HEADER TRANSFERASE 21-JUL-13 2MAX TITLE NMR STRUCTURE OF THE RNA POLYMERASE ALPHA SUBUNIT C-TERMINAL DOMAIN TITLE 2 FROM HELICOBACTER PYLORI COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-DIRECTED RNA POLYMERASE SUBUNIT ALPHA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RNA POLYMERASE ALPHA SUBUNIT C-TERMINAL DOMAIN; COMPND 5 SYNONYM: RNAP SUBUNIT ALPHA, RNA POLYMERASE SUBUNIT ALPHA, COMPND 6 TRANSCRIPTASE SUBUNIT ALPHA; COMPND 7 EC: 2.7.7.6; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 3 ORGANISM_TAXID: 85963; SOURCE 4 STRAIN: J99; SOURCE 5 GENE: JHP_1213, RPOA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PETBNK KEYWDS RNA POLYMERASE ALPHA SUBUNIT, HP1293, JHP1213, RPOA, DNA-DIRECTED RNA KEYWDS 2 POLYMERASE, NUCLEOTIDYLTRANSFERASE, TRANSCRIPTION, TRANSFERASE EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR B.N.BORIN,A.M.KREZEL REVDAT 2 09-APR-14 2MAX 1 JRNL REVDAT 1 12-MAR-14 2MAX 0 JRNL AUTH B.N.BORIN,W.TANG,A.M.KREZEL JRNL TITL HELICOBACTER PYLORI RNA POLYMERASE ALPHA-SUBUNIT C-TERMINAL JRNL TITL 2 DOMAIN SHOWS FEATURES UNIQUE TO -PROTEOBACTERIA AND BINDS JRNL TITL 3 NIKR/DNA COMPLEXES. JRNL REF PROTEIN SCI. V. 23 454 2014 JRNL REFN ISSN 0961-8368 JRNL PMID 24442709 JRNL DOI 10.1002/PRO.2427 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER, CYANA REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN (AMBER), GUNTERT, REMARK 3 MUMENTHALER AND WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MAX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUL-13. REMARK 100 THE RCSB ID CODE IS RCSB103424. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.3 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-15N] RNAP ALPHA SUBUNIT REMARK 210 CTD, 25 MM POTASSIUM PHOSPHATE, REMARK 210 225 MM POTASSIUM CHLORIDE, 1 MM REMARK 210 TCEP, 90% H2O/10% D2O; 1 MM [U- REMARK 210 13C; U-15N] RNAP ALPHA SUBUNIT REMARK 210 CTD, 25 MM POTASSIUM PHOSPHATE, REMARK 210 225 MM POTASSIUM CHLORIDE, 1 MM REMARK 210 TCEP, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D CBCANH; 3D REMARK 210 C(CO)NH; 3D H(CCO)NH; 3D HCCH REMARK 210 TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, SPARKY, CYANA, TALOS, REMARK 210 PROCHECKNMR REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: A 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-15 REMARK 465 RES C SSSEQI REMARK 465 MET A 219 REMARK 465 ARG A 220 REMARK 465 GLY A 221 REMARK 465 SER A 222 REMARK 465 HIS A 223 REMARK 465 HIS A 224 REMARK 465 HIS A 225 REMARK 465 HIS A 226 REMARK 465 HIS A 227 REMARK 465 HIS A 228 REMARK 465 GLY A 229 REMARK 465 SER A 230 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 6 ARG A 327 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 8 ARG A 269 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 10 ARG A 327 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 11 ARG A 237 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 11 VAL A 296 CA - CB - CG2 ANGL. DEV. = 9.1 DEGREES REMARK 500 14 ARG A 327 NE - CZ - NH1 ANGL. DEV. = 3.7 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 1 MET A 288 76.51 -69.13 REMARK 500 1 THR A 320 78.76 -67.58 REMARK 500 1 GLU A 321 67.80 -119.04 REMARK 500 1 SER A 323 66.51 -156.22 REMARK 500 1 LYS A 340 -45.76 -149.26 REMARK 500 2 ALA A 254 0.17 -69.21 REMARK 500 2 MET A 288 77.46 -66.46 REMARK 500 2 SER A 289 154.52 -49.09 REMARK 500 2 LYS A 294 8.38 -68.34 REMARK 500 2 SER A 323 68.59 -175.87 REMARK 500 3 ASN A 241 32.18 -141.91 REMARK 500 3 GLU A 262 3.39 -68.82 REMARK 500 3 MET A 288 77.12 -63.83 REMARK 500 3 SER A 289 150.80 -49.87 REMARK 500 3 VAL A 296 170.97 -58.96 REMARK 500 3 ASN A 298 34.70 -142.45 REMARK 500 3 GLU A 321 31.24 -151.05 REMARK 500 3 SER A 323 39.98 -168.69 REMARK 500 3 PRO A 324 29.38 -78.24 REMARK 500 4 MET A 288 79.65 -65.87 REMARK 500 4 SER A 323 65.70 -172.33 REMARK 500 5 ASN A 241 -32.64 -150.12 REMARK 500 5 GLN A 250 -68.08 -126.99 REMARK 500 5 SER A 258 0.70 -68.09 REMARK 500 5 MET A 288 73.92 -65.21 REMARK 500 5 VAL A 296 173.53 -56.21 REMARK 500 5 SER A 323 51.34 -173.93 REMARK 500 5 PRO A 324 38.24 -77.60 REMARK 500 6 GLU A 243 -12.76 -143.13 REMARK 500 6 MET A 288 80.46 -65.83 REMARK 500 6 ASN A 298 41.26 -145.28 REMARK 500 6 SER A 323 68.50 -175.04 REMARK 500 7 GLN A 250 89.22 -34.28 REMARK 500 7 MET A 288 76.89 -66.87 REMARK 500 7 SER A 289 150.86 -47.11 REMARK 500 7 ASN A 298 45.67 -140.33 REMARK 500 7 GLU A 321 51.92 -152.50 REMARK 500 7 SER A 323 60.10 -164.83 REMARK 500 7 PRO A 324 38.77 -83.01 REMARK 500 8 GLU A 262 -9.24 -56.74 REMARK 500 8 MET A 288 81.75 -68.80 REMARK 500 8 GLU A 321 24.14 -140.01 REMARK 500 8 SER A 323 55.87 -158.34 REMARK 500 8 ASN A 343 13.21 -146.48 REMARK 500 9 ASP A 252 2.99 -67.23 REMARK 500 9 ASN A 265 36.69 -75.70 REMARK 500 9 MET A 288 78.50 -61.24 REMARK 500 9 SER A 289 150.10 -47.10 REMARK 500 9 LEU A 322 -67.46 -131.66 REMARK 500 9 SER A 323 55.40 -154.98 REMARK 500 REMARK 500 THIS ENTRY HAS 80 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA A 249 GLN A 250 7 -149.26 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 2 TYR A 304 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19380 RELATED DB: BMRB DBREF 2MAX A 231 344 UNP Q9ZJT5 RPOA_HELPJ 231 344 SEQADV 2MAX MET A 219 UNP Q9ZJT5 EXPRESSION TAG SEQADV 2MAX ARG A 220 UNP Q9ZJT5 EXPRESSION TAG SEQADV 2MAX GLY A 221 UNP Q9ZJT5 EXPRESSION TAG SEQADV 2MAX SER A 222 UNP Q9ZJT5 EXPRESSION TAG SEQADV 2MAX HIS A 223 UNP Q9ZJT5 EXPRESSION TAG SEQADV 2MAX HIS A 224 UNP Q9ZJT5 EXPRESSION TAG SEQADV 2MAX HIS A 225 UNP Q9ZJT5 EXPRESSION TAG SEQADV 2MAX HIS A 226 UNP Q9ZJT5 EXPRESSION TAG SEQADV 2MAX HIS A 227 UNP Q9ZJT5 EXPRESSION TAG SEQADV 2MAX HIS A 228 UNP Q9ZJT5 EXPRESSION TAG SEQADV 2MAX GLY A 229 UNP Q9ZJT5 EXPRESSION TAG SEQADV 2MAX SER A 230 UNP Q9ZJT5 EXPRESSION TAG SEQRES 1 A 126 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER LEU SEQRES 2 A 126 GLY VAL PHE GLY GLU ARG PRO ILE ALA ASN THR GLU TYR SEQRES 3 A 126 SER GLY ASP TYR ALA GLN ARG ASP ASP ALA LYS ASP LEU SEQRES 4 A 126 SER ALA LYS ILE GLU SER MET ASN LEU SER ALA ARG CYS SEQRES 5 A 126 PHE ASN CYS LEU ASP LYS ILE GLY ILE LYS TYR VAL GLY SEQRES 6 A 126 GLU LEU VAL LEU MET SER GLU GLU GLU LEU LYS GLY VAL SEQRES 7 A 126 LYS ASN MET GLY LYS LYS SER TYR ASP GLU ILE ALA GLU SEQRES 8 A 126 LYS LEU ASN ASP LEU GLY TYR PRO VAL GLY THR GLU LEU SEQRES 9 A 126 SER PRO GLU GLN ARG GLU SER LEU LYS LYS ARG LEU GLU SEQRES 10 A 126 LYS LEU GLU ASP LYS GLY GLY ASN ASP HELIX 1 1 ARG A 251 ALA A 259 5 9 HELIX 2 2 LYS A 260 ASN A 265 5 6 HELIX 3 3 SER A 267 GLY A 278 1 12 HELIX 4 4 TYR A 281 MET A 288 1 8 HELIX 5 5 SER A 289 LYS A 294 1 6 HELIX 6 6 GLY A 300 LEU A 314 1 15 HELIX 7 7 GLN A 326 GLU A 335 1 10 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1