 -1.000000 0.000000 0.000000 175.73000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 320.20000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH E 101 LIES ON A SPECIAL POSITION. 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 VAL A 1 REMARK 465 LEU A 2 REMARK 465 GLY A 3 REMARK 465 LYS A 4 REMARK 465 PRO A 5 REMARK 465 GLN A 6 REMARK 465 LYS B 246 REMARK 465 PRO B 247 REMARK 465 GLU B 248 REMARK 465 PRO B 323 REMARK 465 ALA B 324 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 PRO C 323 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 THR A 7 OG1 CG2 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 D 18 O4' - C4' - C3' ANGL. DEV. = -2.7 DEGREES REMARK 500 DG D 18 C4' - C3' - C2' ANGL. DEV. = -4.5 DEGREES REMARK 500 DG D 18 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES REMARK 500 DG E 24 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DC E 29 O4' - C1' - N1 ANGL. DEV. = 1.8 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 GLU A 37 -0.93 -141.83 REMARK 500 ASN A 109 99.07 -161.76 REMARK 500 ASN A 194 47.61 39.45 REMARK 500 GLU B 261 71.25 51.20 REMARK 500 ALA B 274 34.67 72.03 REMARK 500 ASN B 320 70.32 54.07 REMARK 500 GLU C 261 70.98 51.04 REMARK 500 ALA C 274 34.66 71.66 REMARK 500 ASN C 320 70.31 53.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 CMP D 100 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CMP A 210 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CMP D 100 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LB2 RELATED DB: PDB REMARK 900 THIS ENTRY IS A RE-DETERMINATION OF THE 1LB2 CAP-ALPHA CTD-DNA REMARK 900 COMPLEX USING NEW DIFFRACTION DATA 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 900 RELATED ID: 3N97 RELATED DB: PDB REMARK 900 RNA POLYMERASE ALPHA C-TERMINAL DOMAIN (E. COLI) AND SIGMA REGION 4 REMARK 900 (T. AQ. MUTANT) BOUND TO (UP,-35 ELEMENT) DNA DBREF 3N4M A 1 209 UNP P0ACJ8 CRP_ECOLI 2 210 DBREF 3N4M B 246 329 UNP P0A7Z4 RPOA_ECOLI 246 329 DBREF 3N4M C 246 329 UNP P0A7Z4 RPOA_ECOLI 246 329 DBREF 3N4M D 1 20 PDB 3N4M 3N4M 1 20 DBREF 3N4M E 21 44 PDB 3N4M 3N4M 21 44 SEQRES 1 A 209 VAL LEU GLY LYS PRO GLN THR ASP PRO THR LEU GLU TRP SEQRES 2 A 209 PHE LEU SER HIS CYS HIS ILE HIS LYS TYR PRO SER LYS SEQRES 3 A 209 SER THR LEU ILE HIS GLN GLY GLU LYS ALA GLU THR LEU SEQRES 4 A 209 TYR TYR ILE VAL LYS GLY SER VAL ALA VAL LEU ILE LYS SEQRES 5 A 209 ASP GLU GLU GLY LYS GLU MET ILE LEU SER TYR LEU ASN SEQRES 6 A 209 GLN GLY ASP PHE ILE GLY GLU LEU GLY LEU PHE GLU GLU SEQRES 7 A 209 GLY GLN GLU ARG SER ALA TRP VAL ARG ALA LYS THR ALA SEQRES 8 A 209 CYS GLU VAL ALA GLU ILE SER TYR LYS LYS PHE ARG GLN SEQRES 9 A 209 LEU ILE GLN VAL ASN PRO ASP ILE LEU MET ARG LEU SER SEQRES 10 A 209 ALA GLN MET ALA ARG ARG LEU GLN VAL THR SER GLU LYS SEQRES 11 A 209 VAL GLY ASN LEU ALA PHE LEU ASP VAL THR GLY ARG ILE SEQRES 12 A 209 ALA GLN THR LEU LEU ASN LEU ALA LYS GLN PRO ASP ALA SEQRES 13 A 209 MET THR HIS PRO ASP GLY MET GLN ILE LYS ILE THR ARG SEQRES 14 A 209 GLN GLU ILE GLY GLN ILE VAL GLY CYS SER ARG GLU THR SEQRES 15 A 209 VAL GLY ARG ILE LEU LYS MET LEU GLU ASP GLN ASN LEU SEQRES 16 A 209 ILE SER ALA HIS GLY LYS THR ILE VAL VAL TYR GLY THR SEQRES 17 A 209 ARG 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 D 20 DC DT DT DT DT DT DT DC DC DT DA DA DA SEQRES 2 D 20 DA DT DG DT DG DA DT SEQRES 1 E 24 DC DT DA DG DA DT DC DA DC DA DT DT DT SEQRES 2 E 24 DT DA DG DG DA DA DA DA DA DA DG HET CMP A 210 22 HET PEG A 501 7 HET PEG A 502 7 HET CMP D 100 11 HETNAM CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN CMP CYCLIC AMP; CAMP FORMUL 6 CMP 2(C10 H12 N5 O6 P) FORMUL 7 PEG 2(C4 H10 O3) FORMUL 10 HOH *35(H2 O) HELIX 1 1 ASP A 8 SER A 16 1 9 HELIX 2 2 GLU A 72 PHE A 76 5 5 HELIX 3 3 TYR A 99 GLN A 107 1 9 HELIX 4 4 PRO A 110 LEU A 137 1 28 HELIX 5 5 ASP A 138 ALA A 151 1 14 HELIX 6 6 THR A 168 GLY A 177 1 10 HELIX 7 7 SER A 179 GLN A 193 1 15 HELIX 8 8 PRO B 251 ARG B 255 5 5 HELIX 9 9 PRO B 256 GLU B 261 5 6 HELIX 10 10 THR B 263 LYS B 271 1 9 HELIX 11 11 TYR B 277 ARG B 284 1 8 HELIX 12 12 THR B 285 LYS B 291 1 7 HELIX 13 13 GLY B 296 SER B 309 1 14 HELIX 14 14 PRO C 251 ARG C 255 5 5 HELIX 15 15 PRO C 256 GLU C 261 5 6 HELIX 16 16 THR C 263 LYS C 271 1 9 HELIX 17 17 TYR C 277 ARG C 284 1 8 HELIX 18 18 THR C 285 LYS C 291 1 7 HELIX 19 19 GLY C 296 SER C 309 1 14 SHEET 1 A 4 HIS A 19 TYR A 23 0 SHEET 2 A 4 CYS A 92 SER A 98 -1 O CYS A 92 N TYR A 23 SHEET 3 A 4 THR A 38 LYS A 44 -1 N LEU A 39 O ILE A 97 SHEET 4 A 4 PHE A 69 ILE A 70 -1 O ILE A 70 N TYR A 40 SHEET 1 B 4 THR A 28 ILE A 30 0 SHEET 2 B 4 TRP A 85 ALA A 88 -1 O VAL A 86 N LEU A 29 SHEET 3 B 4 SER A 46 LYS A 52 -1 N ALA A 48 O ARG A 87 SHEET 4 B 4 GLU A 58 ASN A 65 -1 O SER A 62 N VAL A 49 SHEET 1 C 3 GLY A 162 LYS A 166 0 SHEET 2 C 3 THR A 202 TYR A 206 -1 O ILE A 203 N ILE A 165 SHEET 3 C 3 ILE A 196 HIS A 199 -1 N SER A 197 O VAL A 204 CISPEP 1 TRP B 321 PRO B 322 0 -0.81 CISPEP 2 TRP C 321 PRO C 322 0 -0.93 SITE 1 AC1 13 VAL A 49 LEU A 61 GLY A 71 GLU A 72 SITE 2 AC1 13 LEU A 73 GLY A 74 ARG A 82 SER A 83 SITE 3 AC1 13 ALA A 84 ARG A 123 LEU A 124 THR A 127 SITE 4 AC1 13 SER A 128 SITE 1 AC2 2 THR A 10 ASN A 109 SITE 1 AC3 1 ASP A 161 SITE 1 AC4 3 DT D 17 DC E 27 DA E 28 CRYST1 175.730 175.730 160.100 90.00 90.00 120.00 P 62 2 2 24 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 0.005691 0.003285 0.000000 0.00000 SCALE2 0.000000 0.006571 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006246 0.00000 MTRIX1 1 0.709049 -0.218932 -0.670312 117.99700 1 MTRIX2 1 -0.459989 0.576888 -0.674989 121.58100 1 MTRIX3 1 0.534472 0.786937 0.308335 68.51630 1