HEADER TRANSFERASE 21-NOV-05 2F3I TITLE SOLUTION STRUCTURE OF A SUBUNIT OF RNA POLYMERASE II CAVEAT 2F3I CHIRALITAY ERROR AT CA CENTER AT ILE A 4 IN MODEL 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-DIRECTED RNA POLYMERASES I, II, AND III 17.1 KDA COMPND 3 POLYPEPTIDE; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: RNA POLYMERASE II SUBUNIT, RPB17, RPB8, RPABC3; COMPND 6 EC: 2.7.7.6; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET24A KEYWDS RNA POLYMERASE II, TRANSFERASE EXPDTA SOLUTION NMR NUMMDL 21 MDLTYP MINIMIZED AVERAGE AUTHOR X.KANG,C.JIN REVDAT 4 09-MAR-22 2F3I 1 REMARK REVDAT 3 24-FEB-09 2F3I 1 VERSN REVDAT 2 26-SEP-06 2F3I 1 JRNL REVDAT 1 02-MAY-06 2F3I 0 JRNL AUTH X.KANG,Y.HU,Y.LI,X.GUO,X.JIANG,L.LAI,B.XIA,C.JIN JRNL TITL STRUCTURAL, BIOCHEMICAL, AND DYNAMIC CHARACTERIZATIONS OF JRNL TITL 2 THE HRPB8 SUBUNIT OF HUMAN RNA POLYMERASES JRNL REF J.BIOL.CHEM. V. 281 18216 2006 JRNL REFN ISSN 0021-9258 JRNL PMID 16632472 JRNL DOI 10.1074/JBC.M513241200 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.5, AMBER 7.0 REMARK 3 AUTHORS : BRUKER (XWINNMR), DAVID CASE (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2F3I COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-NOV-05. REMARK 100 THE DEPOSITION ID IS D_1000035406. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.3 REMARK 210 IONIC STRENGTH : 50MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5MM RNA POLYMERASE II SUBUNIT REMARK 210 U-15N,13C REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; 2D_15N-EDITED_ REMARK 210 HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.1, NMRVIEW 5, CYANA REMARK 210 1.0.6 REMARK 210 METHOD USED : SIMULATED ANNEALING MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 21 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 3D REMARK 210 HETERONUCLEAR TECHNIQUES. 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 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 1 ARG A 27 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 15 ARG A 57 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 18 ARG A 27 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 19 TYR A 118 CB - CG - CD2 ANGL. DEV. = -3.8 DEGREES REMARK 500 20 ARG A 27 NE - CZ - NH2 ANGL. DEV. = -3.5 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 ILE A 4 -157.19 67.46 REMARK 500 1 LEU A 5 15.59 -149.33 REMARK 500 1 PRO A 17 30.88 -67.48 REMARK 500 1 PHE A 35 -134.08 -126.01 REMARK 500 1 LYS A 36 13.54 -143.61 REMARK 500 1 VAL A 50 -143.77 -152.67 REMARK 500 1 THR A 63 -89.67 -94.47 REMARK 500 1 LEU A 64 -37.87 -153.45 REMARK 500 1 ASP A 67 -78.51 -120.20 REMARK 500 1 LEU A 70 -42.54 -132.69 REMARK 500 1 GLU A 74 -143.87 -95.72 REMARK 500 1 TYR A 75 -7.42 62.84 REMARK 500 1 PRO A 77 -157.43 -87.29 REMARK 500 1 THR A 78 1.62 -30.54 REMARK 500 1 ASP A 80 -142.59 -143.89 REMARK 500 1 ARG A 81 -109.42 53.19 REMARK 500 1 ALA A 85 80.01 -55.88 REMARK 500 1 ASP A 86 -41.80 -154.69 REMARK 500 1 PHE A 88 73.22 -167.39 REMARK 500 1 GLU A 89 -33.23 -39.03 REMARK 500 1 GLU A 103 15.25 -143.43 REMARK 500 1 SER A 105 -36.58 117.77 REMARK 500 1 THR A 106 -29.55 -151.10 REMARK 500 1 ALA A 109 103.05 -1.28 REMARK 500 2 ARG A 24 2.17 -68.64 REMARK 500 2 PHE A 35 -102.16 -124.20 REMARK 500 2 LYS A 36 10.80 -168.19 REMARK 500 2 ASN A 44 90.71 -68.48 REMARK 500 2 ILE A 45 3.88 -69.65 REMARK 500 2 SER A 62 51.85 -145.05 REMARK 500 2 THR A 63 105.29 -43.87 REMARK 500 2 GLU A 74 40.96 -80.60 REMARK 500 2 PRO A 82 58.07 23.36 REMARK 500 2 SER A 83 22.49 -65.77 REMARK 500 2 ASP A 86 -32.55 -159.45 REMARK 500 2 TYR A 97 58.59 -143.34 REMARK 500 2 ASP A 102 -97.77 -147.49 REMARK 500 2 GLU A 103 74.60 -167.85 REMARK 500 2 THR A 104 -159.79 -150.15 REMARK 500 2 THR A 106 38.41 109.77 REMARK 500 3 LYS A 20 25.97 -73.03 REMARK 500 3 LYS A 21 -59.84 68.02 REMARK 500 3 ASP A 54 -64.06 -141.77 REMARK 500 3 ALA A 61 175.43 57.55 REMARK 500 3 THR A 63 -179.18 62.66 REMARK 500 3 ASP A 80 -49.05 -152.25 REMARK 500 3 ALA A 85 24.11 -75.05 REMARK 500 3 ASP A 86 35.26 -82.32 REMARK 500 3 PHE A 88 38.27 -75.35 REMARK 500 3 SER A 105 -15.41 121.46 REMARK 500 REMARK 500 THIS ENTRY HAS 332 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 ASP A 51 LEU A 52 1 -147.93 REMARK 500 THR A 63 LEU A 64 1 110.77 REMARK 500 LEU A 64 TYR A 65 1 -71.99 REMARK 500 GLU A 66 ASP A 67 1 -149.15 REMARK 500 ARG A 84 ALA A 85 1 131.84 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 1 TYR A 65 0.09 SIDE CHAIN REMARK 500 1 TYR A 75 0.08 SIDE CHAIN REMARK 500 1 ARG A 98 0.12 SIDE CHAIN REMARK 500 5 TYR A 118 0.07 SIDE CHAIN REMARK 500 7 TYR A 65 0.07 SIDE CHAIN REMARK 500 10 ARG A 140 0.11 SIDE CHAIN REMARK 500 13 ARG A 124 0.10 SIDE CHAIN REMARK 500 16 ARG A 140 0.10 SIDE CHAIN REMARK 500 19 ARG A 98 0.11 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 2F3I A 1 150 UNP P52434 RPB8_HUMAN 1 150 SEQRES 1 A 150 MET ALA GLY ILE LEU PHE GLU ASP ILE PHE ASP VAL LYS SEQRES 2 A 150 ASP ILE ASP PRO GLU GLY LYS LYS PHE ASP ARG VAL SER SEQRES 3 A 150 ARG LEU HIS CYS GLU SER GLU SER PHE LYS MET ASP LEU SEQRES 4 A 150 ILE LEU ASP VAL ASN ILE GLN ILE TYR PRO VAL ASP LEU SEQRES 5 A 150 GLY ASP LYS PHE ARG LEU VAL ILE ALA SER THR LEU TYR SEQRES 6 A 150 GLU ASP GLY THR LEU ASP ASP GLY GLU TYR ASN PRO THR SEQRES 7 A 150 ASP ASP ARG PRO SER ARG ALA ASP GLN PHE GLU TYR VAL SEQRES 8 A 150 MET TYR GLY LYS VAL TYR ARG ILE GLU GLY ASP GLU THR SEQRES 9 A 150 SER THR GLU ALA ALA THR ARG LEU SER ALA TYR VAL SER SEQRES 10 A 150 TYR GLY GLY LEU LEU MET ARG LEU GLN GLY ASP ALA ASN SEQRES 11 A 150 ASN LEU HIS GLY PHE GLU VAL ASP SER ARG VAL TYR LEU SEQRES 12 A 150 LEU MET LYS LYS LEU ALA PHE HELIX 1 1 ASP A 128 HIS A 133 1 6 SHEET 1 A 9 TYR A 90 MET A 92 0 SHEET 2 A 9 LEU A 143 LYS A 147 -1 O MET A 145 N TYR A 90 SHEET 3 A 9 PHE A 56 VAL A 59 -1 N ARG A 57 O LYS A 146 SHEET 4 A 9 GLU A 7 ASP A 16 -1 N ASP A 8 O LEU A 58 SHEET 5 A 9 VAL A 25 SER A 32 -1 O HIS A 29 N LYS A 13 SHEET 6 A 9 ASP A 38 ASN A 44 -1 O LEU A 39 N CYS A 30 SHEET 7 A 9 LEU A 121 GLY A 127 -1 O LEU A 122 N ASP A 42 SHEET 8 A 9 LEU A 112 TYR A 118 -1 N ALA A 114 O LEU A 125 SHEET 9 A 9 GLY A 94 TYR A 97 -1 N LYS A 95 O SER A 117 CISPEP 1 ILE A 4 LEU A 5 1 19.61 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