0.009989 0.000000 0.000000 0.000000 0.009989 0.000000 0.000000 0.000000 0.009989 0.00000 0.00000 0.00000 Joint Center for Structural Genomics (JCSG) http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 24 90.00 90.00 90.00 100.110 100.110 100.110 C10 H15 N5 O10 P2 427.201 n ADENOSINE-5'-DIPHOSPHATE non-polymer 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 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 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 C5 H11 N O2 Se 196.106 n SELENOMETHIONINE 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 O4 S -2 96.063 SULFATE ION non-polymer 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 US Proteins PSFGEY 0867 0887-3585 54 810 813 10.1002/prot.10647 14997579 Crystal structure of a putative PII-like signaling protein (TM0021) from Thermotoga maritima at 2.5 A resolution 2004 10.2210/pdb1o51/pdb pdb_00001o51 100.0 1 WATER COOLED FOCUSING 2ND CRYSTAL, ROSENBAUM-ROCK VERTICAL FOCUSING MIRROR CCD 2002-10-27 APS-1 ROSENBAUM-ROCK DOUBLE-CRYSTAL MONOCHROMATOR SINGLE WAVELENGTH M x-ray 1 0.97914 1.0 0.97934 1.0 19-BM APS 0.97914, 0.97934 SYNCHROTRON APS BEAMLINE 19-BM 13425.157 Hypothetical protein TM0021 1 man polymer 96.063 SULFATE ION 2 syn non-polymer 427.201 ADENOSINE-5'-DIPHOSPHATE 1 syn non-polymer 18.015 water 39 nat water no yes MGSDKIHHHHHH(MSE)KLLKIYLGEKDKHSGKPLFEYLVKRAYELG(MSE)KGVTVYRGI(MSE)GFGHKRHMHRSDFF SLSPDLPIVLEIVDEEERINLFLKEIDNIDFDGLVFTADVNVVKMG MGSDKIHHHHHHMKLLKIYLGEKDKHSGKPLFEYLVKRAYELGMKGVTVYRGIMGFGHKRHMHRSDFFSLSPDLPIVLEI VDEEERINLFLKEIDNIDFDGLVFTADVNVVKMG A 281902 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 Thermotoga Escherichia sample TM0021 2336 Thermotoga maritima 562 Escherichia coli Plasmid 1 3.80 67.37 5.60 2M ammonium sulfate, 0.1M tri-sodium citrate dihydrate pH 5.6, 0.2M potassium sodium tartrate tetrahydrate, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K, pH 5.60 293 Joint Center for Structural Genomics JCSG PSI, Protein Structure Initiative software pdbx_database_related pdbx_struct_special_symmetry database_2 struct_conn struct_ref_seq_dif struct_site repository Initial release Version format compliance Advisory Derived calculations Version format compliance Refinement description Data collection Database references Derived calculations Database references Derived calculations 1 0 2003-08-19 1 1 2008-04-26 1 2 2011-07-13 1 3 2017-10-04 1 4 2018-07-18 1 5 2023-01-25 _software.name _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag _struct_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id 2003-08-19 SPRSDE Y RCSB Y RCSB 2003-08-01 REL REL SO4 SULFATE ION ADP ADENOSINE-5'-DIPHOSPHATE HOH water SO4 301 2 SO4 SO4 301 A SO4 302 2 SO4 SO4 302 A ADP 200 3 ADP ADP 200 A HOH 1 4 HOH HOH 303 A HOH 2 4 HOH HOH 304 A HOH 3 4 HOH HOH 305 A HOH 4 4 HOH HOH 306 A HOH 5 4 HOH HOH 307 A HOH 6 4 HOH HOH 308 A HOH 7 4 HOH HOH 309 A HOH 8 4 HOH HOH 310 A HOH 9 4 HOH HOH 311 A HOH 10 4 HOH HOH 312 A HOH 11 4 HOH HOH 313 A HOH 12 4 HOH HOH 314 A HOH 13 4 HOH HOH 315 A HOH 16 4 HOH HOH 316 A HOH 18 4 HOH HOH 317 A HOH 19 4 HOH HOH 318 A HOH 20 4 HOH HOH 319 A HOH 21 4 HOH HOH 320 A HOH 22 4 HOH HOH 321 A HOH 24 4 HOH HOH 322 A HOH 25 4 HOH HOH 323 A HOH 29 4 HOH HOH 324 A HOH 31 4 HOH HOH 325 A HOH 34 4 HOH HOH 326 A HOH 36 4 HOH HOH 327 A HOH 37 4 HOH HOH 328 A HOH 38 4 HOH HOH 329 A HOH 39 4 HOH HOH 330 A HOH 40 4 HOH HOH 331 A HOH 41 4 HOH HOH 332 A HOH 42 4 HOH HOH 333 A HOH 43 4 HOH HOH 334 A HOH 44 4 HOH HOH 335 A HOH 46 4 HOH HOH 336 A HOH 47 4 HOH HOH 337 A HOH 48 4 HOH HOH 338 A HOH 49 4 HOH HOH 339 A HOH 50 4 HOH HOH 340 A HOH 52 4 HOH HOH 341 A n 1 -11 A n 2 -10 A n 3 -9 A n 4 -8 A n 5 -7 A n 6 -6 A n 7 -5 A n 8 -4 A n 9 -3 A n 10 -2 A HIS -1 n 11 HIS -1 A HIS 0 n 12 HIS 0 A MSE 1 n 13 MSE 1 A LYS 2 n 14 LYS 2 A LEU 3 n 15 LEU 3 A LEU 4 n 16 LEU 4 A LYS 5 n 17 LYS 5 A ILE 6 n 18 ILE 6 A TYR 7 n 19 TYR 7 A LEU 8 n 20 LEU 8 A GLY 9 n 21 GLY 9 A GLU 10 n 22 GLU 10 A LYS 11 n 23 LYS 11 A ASP 12 n 24 ASP 12 A LYS 13 n 25 LYS 13 A HIS 14 n 26 HIS 14 A SER 15 n 27 SER 15 A GLY 16 n 28 GLY 16 A LYS 17 n 29 LYS 17 A PRO 18 n 30 PRO 18 A LEU 19 n 31 LEU 19 A PHE 20 n 32 PHE 20 A GLU 21 n 33 GLU 21 A TYR 22 n 34 TYR 22 A LEU 23 n 35 LEU 23 A VAL 24 n 36 VAL 24 A LYS 25 n 37 LYS 25 A ARG 26 n 38 ARG 26 A ALA 27 n 39 ALA 27 A TYR 28 n 40 TYR 28 A GLU 29 n 41 GLU 29 A LEU 30 n 42 LEU 30 A GLY 31 n 43 GLY 31 A MSE 32 n 44 MSE 32 A LYS 33 n 45 LYS 33 A GLY 34 n 46 GLY 34 A VAL 35 n 47 VAL 35 A THR 36 n 48 THR 36 A VAL 37 n 49 VAL 37 A TYR 38 n 50 TYR 38 A ARG 39 n 51 ARG 39 A GLY 40 n 52 GLY 40 A ILE 41 n 53 ILE 41 A MSE 42 n 54 MSE 42 A GLY 43 n 55 GLY 43 A PHE 44 n 56 PHE 44 A GLY 45 n 57 GLY 45 A HIS 46 n 58 HIS 46 A n 59 47 A n 60 48 A n 61 49 A n 62 50 A n 63 51 A n 64 52 A n 65 53 A n 66 54 A n 67 55 A n 68 56 A n 69 57 A n 70 58 A n 71 59 A PRO 60 n 72 PRO 60 A ASP 61 n 73 ASP 61 A LEU 62 n 74 LEU 62 A PRO 63 n 75 PRO 63 A ILE 64 n 76 ILE 64 A VAL 65 n 77 VAL 65 A LEU 66 n 78 LEU 66 A GLU 67 n 79 GLU 67 A ILE 68 n 80 ILE 68 A VAL 69 n 81 VAL 69 A ASP 70 n 82 ASP 70 A GLU 71 n 83 GLU 71 A GLU 72 n 84 GLU 72 A GLU 73 n 85 GLU 73 A ARG 74 n 86 ARG 74 A ILE 75 n 87 ILE 75 A ASN 76 n 88 ASN 76 A LEU 77 n 89 LEU 77 A PHE 78 n 90 PHE 78 A LEU 79 n 91 LEU 79 A LYS 80 n 92 LYS 80 A GLU 81 n 93 GLU 81 A ILE 82 n 94 ILE 82 A ASP 83 n 95 ASP 83 A ASN 84 n 96 ASN 84 A ILE 85 n 97 ILE 85 A ASP 86 n 98 ASP 86 A PHE 87 n 99 PHE 87 A ASP 88 n 100 ASP 88 A GLY 89 n 101 GLY 89 A LEU 90 n 102 LEU 90 A VAL 91 n 103 VAL 91 A PHE 92 n 104 PHE 92 A THR 93 n 105 THR 93 A ALA 94 n 106 ALA 94 A ASP 95 n 107 ASP 95 A VAL 96 n 108 VAL 96 A ASN 97 n 109 ASN 97 A VAL 98 n 110 VAL 98 A VAL 99 n 111 VAL 99 A LYS 100 n 112 LYS 100 A n 113 101 A n 114 102 A 5.7424 -0.0523 2.4899 3.7382 -1.3634 4.8187 -0.2259 -0.3676 0.4388 0.5771 0.0022 0.1537 -0.7102 -0.1453 0.2237 -0.0264 -0.0201 0.0034 -0.2146 -0.0658 -0.1646 refined 48.2120 12.3870 4.3480 X-RAY DIFFRACTION A -1 A 11 A 100 A 112 X-RAY DIFFRACTION 1 author_and_software_defined_assembly PISA,PQS 3 trimeric 8630 -187 12380 A MSE 1 SELENOMETHIONINE A MSE 13 MET A MSE 32 SELENOMETHIONINE A MSE 44 MET A MSE 42 SELENOMETHIONINE A MSE 54 MET 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 0.0000000000 0.0000000000 1.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 6_555 z+1/2,-x+1/2,-y crystal symmetry operation 50.0550000000 50.0550000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 1.0000000000 0.0000000000 0.0000000000 12_554 -y+1/2,-z,x-1/2 crystal symmetry operation 50.0550000000 0.0000000000 -50.0550000000 A N TYR 38 A N TYR 50 A O VAL 65 A O VAL 77 A O ILE 68 A O ILE 80 A N LEU 4 A N LEU 16 A N LYS 5 A N LYS 17 A O PHE 92 A O PHE 104 A N HIS 14 A N HIS 26 A O LYS 17 A O LYS 29 1 A SO4 302 C SO4 1 A HOH 304 E HOH 1 A HOH 328 E HOH 1 A CE LYS 11 A CE LYS 23 1 Y 1 A NZ LYS 11 A NZ LYS 23 1 Y 1 A NZ LYS 17 A NZ LYS 29 1 Y 1 A CE LYS 25 A CE LYS 37 1 Y 1 A NZ LYS 25 A NZ LYS 37 1 Y 1 A CG MSE 32 A CG MSE 44 1 Y 1 A SE MSE 32 A SE MSE 44 1 Y 1 A CE MSE 32 A CE MSE 44 1 Y 1 A CD LYS 80 A CD LYS 92 1 Y 1 A CE LYS 80 A CE LYS 92 1 Y 1 A NZ LYS 80 A NZ LYS 92 1 Y 1 A CG ASN 84 A CG ASN 96 1 Y 1 A OD1 ASN 84 A OD1 ASN 96 1 Y 1 A ND2 ASN 84 A ND2 ASN 96 1 Y 1 A CG ASP 86 A CG ASP 98 1 Y 1 A OD1 ASP 86 A OD1 ASP 98 1 Y 1 A OD2 ASP 86 A OD2 ASP 98 1 Y 1 A CG ASP 88 A CG ASP 100 1 Y 1 A OD1 ASP 88 A OD1 ASP 100 1 Y 1 A OD2 ASP 88 A OD2 ASP 100 1 Y 1 A MET -11 A MET 1 1 Y 1 A GLY -10 A GLY 2 1 Y 1 A SER -9 A SER 3 1 Y 1 A ASP -8 A ASP 4 1 Y 1 A LYS -7 A LYS 5 1 Y 1 A ILE -6 A ILE 6 1 Y 1 A HIS -5 A HIS 7 1 Y 1 A HIS -4 A HIS 8 1 Y 1 A HIS -3 A HIS 9 1 Y 1 A HIS -2 A HIS 10 1 Y 1 A LYS 47 A LYS 59 1 Y 1 A ARG 48 A ARG 60 1 Y 1 A HIS 49 A HIS 61 1 Y 1 A MET 50 A MET 62 1 Y 1 A HIS 51 A HIS 63 1 Y 1 A ARG 52 A ARG 64 1 Y 1 A SER 53 A SER 65 1 Y 1 A ASP 54 A ASP 66 1 Y 1 A PHE 55 A PHE 67 1 Y 1 A PHE 56 A PHE 68 1 Y 1 A SER 57 A SER 69 1 Y 1 A LEU 58 A LEU 70 1 Y 1 A SER 59 A SER 71 1 Y 1 A MET 101 A MET 113 1 Y 1 A GLY 102 A GLY 114 1 Y 1 7.71 0.90 118.30 126.01 A A A CB CG OD2 ASP ASP ASP 12 12 12 N 1 A ASP 88 -88.09 -100.19 35.09 0.940 0.923 1, PROMINENT DIFFERENCE DENSITY ON THE CRYSTALLOGRAPHIC (AND BIOLOGICAL) THREE-FOLD AXIS WAS INTERPRETED AS TWO SULFATE IONS, EVEN THOUGH BOTH ARE REFINED TO HIGH B-FACTORS.2, THERE IS WEAK AND AMBIGUOUS DENSITY INDICATING THE GENERAL LOCATION OF THE LAST RESIDUE OMITTED IN THE CHAIN BREAK, SER59A.3, HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 0.229 0.184 0.19 2.50 44.77 787 5544 12.400 100.0 11.317 0.129 RANDOM LIKELY RESIDUAL 1 ISOTROPIC THROUGHOUT SAD 0.276 0.226 0.80 0.80 1.40 MAXIMUM LIKELIHOOD BABINET MODEL WITH MASK 2.50 44.77 39 779 37 0 703 0.018 0.022 761 0.001 0.020 698 1.784 2.026 1033 0.873 3.000 1613 6.913 5.000 89 30.257 24.062 32 17.152 15.000 129 25.487 15.000 3 0.092 0.200 115 0.006 0.020 799 0.001 0.020 150 0.241 0.200 113 0.190 0.200 633 0.091 0.200 506 0.200 0.200 24 0.178 0.200 14 0.222 0.200 41 0.171 0.200 20 0.858 1.500 441 1.685 2.000 708 2.586 3.000 320 4.231 4.500 324 0.247 0.171 2.57 76 371 20 51.99 2.500 50.000 1O51 6359 0.109 1 70.0500 43.830 100.0 2.50 2.59 10.640 0.588 1 0.57 100.0 data reduction DENZO data scaling SCALEPACK model building RESOLVE phasing SOLVE refinement REFMAC 5.1.9999 phasing RESOLVE Crystal structure of a putative PII-like signaling protein (TM0021) from Thermotoga maritima at 2.50 A resolution 1 N N 2 N N 2 N N 3 N N 4 N N A LEU 19 A LEU 31 HELX_P A LEU 30 A LEU 42 1 1 12 A GLU 71 A GLU 83 HELX_P A ASN 84 A ASN 96 1 2 14 covale 1.325 both A HIS 0 A C HIS 12 1_555 A MSE 1 A N MSE 13 1_555 covale 1.328 both A MSE 1 A C MSE 13 1_555 A LYS 2 A N LYS 14 1_555 covale 1.343 both A GLY 31 A C GLY 43 1_555 A MSE 32 A N MSE 44 1_555 covale 1.324 both A MSE 32 A C MSE 44 1_555 A LYS 33 A N LYS 45 1_555 covale 1.326 both A ILE 41 A C ILE 53 1_555 A MSE 42 A N MSE 54 1_555 covale 1.320 both A MSE 42 A C MSE 54 1_555 A GLY 43 A N GLY 55 1_555 SIGNALING PROTEIN Ferredoxin-like fold, structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI, signaling protein Y021_THEMA UNP 1 1 Q9WXM9 MKLLKIYLGEKDKHSGKPLFEYLVKRAYELGMKGVTVYRGIMGFGHKRHMHRSDFFSLSPDLPIVLEIVDEEERINLFLK EIDNIDFDGLVFTADVNVVKMG 1 102 1O51 1 102 Q9WXM9 A 1 13 114 1 expression tag MET -11 1O51 A Q9WXM9 UNP 1 1 expression tag GLY -10 1O51 A Q9WXM9 UNP 2 1 expression tag SER -9 1O51 A Q9WXM9 UNP 3 1 expression tag ASP -8 1O51 A Q9WXM9 UNP 4 1 expression tag LYS -7 1O51 A Q9WXM9 UNP 5 1 expression tag ILE -6 1O51 A Q9WXM9 UNP 6 1 expression tag HIS -5 1O51 A Q9WXM9 UNP 7 1 expression tag HIS -4 1O51 A Q9WXM9 UNP 8 1 expression tag HIS -3 1O51 A Q9WXM9 UNP 9 1 expression tag HIS -2 1O51 A Q9WXM9 UNP 10 1 expression tag HIS -1 1O51 A Q9WXM9 UNP 11 1 expression tag HIS 0 1O51 A Q9WXM9 UNP 12 1 MET modified residue MSE 1 1O51 A Q9WXM9 UNP 1 13 1 MET modified residue MSE 32 1O51 A Q9WXM9 UNP 32 44 1 MET modified residue MSE 42 1O51 A Q9WXM9 UNP 42 54 4 2 anti-parallel anti-parallel anti-parallel anti-parallel A THR 36 A THR 48 A ARG 39 A ARG 51 A PRO 63 A PRO 75 A ASP 70 A ASP 82 A HIS 0 A HIS 12 A GLY 9 A GLY 21 A LEU 90 A LEU 102 A ASN 97 A ASN 109 A LYS 13 A LYS 25 A HIS 14 A HIS 26 A LYS 17 A LYS 29 A PRO 18 A PRO 30 BINDING SITE FOR RESIDUE SO4 A 301 A SO4 301 Software 11 BINDING SITE FOR RESIDUE SO4 A 302 A SO4 302 Software 14 BINDING SITE FOR RESIDUE ADP A 200 A ADP 200 Software 18 A LYS 5 A LYS 17 11 6_555 A LYS 5 A LYS 17 11 1_555 A LYS 5 A LYS 17 11 12_554 A TYR 38 A TYR 50 11 1_555 A TYR 38 A TYR 50 11 12_554 A GLU 67 A GLU 79 11 12_554 A GLU 67 A GLU 79 11 6_555 A GLU 67 A GLU 79 11 1_555 A SO4 302 C SO4 11 6_555 A SO4 302 C SO4 11 12_554 A SO4 302 C SO4 11 1_555 A LEU 3 A LEU 15 14 12_554 A LEU 3 A LEU 15 14 6_555 A LYS 5 A LYS 17 14 1_555 A LYS 5 A LYS 17 14 12_554 A LYS 5 A LYS 17 14 6_555 A GLU 67 A GLU 79 14 6_555 A GLU 67 A GLU 79 14 12_554 A PHE 92 A PHE 104 14 12_554 A SO4 301 B SO4 14 12_554 A SO4 301 B SO4 14 6_555 A SO4 301 B SO4 14 1_555 A HOH 341 E HOH 14 6_555 A HOH 341 E HOH 14 1_555 A HOH 341 E HOH 14 12_554 A TYR 7 A TYR 19 18 1_555 A GLY 34 A GLY 46 18 12_554 A VAL 35 A VAL 47 18 12_554 A THR 36 A THR 48 18 12_554 A GLY 43 A GLY 55 18 1_555 A PHE 44 A PHE 56 18 1_555 A GLY 45 A GLY 57 18 1_555 A HIS 46 A HIS 58 18 1_555 A PRO 63 A PRO 75 18 1_555 A GLU 67 A GLU 79 18 12_554 A VAL 69 A VAL 81 18 12_554 A ASP 88 A ASP 100 18 1_555 A GLY 89 A GLY 101 18 1_555 A HOH 311 E HOH 18 12_554 A HOH 319 E HOH 18 1_555 A HOH 336 E HOH 18 1_555 A HOH 337 E HOH 18 1_555 A HOH 339 E HOH 18 1_555 212 P 43 3 2