HEADER GENE REGULATION/DNA 13-JUL-15 5CIZ TITLE E. COLI RNA POLYMERASE ALPHA SUBUNIT CTD IN COMPLEX WITH CAP AND DNA: TITLE 2 A(5)-TRACT BINDING SITE FOR ALPHA CTD COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAMP-ACTIVATED GLOBAL TRANSCRIPTIONAL REGULATOR CRP; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CATABOLITE ACTIVATOR PROTEIN,CAP,CATABOLITE GENE ACTIVATOR, COMPND 5 CAMP RECEPTOR PROTEIN,CRP,CAMP REGULATORY PROTEIN; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA-DIRECTED RNA POLYMERASE SUBUNIT ALPHA; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: RNAP SUBUNIT ALPHA,RNA POLYMERASE SUBUNIT ALPHA, COMPND 11 TRANSCRIPTASE 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*GP*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*CP*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 (STRAIN K12); SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: CRP, CAP, CSM, B3357, JW5702; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI (STRAIN K12); SOURCE 10 ORGANISM_TAXID: 83333; SOURCE 11 STRAIN: K12; SOURCE 12 GENE: RPOA, PEZ, PHS, SEZ, B3295, JW3257; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 14 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 18 ORGANISM_TAXID: 562; SOURCE 19 MOL_ID: 4; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 22 ORGANISM_TAXID: 562 KEYWDS PROTEIN-PROTEIN INTERACTIONS, PROTEIN-DNA INTERACTIONS, GENE KEYWDS 2 REGULATION-DNA COMPLEX, KNOCK OUT EXPDTA X-RAY DIFFRACTION AUTHOR A.A.NAPOLI,C.L.LAWSON REVDAT 4 25-NOV-20 5CIZ 1 JRNL REVDAT 3 25-DEC-19 5CIZ 1 REMARK REVDAT 2 06-SEP-17 5CIZ 1 REMARK REVDAT 1 29-JUN-16 5CIZ 0 JRNL AUTH S.LARA-GONZALEZ,A.C.D.MACHADO,S.RAO,A.A.NAPOLI,J.BIRKTOFT, JRNL AUTH 2 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 2020 JRNL REFN ISSN 0006-2960 JRNL DOI 10.1021/ACS.BIOCHEM.0C00571 REMARK 2 REMARK 2 RESOLUTION. 5.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) 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) : 5.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 6615 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.020 REMARK 3 FREE R VALUE TEST SET COUNT : 663 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 49.9294 - 8.5552 0.98 1268 143 0.1620 0.1962 REMARK 3 2 8.5552 - 6.7959 1.00 1190 132 0.1795 0.1855 REMARK 3 3 6.7959 - 5.9385 1.00 1173 131 0.1782 0.2439 REMARK 3 4 5.9385 - 5.3962 1.00 1176 130 0.2103 0.2447 REMARK 3 5 5.3962 - 5.0098 0.99 1145 127 0.2312 0.3152 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.600 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.940 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 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 : 0.013 3243 REMARK 3 ANGLE : 1.660 4573 REMARK 3 CHIRALITY : 0.074 526 REMARK 3 PLANARITY : 0.008 425 REMARK 3 DIHEDRAL : 23.092 1286 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): 108.1332 -53.8316 148.3464 REMARK 3 T TENSOR REMARK 3 T11: 2.3502 T22: 2.0826 REMARK 3 T33: 2.0273 T12: 0.0920 REMARK 3 T13: -0.0495 T23: -0.0298 REMARK 3 L TENSOR REMARK 3 L11: 4.2900 L22: 1.9922 REMARK 3 L33: 2.7134 L12: 0.2151 REMARK 3 L13: -0.7910 L23: -0.1293 REMARK 3 S TENSOR REMARK 3 S11: 0.0012 S12: 0.0454 S13: 0.5036 REMARK 3 S21: 0.1287 S22: -0.0102 S23: -0.3672 REMARK 3 S31: -0.0082 S32: 0.4145 S33: 0.0143 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5CIZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000211725. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-FEB-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : NULL 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) : 1.10 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6646 REMARK 200 RESOLUTION RANGE HIGH (A) : 5.010 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 18.70 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 5.01 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 5.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 19.20 REMARK 200 R MERGE FOR SHELL (I) : 0.73300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 1LB2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL 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 298K 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 105.66200 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 52.83100 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 105.66200 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 52.83100 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 105.66200 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 52.83100 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 105.66200 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 52.83100 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: OCTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 13570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 40150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -94.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 176.31200 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 316.98600 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 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 470 ARG A 122 CG CD NE CZ NH1 NH2 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 OG SER B 266 OE1 GLU B 302 2.12 REMARK 500 ND2 ASN B 268 OP1 DG E 44 2.15 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 DC D 8 O3' DC D 8 C3' -0.041 REMARK 500 DT D 10 O3' DT D 10 C3' -0.042 REMARK 500 DA D 12 O3' DA D 12 C3' -0.036 REMARK 500 DT D 17 O3' DT D 17 C3' -0.063 REMARK 500 DT E 22 O3' DT E 22 C3' -0.057 REMARK 500 DA E 23 O3' DA E 23 C3' -0.071 REMARK 500 DC E 29 O3' DC E 29 C3' -0.037 REMARK 500 DA E 40 O3' DA E 40 C3' -0.038 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 PRO A 9 C - N - CA ANGL. DEV. = 12.3 DEGREES REMARK 500 PRO B 322 C - N - CA ANGL. DEV. = 15.7 DEGREES REMARK 500 DA D 13 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG D 18 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DT E 31 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG E 36 O4' - C1' - N9 ANGL. DEV. = 3.4 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 -0.65 -140.28 REMARK 500 ASN A 109 93.82 -160.76 REMARK 500 ASN A 194 48.22 38.58 REMARK 500 GLU B 261 70.30 52.16 REMARK 500 ALA B 274 34.11 71.80 REMARK 500 ASN B 320 72.34 57.76 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 CMP A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3N4M RELATED DB: PDB REMARK 900 THE REFERENCE MODEL USED IN THE LOW-RESOLUTION REFINEMENT OF THIS " REMARK 900 KNOCK-OUT" VARIANT. DBREF 5CIZ A 1 209 UNP P0ACJ8 CRP_ECOLI 2 210 DBREF 5CIZ B 246 329 UNP P0A7Z4 RPOA_ECOLI 246 329 DBREF 5CIZ D 1 20 PDB 5CIZ 5CIZ 1 20 DBREF 5CIZ E 21 44 PDB 5CIZ 5CIZ 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 D 20 DC DT DT DT DT DT DG 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 DC DA DA DA DA DA DG HET CMP A 301 22 HETNAM CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE HETSYN CMP CYCLIC AMP; CAMP FORMUL 5 CMP C10 H12 N5 O6 P HELIX 1 AA1 ASP A 8 SER A 16 1 9 HELIX 2 AA2 GLU A 72 PHE A 76 5 5 HELIX 3 AA3 TYR A 99 GLN A 107 1 9 HELIX 4 AA4 ASN A 109 LEU A 137 1 29 HELIX 5 AA5 ASP A 138 LEU A 150 1 13 HELIX 6 AA6 THR A 168 GLY A 177 1 10 HELIX 7 AA7 SER A 179 GLN A 193 1 15 HELIX 8 AA8 PRO B 251 ARG B 255 5 5 HELIX 9 AA9 PRO B 256 GLU B 261 5 6 HELIX 10 AB1 THR B 263 LYS B 271 1 9 HELIX 11 AB2 TYR B 277 ARG B 284 1 8 HELIX 12 AB3 THR B 285 THR B 292 1 8 HELIX 13 AB4 GLY B 296 SER B 309 1 14 SHEET 1 AA1 4 HIS A 19 TYR A 23 0 SHEET 2 AA1 4 CYS A 92 SER A 98 -1 O CYS A 92 N TYR A 23 SHEET 3 AA1 4 THR A 38 LYS A 44 -1 N LEU A 39 O ILE A 97 SHEET 4 AA1 4 PHE A 69 ILE A 70 -1 O ILE A 70 N TYR A 40 SHEET 1 AA2 4 THR A 28 ILE A 30 0 SHEET 2 AA2 4 TRP A 85 ALA A 88 -1 O VAL A 86 N ILE A 30 SHEET 3 AA2 4 SER A 46 LYS A 52 -1 N ALA A 48 O ARG A 87 SHEET 4 AA2 4 GLU A 58 ASN A 65 -1 O LEU A 61 N VAL A 49 SHEET 1 AA3 4 MET A 157 THR A 158 0 SHEET 2 AA3 4 GLY A 162 LYS A 166 -1 O GLN A 164 N MET A 157 SHEET 3 AA3 4 THR A 202 TYR A 206 -1 O ILE A 203 N ILE A 165 SHEET 4 AA3 4 ILE A 196 HIS A 199 -1 N SER A 197 O VAL A 204 CISPEP 1 TRP B 321 PRO B 322 0 -4.13 SITE 1 AC1 12 VAL A 49 LEU A 61 ILE A 70 GLY A 71 SITE 2 AC1 12 GLU A 72 LEU A 73 ARG A 82 SER A 83 SITE 3 AC1 12 ALA A 84 VAL A 86 THR A 127 SER A 128 CRYST1 176.312 176.312 158.493 90.00 90.00 120.00 P 62 2 2 12 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 0.005672 0.003275 0.000000 0.00000 SCALE2 0.000000 0.006549 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006309 0.00000 MASTER 372 0 1 13 12 0 3 6 0 0 0 28 END