0.012551 0.000000 0.000000 0.000000 0.010772 0.000000 0.000000 0.000000 0.027182 0.00000 0.00000 0.00000 Bent, C.J. Isaacs, N.W. Mitchell, T.J. Riboldi-Tunnicliffe, A. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 79.673 92.829 36.789 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 H2 O 18.015 WATER non-polymer 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 C4 H8 N O7 P 213.083 n ASPARTYL PHOSPHATE 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 C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking Xe 131.293 XENON non-polymer US J.Bacteriol. JOBAAY 0767 0021-9193 186 2872 2879 10.1128/JB.186.9.2872-2879.2004 15090529 Crystal structure of the response regulator 02 receiver domain, the essential YycF two-component system of Streptococcus pneumoniae in both complexed and native states. 2004 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100 1 CCD 2002-09-29 MARRESEARCH 1.8 SAD using Sulphur and Xenon M x-ray 1 1.8 1.0 5.2R ELETTRA 1.8 SYNCHROTRON ELETTRA BEAMLINE 5.2R 13680.710 DNA-binding response regulator MicA receiver Domain 1 man polymer 131.293 XENON 1 syn non-polymer 18.015 water 30 nat water no yes MKKILIVDDEKPISDIIKFNMTKEGYEVVTAFNGREALEQFEAEQPDIIIL(PHD)LMLPEIDGLEVAKTIRKTSSVPIL MLSAKDSEFDKVIGLELGADDYVTKPFSNRELQARVKALLRRSQ MKKILIVDDEKPISDIIKFNMTKEGYEVVTAFNGREALEQFEAEQPDIIILDLMLPEIDGLEVAKTIRKTSSVPILMLSA KDSEFDKVIGLELGADDYVTKPFSNRELQARVKALLRRSQ 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 n n n n n n n n n n n n n n n n n n n n n Streptococcus Streptococcus pneumoniae TIGR4 Escherichia Escherichia coli sample 170187 Streptococcus pneumoniae 469008 Escherichia coli BL21(DE3) BL21(DE3) Plasmid Pet33B 1 2.54 51.22 VAPOR DIFFUSION, SITTING DROP 4.0 40%v/v PEG 300, 100mM Phosphate Citrate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K 293 repository Initial release Version format compliance Advisory Source and taxonomy Version format compliance 1 0 2004-02-17 1 1 2008-04-29 1 2 2011-07-13 RCSB Y RCSB 2003-02-11 REL REL XE XENON HOH water XE 101 2 XE XE 121 A HOH 1 3 HOH HOH 122 A HOH 2 3 HOH HOH 123 A HOH 3 3 HOH HOH 124 A HOH 4 3 HOH HOH 125 A HOH 5 3 HOH HOH 126 A HOH 6 3 HOH HOH 127 A HOH 7 3 HOH HOH 128 A HOH 8 3 HOH HOH 129 A HOH 9 3 HOH HOH 130 A HOH 10 3 HOH HOH 131 A HOH 11 3 HOH HOH 132 A HOH 12 3 HOH HOH 133 A HOH 13 3 HOH HOH 134 A HOH 14 3 HOH HOH 135 A HOH 15 3 HOH HOH 136 A HOH 16 3 HOH HOH 137 A HOH 17 3 HOH HOH 138 A HOH 18 3 HOH HOH 139 A HOH 19 3 HOH HOH 140 A HOH 20 3 HOH HOH 141 A HOH 21 3 HOH HOH 142 A HOH 22 3 HOH HOH 143 A HOH 23 3 HOH HOH 144 A HOH 24 3 HOH HOH 145 A HOH 25 3 HOH HOH 146 A HOH 26 3 HOH HOH 147 A HOH 27 3 HOH HOH 148 A HOH 28 3 HOH HOH 149 A HOH 29 3 HOH HOH 150 A HOH 30 3 HOH HOH 151 A n 1 1 A LYS 2 n 2 LYS 2 A LYS 3 n 3 LYS 3 A ILE 4 n 4 ILE 4 A LEU 5 n 5 LEU 5 A ILE 6 n 6 ILE 6 A VAL 7 n 7 VAL 7 A ASP 8 n 8 ASP 8 A ASP 9 n 9 ASP 9 A GLU 10 n 10 GLU 10 A LYS 11 n 11 LYS 11 A PRO 12 n 12 PRO 12 A ILE 13 n 13 ILE 13 A SER 14 n 14 SER 14 A ASP 15 n 15 ASP 15 A ILE 16 n 16 ILE 16 A ILE 17 n 17 ILE 17 A LYS 18 n 18 LYS 18 A PHE 19 n 19 PHE 19 A ASN 20 n 20 ASN 20 A MET 21 n 21 MET 21 A THR 22 n 22 THR 22 A LYS 23 n 23 LYS 23 A GLU 24 n 24 GLU 24 A GLY 25 n 25 GLY 25 A TYR 26 n 26 TYR 26 A GLU 27 n 27 GLU 27 A VAL 28 n 28 VAL 28 A VAL 29 n 29 VAL 29 A THR 30 n 30 THR 30 A ALA 31 n 31 ALA 31 A PHE 32 n 32 PHE 32 A ASN 33 n 33 ASN 33 A GLY 34 n 34 GLY 34 A ARG 35 n 35 ARG 35 A GLU 36 n 36 GLU 36 A ALA 37 n 37 ALA 37 A LEU 38 n 38 LEU 38 A GLU 39 n 39 GLU 39 A GLN 40 n 40 GLN 40 A PHE 41 n 41 PHE 41 A GLU 42 n 42 GLU 42 A ALA 43 n 43 ALA 43 A GLU 44 n 44 GLU 44 A GLN 45 n 45 GLN 45 A PRO 46 n 46 PRO 46 A ASP 47 n 47 ASP 47 A ILE 48 n 48 ILE 48 A ILE 49 n 49 ILE 49 A ILE 50 n 50 ILE 50 A LEU 51 n 51 LEU 51 A PHD 52 n 52 PHD 52 A LEU 53 n 53 LEU 53 A MET 54 n 54 MET 54 A LEU 55 n 55 LEU 55 A PRO 56 n 56 PRO 56 A n 57 57 A n 58 58 A ASP 59 n 59 ASP 59 A GLY 60 n 60 GLY 60 A LEU 61 n 61 LEU 61 A GLU 62 n 62 GLU 62 A VAL 63 n 63 VAL 63 A ALA 64 n 64 ALA 64 A LYS 65 n 65 LYS 65 A THR 66 n 66 THR 66 A ILE 67 n 67 ILE 67 A ARG 68 n 68 ARG 68 A LYS 69 n 69 LYS 69 A THR 70 n 70 THR 70 A SER 71 n 71 SER 71 A SER 72 n 72 SER 72 A VAL 73 n 73 VAL 73 A PRO 74 n 74 PRO 74 A ILE 75 n 75 ILE 75 A LEU 76 n 76 LEU 76 A MET 77 n 77 MET 77 A LEU 78 n 78 LEU 78 A SER 79 n 79 SER 79 A ALA 80 n 80 ALA 80 A LYS 81 n 81 LYS 81 A ASP 82 n 82 ASP 82 A SER 83 n 83 SER 83 A GLU 84 n 84 GLU 84 A PHE 85 n 85 PHE 85 A ASP 86 n 86 ASP 86 A LYS 87 n 87 LYS 87 A VAL 88 n 88 VAL 88 A ILE 89 n 89 ILE 89 A GLY 90 n 90 GLY 90 A LEU 91 n 91 LEU 91 A GLU 92 n 92 GLU 92 A LEU 93 n 93 LEU 93 A GLY 94 n 94 GLY 94 A ALA 95 n 95 ALA 95 A ASP 96 n 96 ASP 96 A ASP 97 n 97 ASP 97 A TYR 98 n 98 TYR 98 A VAL 99 n 99 VAL 99 A THR 100 n 100 THR 100 A LYS 101 n 101 LYS 101 A PRO 102 n 102 PRO 102 A PHE 103 n 103 PHE 103 A SER 104 n 104 SER 104 A ASN 105 n 105 ASN 105 A ARG 106 n 106 ARG 106 A GLU 107 n 107 GLU 107 A LEU 108 n 108 LEU 108 A GLN 109 n 109 GLN 109 A ALA 110 n 110 ALA 110 A ARG 111 n 111 ARG 111 A VAL 112 n 112 VAL 112 A LYS 113 n 113 LYS 113 A ALA 114 n 114 ALA 114 A LEU 115 n 115 LEU 115 A LEU 116 n 116 LEU 116 A ARG 117 n 117 ARG 117 A ARG 118 n 118 ARG 118 A SER 119 n 119 SER 119 A n 120 120 A 0.3313 -0.2105 -0.0590 1.0424 0.2223 0.1837 -0.0060 0.0129 0.0078 0.0320 0.0128 -0.0424 0.0015 -0.0309 -0.0067 0.0151 0.0112 -0.0047 0.0109 -0.0006 0.0047 refined 64.7686 57.3347 5.4721 X-RAY DIFFRACTION A 2 A 2 A 24 A 24 X-RAY DIFFRACTION 1 A 25 A 25 A 44 A 44 X-RAY DIFFRACTION 1 A 45 A 45 A 54 A 54 X-RAY DIFFRACTION 1 A 59 A 59 A 70 A 70 X-RAY DIFFRACTION 1 A 71 A 71 A 94 A 94 X-RAY DIFFRACTION 1 A 95 A 95 A 119 A 119 X-RAY DIFFRACTION 1 author_defined_assembly 2 dimeric A PHD 52 ASPARTYL PHOSPHATE A PHD 52 ASP 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 1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 4_566 x,-y+1,-z+1 crystal symmetry operation 0.0000000000 92.8290000000 36.7890000000 A O GLU 27 A O GLU 27 A N ILE 4 A N ILE 4 A N VAL 7 A N VAL 7 A O ILE 50 A O ILE 50 A N ILE 49 A N ILE 49 A O LEU 76 A O LEU 76 A N MET 77 A N MET 77 A O VAL 99 A O VAL 99 1 A CD GLU 42 A CD GLU 42 0 Y 1 A OE1 GLU 42 A OE1 GLU 42 0 Y 1 A OE2 GLU 42 A OE2 GLU 42 0 Y 1 A C PRO 56 A C PRO 56 0 Y 1 A O PRO 56 A O PRO 56 0 Y 1 A CG GLU 92 A CG GLU 92 0 Y 1 A CD GLU 92 A CD GLU 92 0 Y 1 A OE1 GLU 92 A OE1 GLU 92 0 Y 1 A OE2 GLU 92 A OE2 GLU 92 0 Y 1 A CG LYS 113 A CG LYS 113 0 Y 1 A CD LYS 113 A CD LYS 113 0 Y 1 A CE LYS 113 A CE LYS 113 0 Y 1 A NZ LYS 113 A NZ LYS 113 0 Y 1 A MET 1 A MET 1 1 Y 1 A GLU 57 A GLU 57 1 Y 1 A ILE 58 A ILE 58 1 Y 1 A GLN 120 A GLN 120 1 Y 1 A A O O HOH HOH 149 150 1.48 1 A A O O HOH HOH 135 137 2.17 1 A ARG 118 -36.31 1 5.64 0.90 118.30 123.94 A A A CB CG OD2 ASP ASP ASP 15 15 15 N 1 17.22 2.70 114.20 131.42 A A A CB CG CD GLU GLU GLU 42 42 42 N 1 -15.05 2.00 118.30 103.25 A A A CG CD OE1 GLU GLU GLU 42 42 42 N 1 14.89 2.00 118.30 133.19 A A A CG CD OE2 GLU GLU GLU 42 42 42 N 1 6.37 0.90 118.30 124.67 A A A CB CG OD2 ASP ASP ASP 59 59 59 N 1 15.03 2.20 113.40 128.43 A A A CA CB CG GLU GLU GLU 92 92 92 N 1 -20.10 2.10 120.10 100.00 A A A CA C O ARG ARG ARG 118 118 118 N 1 -14.24 1.60 122.70 108.46 A A A O C N ARG ARG SER 118 118 119 Y 1 A A CG CD GLU GLU 42 42 -0.102 0.015 1.515 1.413 N 1 A A CB CG GLU GLU 92 92 -0.232 0.019 1.517 1.285 N 1 A A C O ARG ARG 118 118 -0.213 0.019 1.229 1.016 N 39.556 2.61 0.00 0.00 -1.28 0.00 -1.33 0.934 0.911 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 0.23556 0.2141 0.21614 2.34 30.86 579 5398 9.7 98.96 11.526 0.259 RANDOM LIKELY RESIDUAL 1 THROUGHOUT 2.0 2.0 SAD Xenon/Sulphur 0.396 0.239 0.80 0.80 1.40 BABINET MODEL WITH MASK 2.34 30.86 30 953 1 0 922 0.022 0.022 921 0.000 0.020 889 1.838 2.013 1239 3.788 3.000 2068 6.476 5.000 114 0.112 0.200 147 0.011 0.020 983 0.013 0.020 167 0.222 0.200 198 0.279 0.200 906 0.110 0.200 473 0.331 0.200 25 0.216 0.200 13 0.303 0.200 51 0.235 0.200 5 1.058 1.500 575 1.972 2.000 931 2.928 3.000 346 5.368 4.500 308 0.247 0.301 2.402 41 357 20 39.55 2.34 30.86 1NXT 5398 2.0 2.0 0.052 1 11.6 98.96 2.342 2.402 5.1 0.116 1 97.3 refinement REFMAC 5.1.27 data reduction MOSFLM data scaling CCP4 (SCALA) phasing SHARP DNA-binding response regulator MicArec pH 4.0 1 N N 2 N N 3 N N he second part of the biological assembly is generated by the two fold axis: X, -y, -z A GLU 10 A GLU 10 HELX_P A GLU 24 A GLU 24 1 1 15 A ASN 33 A ASN 33 HELX_P A GLN 45 A GLN 45 1 2 13 A ASP 59 A ASP 59 HELX_P A SER 71 A SER 71 1 3 13 A SER 83 A SER 83 HELX_P A LEU 93 A LEU 93 1 4 11 A SER 104 A SER 104 HELX_P A ARG 118 A ARG 118 1 5 15 covale 1.321 A A LEU 51 A C LEU 51 1_555 A PHD 52 A N PHD 52 1_555 covale 1.347 A A PHD 52 A C PHD 52 1_555 A LEU 53 A N LEU 53 1_555 SIGNALING PROTEIN doubly wound 5 alpha, 5 beta fold, SIGNALING PROTEIN A LYS 101 A LYS 101 1 A PRO 102 A PRO 102 4.38 Q9S1K0_STRPN UNP 1 1 Q9S1K0 MKKILIVDDEKPISDIIKFNMTKEGYEVVTAFNGREALEQFEAEQPDIIILDLMLPEIDGLEVAKTIRKTSSVPILMLSA KDSEFDKVIGLELGADDYVTKPFSNRELQARVKALLRRSQ 1 120 1NXT 1 120 Q9S1K0 A 1 1 120 1 ASP MODIFIED RESIDUE PHD 52 1NXT A Q9S1K0 UNP 52 52 5 parallel parallel parallel parallel A GLU 27 A GLU 27 A ALA 31 A ALA 31 A LYS 3 A LYS 3 A VAL 7 A VAL 7 A ILE 48 A ILE 48 A PHD 52 A PHD 52 A ILE 75 A ILE 75 A SER 79 A SER 79 A ASP 97 A ASP 97 A THR 100 A THR 100 20 C 2 2 21