1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Motackova, V. Sanderova, H. Zidek, L. Novacek, J. Padrta, P. Svenkova, A. Jonak, J. Krasny, L. Sklenar, V. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking US Proteins PSFGEY 0867 0887-3585 78 1807 1810 10.1002/prot.22708 20310067 Solution structure of the N-terminal domain of Bacillus subtilis delta subunit of RNA polymerase and its classification based on structural homologs 2010 10.2210/pdb2krc/pdb pdb_00002krc 11769.083 DNA-directed RNA polymerase subunit delta residues 2-92 1 man polymer N delta, RNAP delta factor no no GIKQYSQEELKEMALVEIAHELFEEHKKPVPFQELLNEIASLLGVKKEELGDRIAQFYTDLNIDGRFLALSDQTWGLRSW YPYDQLDEETQLEHHHHHH GIKQYSQEELKEMALVEIAHELFEEHKKPVPFQELLNEIASLLGVKKEELGDRIAQFYTDLNIDGRFLALSDQTWGLRSW YPYDQLDEETQLEHHHHHH A polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n sample 1423 Bacillus subtilis 469008 Escherichia coli BL21(DE3) pET22b vector database_2 pdbx_nmr_software pdbx_nmr_spectrometer pdbx_struct_assembly pdbx_struct_oper_list struct_ref_seq_dif repository Initial release Version format compliance Data collection Database references Derived calculations 1 0 2010-04-07 1 1 2011-07-13 1 2 2022-03-16 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _pdbx_nmr_spectrometer.model _struct_ref_seq_dif.details BMRB Y PDBJ 2009-12-16 REL REL 2341 734 544 564 499 0 0 66 66 structures with the lowest energy 100 10 1 2D 1H-15N HSQC 2D 1H-13C HMQC 3D CBCA(CO)NH 3D HNCACB 3D HNCA 3D HN(CO)CA 3D HNCO 3D HNHA 3D HCCH-TOCSY 3D 1H-15N NOESY 3D 1H-13C NOESY (HB)CB(CGCD)HD 2D 1H-15N IPAP 2D HN[C]-S3E 2D (H)CACO-IPAP 2D 13C-coupled 1H-13C HSQC 2D 1H-15N IPAP 2D HN[C]-S3E 2D (H)CACO-IPAP 2D 13C-coupled 1H-13C HSQC 2D 13C-detected CON 2D 13C-detected CON 2D 1H-15N IPAP 2D HN[C]-S3E 2D (H)CACO-IPAP 2D 13C-coupled 1H-13C HSQC 10 mM 50 uM 20 mM 10 mM 50 uM 20 mM 14.29 mg/mL 10 mM 50 uM 20 mM 5 % 10 6.6 1 atm 301 K molecular dynamics, simulated annealing 1 lowest energy 10 mM sodium chloride-1, 50 uM sodium azide-2, 20 mM phosphate buffer-3, 90% H2O/10% D2O 90% H2O/10% D2O 10 mM sodium chloride-4, 50 uM sodium azide-5, 20 mM phosphate buffer-6, 14.29 mg/mL filamentous Pf1 bacteriophage-7, 90% H2O/10% D2O 90% H2O/10% D2O 10 mM sodium chloride-8, 50 uM sodium azide-9, 20 mM phosphate buffer-10, 5 % polyacrylamide gel-11, 90% H2O/10% D2O 90% H2O/10% D2O Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax processing NMRPipe 3.0 Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax processing NMRDraw 3.0 Goddard chemical shift assignment Sparky 3.111 Goddard peak picking Sparky 3.111 Linge, O'Donoghue and Nilges noe assignment ARIA 2.1 Brunger, Adams, Clore, Gros, Nilges and Read structure solution CNS 1.2 Brunger, Adams, Clore, Gros, Nilges and Read refinement CNS 1.2 Brunger refinement X-PLOR Petr Novak dipolar coupling determination S3EPY Petr Novak peak picking S3EPY 600 Bruker AVANCE Bruker Avance GLY 2 n 1 GLY 2 A ILE 3 n 2 ILE 3 A LYS 4 n 3 LYS 4 A GLN 5 n 4 GLN 5 A TYR 6 n 5 TYR 6 A SER 7 n 6 SER 7 A GLN 8 n 7 GLN 8 A GLU 9 n 8 GLU 9 A GLU 10 n 9 GLU 10 A LEU 11 n 10 LEU 11 A LYS 12 n 11 LYS 12 A GLU 13 n 12 GLU 13 A MET 14 n 13 MET 14 A ALA 15 n 14 ALA 15 A LEU 16 n 15 LEU 16 A VAL 17 n 16 VAL 17 A GLU 18 n 17 GLU 18 A ILE 19 n 18 ILE 19 A ALA 20 n 19 ALA 20 A HIS 21 n 20 HIS 21 A GLU 22 n 21 GLU 22 A LEU 23 n 22 LEU 23 A PHE 24 n 23 PHE 24 A GLU 25 n 24 GLU 25 A GLU 26 n 25 GLU 26 A HIS 27 n 26 HIS 27 A LYS 28 n 27 LYS 28 A LYS 29 n 28 LYS 29 A PRO 30 n 29 PRO 30 A VAL 31 n 30 VAL 31 A PRO 32 n 31 PRO 32 A PHE 33 n 32 PHE 33 A GLN 34 n 33 GLN 34 A GLU 35 n 34 GLU 35 A LEU 36 n 35 LEU 36 A LEU 37 n 36 LEU 37 A ASN 38 n 37 ASN 38 A GLU 39 n 38 GLU 39 A ILE 40 n 39 ILE 40 A ALA 41 n 40 ALA 41 A SER 42 n 41 SER 42 A LEU 43 n 42 LEU 43 A LEU 44 n 43 LEU 44 A GLY 45 n 44 GLY 45 A VAL 46 n 45 VAL 46 A LYS 47 n 46 LYS 47 A LYS 48 n 47 LYS 48 A GLU 49 n 48 GLU 49 A GLU 50 n 49 GLU 50 A LEU 51 n 50 LEU 51 A GLY 52 n 51 GLY 52 A ASP 53 n 52 ASP 53 A ARG 54 n 53 ARG 54 A ILE 55 n 54 ILE 55 A ALA 56 n 55 ALA 56 A GLN 57 n 56 GLN 57 A PHE 58 n 57 PHE 58 A TYR 59 n 58 TYR 59 A THR 60 n 59 THR 60 A ASP 61 n 60 ASP 61 A LEU 62 n 61 LEU 62 A ASN 63 n 62 ASN 63 A ILE 64 n 63 ILE 64 A ASP 65 n 64 ASP 65 A GLY 66 n 65 GLY 66 A ARG 67 n 66 ARG 67 A PHE 68 n 67 PHE 68 A LEU 69 n 68 LEU 69 A ALA 70 n 69 ALA 70 A LEU 71 n 70 LEU 71 A SER 72 n 71 SER 72 A ASP 73 n 72 ASP 73 A GLN 74 n 73 GLN 74 A THR 75 n 74 THR 75 A TRP 76 n 75 TRP 76 A GLY 77 n 76 GLY 77 A LEU 78 n 77 LEU 78 A ARG 79 n 78 ARG 79 A SER 80 n 79 SER 80 A TRP 81 n 80 TRP 81 A TYR 82 n 81 TYR 82 A PRO 83 n 82 PRO 83 A TYR 84 n 83 TYR 84 A ASP 85 n 84 ASP 85 A GLN 86 n 85 GLN 86 A LEU 87 n 86 LEU 87 A ASP 88 n 87 ASP 88 A GLU 89 n 88 GLU 89 A GLU 90 n 89 GLU 90 A THR 91 n 90 THR 91 A GLN 92 n 91 GLN 92 A LEU 93 n 92 LEU 93 A GLU 94 n 93 GLU 94 A HIS 95 n 94 HIS 95 A HIS 96 n 95 HIS 96 A HIS 97 n 96 HIS 97 A HIS 98 n 97 HIS 98 A HIS 99 n 98 HIS 99 A HIS 100 n 99 HIS 100 A author_defined_assembly 1 monomeric 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 A N VAL 31 A N VAL 30 A O TRP 76 A O TRP 75 A O GLY 77 A O GLY 76 A N LEU 69 A N LEU 68 9 A CA GLN 92 PLANAR 1 A A HH21 OE1 ARG GLU 67 94 1.58 1 A A HD1 OE1 HIS GLU 21 22 1.59 2 A A OE1 HD1 GLU HIS 25 95 1.57 2 A A OE2 HZ1 GLU LYS 25 28 1.57 2 A A HZ1 OE2 LYS GLU 12 13 1.59 3 A A OE1 HZ3 GLU LYS 25 28 1.57 3 A A HE2 OE1 HIS GLU 21 89 1.58 3 A A HG OE2 SER GLU 80 89 1.59 3 A A HE2 OE1 HIS GLU 27 39 1.59 4 A A HE2 OE2 HIS GLU 27 39 1.59 4 A A HZ2 OE1 LYS GLU 47 50 1.59 7 A A HZ2 OE1 LYS GLU 4 25 1.58 7 A A HE2 OE1 HIS GLU 27 39 1.59 8 A A HD1 OE2 HIS GLU 21 22 1.56 8 A A OD2 HD1 ASP HIS 85 98 1.58 8 A A HZ3 OE2 LYS GLU 48 49 1.59 9 A A HZ1 OE1 LYS GLU 4 25 1.58 10 A A H1 OE1 GLY GLU 2 90 1.60 2 A ARG 79 0.092 SIDE CHAIN 4 A ARG 67 0.108 SIDE CHAIN 1 A ILE 3 63.72 -96.28 1 A GLN 5 -161.20 21.65 1 A PHE 68 62.35 146.27 1 A LEU 71 -78.06 -84.40 1 A SER 72 -90.80 -61.32 1 A ASP 73 -162.03 -61.57 1 A TYR 84 177.82 -70.27 1 A ASP 85 -147.19 10.75 1 A GLN 86 -173.48 117.66 1 A LEU 93 61.38 89.24 1 A GLU 94 49.77 105.16 1 A HIS 97 52.45 74.17 1 A HIS 99 -156.94 -55.89 2 A LYS 4 -68.03 1.73 2 A LEU 71 -76.45 -83.24 2 A ASP 73 -153.35 -52.68 2 A ARG 79 -63.80 0.16 2 A GLU 90 -75.90 21.70 2 A GLN 92 -126.25 -64.63 2 A LEU 93 -144.14 -153.11 2 A HIS 97 70.40 -70.93 2 A HIS 98 -162.26 42.26 2 A HIS 99 78.91 -48.00 3 A ARG 67 -101.18 -157.03 3 A PHE 68 48.80 107.90 3 A LEU 71 -98.53 -90.12 3 A SER 72 -91.38 -61.52 3 A GLN 74 68.87 -12.03 3 A TYR 84 175.70 77.35 3 A ASP 85 64.60 -63.36 3 A GLN 86 -91.09 -70.23 3 A LEU 87 71.29 98.40 3 A ASP 88 76.12 80.42 3 A LEU 93 82.17 83.20 3 A GLU 94 59.52 131.24 3 A HIS 97 67.00 -81.00 3 A HIS 98 163.73 -178.04 4 A LYS 4 -65.39 15.36 4 A LEU 71 -76.75 -91.05 4 A SER 72 -92.40 -60.34 4 A ASP 73 -157.44 -37.85 4 A TYR 84 -179.40 84.42 4 A ASP 85 70.81 -40.70 4 A GLN 92 -126.06 -62.91 4 A LEU 93 -167.94 -145.30 4 A GLU 94 -68.37 69.16 4 A HIS 97 56.01 -82.17 5 A ILE 3 -135.80 -82.75 5 A GLN 5 -158.80 20.16 5 A LEU 71 -78.93 -80.93 5 A ASP 73 -164.78 -40.45 5 A ARG 79 -75.17 21.52 5 A TYR 84 -169.36 -85.41 5 A ASP 85 -151.29 -18.05 5 A LEU 87 -162.64 93.23 5 A LEU 93 73.04 68.31 5 A GLU 94 65.22 126.88 5 A HIS 97 61.57 76.20 6 A ILE 3 -131.95 -83.07 6 A GLN 5 -150.85 18.82 6 A LEU 71 -82.34 -89.39 6 A ASP 73 -172.60 -36.77 6 A TYR 84 -179.40 -156.60 6 A GLU 89 175.18 155.66 6 A GLN 92 -122.97 -63.14 6 A LEU 93 85.40 64.66 6 A GLU 94 71.44 139.17 6 A HIS 99 69.93 165.70 7 A ILE 3 -138.82 -82.96 7 A GLN 5 -149.13 16.25 7 A LEU 71 -77.95 -87.84 7 A SER 72 -97.43 -60.23 7 A ASP 73 -149.77 -42.06 7 A TYR 84 -172.10 -162.33 7 A LEU 93 85.57 94.25 7 A GLU 94 59.31 -33.21 7 A HIS 96 -39.59 -19.65 7 A HIS 99 176.54 -51.03 8 A ILE 3 63.17 -102.36 8 A GLN 5 -158.62 22.11 8 A ILE 64 -101.27 59.51 8 A LEU 71 -79.84 -88.34 8 A SER 72 -96.34 -60.02 8 A ASP 73 -155.08 -70.83 8 A TYR 84 -172.02 29.19 8 A ASP 85 80.76 173.71 8 A GLN 86 67.56 -60.77 8 A GLU 90 -67.11 21.17 8 A GLN 92 -126.22 -57.07 8 A LEU 93 62.22 85.89 8 A GLU 94 50.13 79.01 8 A HIS 98 -178.15 -41.63 9 A ILE 3 58.81 -93.60 9 A GLN 5 -175.68 22.80 9 A ILE 64 -102.09 65.57 9 A ASP 65 -122.23 -62.85 9 A LEU 71 -103.40 -81.15 9 A SER 72 -94.18 35.79 9 A ASP 73 80.19 -53.08 9 A SER 80 -69.46 2.41 9 A TYR 84 -159.98 64.90 9 A ASP 85 71.74 -49.78 9 A ASP 88 59.52 10.74 9 A GLU 94 58.26 -78.78 9 A HIS 96 -40.12 2.53 9 A HIS 97 -173.15 -72.71 9 A HIS 98 59.61 -80.33 9 A HIS 99 62.15 113.05 10 A ILE 64 -100.25 68.93 10 A ASP 65 -127.34 -76.18 10 A LEU 71 -76.40 -82.35 10 A SER 72 -95.22 -60.63 10 A ASP 73 -153.67 -57.31 10 A TYR 84 -171.56 -169.57 10 A GLU 90 -68.24 21.15 10 A GLN 92 -129.29 -59.35 10 A LEU 93 79.78 74.05 10 A GLU 94 59.61 105.84 10 A HIS 95 -45.19 101.68 10 A HIS 98 -79.75 -85.28 lowest energy, model 1 Solution structure of the N-terminal domain of Bacillus subtilis delta subunit of RNA polymerase 1 N N A SER 7 A SER 6 HELX_P A GLU 13 A GLU 12 1 1 7 A ALA 15 A ALA 14 HELX_P A LYS 28 A LYS 27 1 2 14 A PHE 33 A PHE 32 HELX_P A GLY 45 A GLY 44 1 3 13 A LYS 47 A LYS 46 HELX_P A LEU 51 A LEU 50 5 4 5 A GLY 52 A GLY 51 HELX_P A ILE 64 A ILE 63 1 5 13 A LEU 78 A LEU 77 HELX_P A TYR 82 A TYR 81 5 6 5 TRANSCRIPTION RNA polymerase, delta subunit, gram-positive bacteria, DNA-directed RNA polymerase, Nucleotidyltransferase, Transcription, Transferase RPOE_BACSU UNP 1 2 P12464 GIKQYSQEELKEMALVEIAHELFEEHKKPVPFQELLNEIASLLGVKKEELGDRIAQFYTDLNIDGRFLALSDQTWGLRSW YPYDQLDEETQ 2 92 2KRC 2 92 P12464 A 1 1 91 1 expression tag LEU 93 2KRC A P12464 UNP 92 1 expression tag GLU 94 2KRC A P12464 UNP 93 1 expression tag HIS 95 2KRC A P12464 UNP 94 1 expression tag HIS 96 2KRC A P12464 UNP 95 1 expression tag HIS 97 2KRC A P12464 UNP 96 1 expression tag HIS 98 2KRC A P12464 UNP 97 1 expression tag HIS 99 2KRC A P12464 UNP 98 1 expression tag HIS 100 2KRC A P12464 UNP 99 3 anti-parallel anti-parallel A VAL 31 A VAL 30 A PRO 32 A PRO 31 A THR 75 A THR 74 A GLY 77 A GLY 76 A LEU 69 A LEU 68 A ALA 70 A ALA 69