0.029091 0.000000 0.000000 0.000000 0.028423 0.000000 0.000000 0.000000 0.022730 0.00000 0.00000 0.00000 Cuypers, M.G. Mason, S.A. Blakeley, M.P. Mitchell, E.P. Haertlein, M. Forsyth, V.T. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 90.00 90.00 34.375 35.183 43.994 C3 H7 N O2 89.093 y ALANINE 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 C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking D3 O 1 22.042 trideuteriooxidanium perdeuterated oxonium non-polymer D 1 2.014 deuterium(1+) non-polymer D2 O 20.028 DEUTERATED WATER non-polymer Fe 3 55.845 FE (III) ION non-polymer C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE 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 GE Angew.Chem.Int.Ed.Engl. ACIEAY 0179 1521-3773 52 1022 10.1002/ANIE.201207071 23225503 Near-Atomic Resolution Neutron Crystallography on Perdeuterated Pyrococcus Furiosus Rubredoxin: Implication of Hydronium Ions and Protonation State Equilibria in Redox Changes. 2013 10.2210/pdb4ar4/pdb pdb_00004ar4 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 BORON CARBIDE BEAM DEFINING APERTURES 5ATM 3HE, CURVED 120X30 DEGREES INSTITUT LAUE LANGEVIN DETECTOR GROUP PYROLYTIC GRAPHITE (002) neutron 1 2.42 1.0 D19 ILL 2.42 NUCLEAR REACTOR ILL BEAMLINE D19 REDUCED STATE (FE II), HYDRONIUM IONS, CARBOXYLIC DEUTERONS 6031.728 Rubredoxin 1 man polymer 55.845 FE (III) ION 1 syn non-polymer 2.014 deuterium(1+) 2 syn non-polymer 22.042 trideuteriooxidanium 4 syn non-polymer 18.015 water 104 nat water Rd no no MAKWVCKICGYIYDEDAGDPDNGISPGTKFEELPDDWVCPICGAPKSEFEKLED MAKWVCKICGYIYDEDAGDPDNGISPGTKFEELPDDWVCPICGAPKSEFEKLED 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 ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 sample 1 54 rub, PF1282 186497 Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) 562 Escherichia coli pET28A PLASMID Biological sequence 1 1.46 15.08 NONE 6.2 pH 6.2 reflns chem_comp citation entity entity_name_com entity_src_gen pdbx_database_status pdbx_struct_assembly_prop pdbx_struct_conn_angle struct_conn struct_ref struct_site database_2 repository Initial release Database references Atomic model Atomic model Data collection Structure summary Data collection Database references Derived calculations Non-polymer description Other Source and taxonomy Structure summary Database references 1 0 2013-01-16 1 1 2013-03-06 1 2 2013-08-14 1 3 2017-03-22 1 4 2019-08-28 2 0 2021-06-09 2 1 2023-05-03 _reflns.pdbx_Rrim_I_all _reflns.pdbx_Rsym_value _reflns.pdbx_netI_over_sigmaI _chem_comp.formula _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _entity.pdbx_description _entity_name_com.name _entity_src_gen.gene_src_strain _entity_src_gen.pdbx_beg_seq_num _entity_src_gen.pdbx_end_seq_num _entity_src_gen.pdbx_gene_src_gene _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id _entity_src_gen.pdbx_gene_src_scientific_name _entity_src_gen.pdbx_host_org_scientific_name _entity_src_gen.pdbx_host_org_vector _entity_src_gen.pdbx_seq_type _pdbx_database_status.status_code_sf _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _database_2.pdbx_DOI _database_2.pdbx_database_accession RUBREDOXIN (METHIONINE MUTANT) FROM PYROCOCCUS FURIOSUS RUBREDOXIN (FORMYL METHIONINE MUTANT) FROM PYROCOCCUS FURIOSUS RUBREDOXIN (WILD TYPE) FROM PYROCOCCUS FURIOSUS RUBREDOXIN (OXIDIZED) RUBREDOXIN (REDUCED) X-RAY CRYSTAL STRUCTURE OF THE RUBREDOXIN MUTANT FROMPYROCOCCUS FURIOSUS NEUTRON CRYSTAL STRUCTURE OF THE RUBREDOXIN MUTANT FROMPYROCOCCUS FURIOSUS RUBREDOXIN VARIANT (PFRD-XC4) FOLDS WITHOUT IRON BACKBONE NMR STRUCTURE OF A MUTANT P. FURIOSUS RUBREDOXINUSING RESIDUAL DIPOLAR COUPLINGS NEUTRON CRYSTAL STRUCTURE OF THE WILD TYPE RUBREDOXIN FROMPYROCOCCUS FURIOSUS AT 1.5A RESOLUTION RUBREDOXIN (ZN-SUBSTITUTED) (NMR, 40 STRUCTURES) NEAR-ATOMIC RESOLUTION NEUTRON CRYSTALLOGRAPHY ON THE OXIDISED FORM PERDEUTERATED PYROCOCCUS FURIOSUS RUBREDOXIN. X-RAY CRYSTALLOGRAPHIC STRUCTURE OF THE OXIDISED FORM PERDEUTERATED PYROCOCCUS FURIOSUS RUBREDOXIN IN D2O AT 295K (IN QUARTZ CAPILLARY) TO 1.00 ANGSTROM RESOLUTION. X-RAY CRYSTALLOGRAPHIC STRUCTURE OF THE REDUCED FORM PERDEUTERATED PYROCOCCUS FURIOSUS RUBREDOXIN AT 295 K ( IN QUARTZ CAPILLARY) TO 0.92 ANGSTROMS RESOLUTION. PDBE Y PDBE 2012-04-20 REL REL 1 A O DOD 2034 6.64 1 A O DOD 2085 8.40 1 A O DOD 2088 7.11 1 A O DOD 2091 9.75 1 A O DOD 2096 6.21 1 A O DOD 2097 6.36 1 A O DOD 2098 A 11.81 1 A O DOD 2112 7.40 1 A O DOD 2120 7.16 1 A O DOD 2131 7.19 FE FE (III) ION D8U deuterium(1+) D3O trideuteriooxidanium DOD water M IN POSITION 0 FE 1054 2 FE FE 1054 A D8U 1055 3 D8U D8U 1055 A D8U 1056 3 D8U D8U 1056 A D3O 1057 4 D3O D3O 1057 A D3O 1058 4 D3O D3O 1058 A D3O 1059 4 D3O D3O 1059 A D3O 1060 4 D3O D3O 1060 A DOD 2004 5 DOD DOD 2004 A DOD 2005 5 DOD DOD 2005 A DOD 2006 5 DOD DOD 2006 A DOD 2007 5 DOD DOD 2007 A DOD 2009 5 DOD DOD 2009 A DOD 2010 5 DOD DOD 2010 A DOD 2011 5 DOD DOD 2011 A DOD 2012 5 DOD DOD 2012 A DOD 2013 5 DOD DOD 2013 A DOD 2014 5 DOD DOD 2014 A DOD 2015 5 DOD DOD 2015 A DOD 2016 5 DOD DOD 2016 A DOD 2017 5 DOD DOD 2017 A DOD 2018 5 DOD DOD 2018 A DOD 2020 5 DOD DOD 2020 A DOD 2021 5 DOD DOD 2021 A DOD 2022 5 DOD DOD 2022 A DOD 2023 5 DOD DOD 2023 A DOD 2024 5 DOD DOD 2024 A DOD 2026 5 DOD DOD 2026 A DOD 2027 5 DOD DOD 2027 A DOD 2028 5 DOD DOD 2028 A DOD 2029 5 DOD DOD 2029 A DOD 2030 5 DOD DOD 2030 A DOD 2031 5 DOD DOD 2031 A DOD 2032 5 DOD DOD 2032 A DOD 2033 5 DOD DOD 2033 A DOD 2034 5 DOD DOD 2034 A DOD 2035 5 DOD DOD 2035 A DOD 2036 5 DOD DOD 2036 A DOD 2037 5 DOD DOD 2037 A DOD 2038 5 DOD DOD 2038 A DOD 2039 5 DOD DOD 2039 A DOD 2040 5 DOD DOD 2040 A DOD 2041 5 DOD DOD 2041 A DOD 2042 5 DOD DOD 2042 A DOD 2043 5 DOD DOD 2043 A DOD 2044 5 DOD DOD 2044 A DOD 2045 5 DOD DOD 2045 A DOD 2046 5 DOD DOD 2046 A DOD 2047 5 DOD DOD 2047 A DOD 2048 5 DOD DOD 2048 A DOD 2049 5 DOD DOD 2049 A DOD 2050 5 DOD DOD 2050 A DOD 2051 5 DOD DOD 2051 A DOD 2052 5 DOD DOD 2052 A DOD 2053 5 DOD DOD 2053 A DOD 2054 5 DOD DOD 2054 A DOD 2055 5 DOD DOD 2055 A DOD 2056 5 DOD DOD 2056 A DOD 2057 5 DOD DOD 2057 A DOD 2058 5 DOD DOD 2058 A DOD 2060 5 DOD DOD 2060 A DOD 2063 5 DOD DOD 2063 A DOD 2064 5 DOD DOD 2064 A DOD 2065 5 DOD DOD 2065 A DOD 2066 5 DOD DOD 2066 A DOD 2067 5 DOD DOD 2067 A DOD 2069 5 DOD DOD 2069 A DOD 2070 5 DOD DOD 2070 A DOD 2073 5 DOD DOD 2073 A DOD 2074 5 DOD DOD 2074 A DOD 2075 5 DOD DOD 2075 A DOD 2076 5 DOD DOD 2076 A DOD 2077 5 DOD DOD 2077 A DOD 2080 5 DOD DOD 2080 A DOD 2082 5 DOD DOD 2082 A DOD 2083 5 DOD DOD 2083 A DOD 2085 5 DOD DOD 2085 A DOD 2086 5 DOD DOD 2086 A DOD 2087 5 DOD DOD 2087 A DOD 2088 5 DOD DOD 2088 A DOD 2089 5 DOD DOD 2089 A DOD 2090 5 DOD DOD 2090 A DOD 2091 5 DOD DOD 2091 A DOD 2092 5 DOD DOD 2092 A DOD 2095 5 DOD DOD 2095 A DOD 2096 5 DOD DOD 2096 A DOD 2097 5 DOD DOD 2097 A DOD 2098 5 DOD DOD 2098 A DOD 2099 5 DOD DOD 2099 A DOD 2101 5 DOD DOD 2101 A DOD 2105 5 DOD DOD 2105 A DOD 2109 5 DOD DOD 2109 A DOD 2110 5 DOD DOD 2110 A DOD 2111 5 DOD DOD 2111 A DOD 2112 5 DOD DOD 2112 A DOD 2114 5 DOD DOD 2114 A DOD 2117 5 DOD DOD 2117 A DOD 2118 5 DOD DOD 2118 A DOD 2119 5 DOD DOD 2119 A DOD 2120 5 DOD DOD 2120 A DOD 2121 5 DOD DOD 2121 A DOD 2122 5 DOD DOD 2122 A DOD 2123 5 DOD DOD 2123 A DOD 2124 5 DOD DOD 2124 A DOD 2125 5 DOD DOD 2125 A DOD 2126 5 DOD DOD 2126 A DOD 2127 5 DOD DOD 2127 A DOD 2128 5 DOD DOD 2128 A DOD 2129 5 DOD DOD 2129 A DOD 2130 5 DOD DOD 2130 A DOD 2131 5 DOD DOD 2131 A DOD 2132 5 DOD DOD 2132 A MET 0 n 1 MET 0 A ALA 1 n 2 ALA 1 A LYS 2 n 3 LYS 2 A TRP 3 n 4 TRP 3 A VAL 4 n 5 VAL 4 A CYS 5 n 6 CYS 5 A LYS 6 n 7 LYS 6 A ILE 7 n 8 ILE 7 A CYS 8 n 9 CYS 8 A GLY 9 n 10 GLY 9 A TYR 10 n 11 TYR 10 A ILE 11 n 12 ILE 11 A TYR 12 n 13 TYR 12 A ASP 13 n 14 ASP 13 A GLU 14 n 15 GLU 14 A ASP 15 n 16 ASP 15 A ALA 16 n 17 ALA 16 A GLY 17 n 18 GLY 17 A ASP 18 n 19 ASP 18 A PRO 19 n 20 PRO 19 A ASP 20 n 21 ASP 20 A ASN 21 n 22 ASN 21 A GLY 22 n 23 GLY 22 A ILE 23 n 24 ILE 23 A SER 24 n 25 SER 24 A PRO 25 n 26 PRO 25 A GLY 26 n 27 GLY 26 A THR 27 n 28 THR 27 A LYS 28 n 29 LYS 28 A PHE 29 n 30 PHE 29 A GLU 30 n 31 GLU 30 A GLU 31 n 32 GLU 31 A LEU 32 n 33 LEU 32 A PRO 33 n 34 PRO 33 A ASP 34 n 35 ASP 34 A ASP 35 n 36 ASP 35 A TRP 36 n 37 TRP 36 A VAL 37 n 38 VAL 37 A CYS 38 n 39 CYS 38 A PRO 39 n 40 PRO 39 A ILE 40 n 41 ILE 40 A CYS 41 n 42 CYS 41 A GLY 42 n 43 GLY 42 A ALA 43 n 44 ALA 43 A PRO 44 n 45 PRO 44 A LYS 45 n 46 LYS 45 A SER 46 n 47 SER 46 A GLU 47 n 48 GLU 47 A PHE 48 n 49 PHE 48 A GLU 49 n 50 GLU 49 A LYS 50 n 51 LYS 50 A LEU 51 n 52 LEU 51 A GLU 52 n 53 GLU 52 A ASP 53 n 54 ASP 53 A author_and_software_defined_assembly PISA 1 monomeric 9090 40 6170 A CYS 5 A SG CYS 6 1_555 A FE 1054 B FE FE 1_555 A CYS 8 A SG CYS 9 1_555 112.8 A CYS 5 A SG CYS 6 1_555 A FE 1054 B FE FE 1_555 A CYS 38 A SG CYS 39 1_555 115.4 A CYS 8 A SG CYS 9 1_555 A FE 1054 B FE FE 1_555 A CYS 38 A SG CYS 39 1_555 102.0 A CYS 5 A SG CYS 6 1_555 A FE 1054 B FE FE 1_555 A CYS 41 A SG CYS 42 1_555 108.6 A CYS 8 A SG CYS 9 1_555 A FE 1054 B FE FE 1_555 A CYS 41 A SG CYS 42 1_555 108.4 A CYS 38 A SG CYS 39 1_555 A FE 1054 B FE FE 1_555 A CYS 41 A SG CYS 42 1_555 109.3 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 TYR 12 A N TYR 13 A O TRP 3 A O TRP 4 A N VAL 4 A N VAL 5 A O GLU 49 A O GLU 50 1 A A OE2 O GLU DOD 52 2124 2.16 A 1 A ASP 18 -154.96 66.51 1 A ASP 18 -154.96 65.82 1 A GLU 52 B -175.96 142.66 11.52 -0.5527 0.0000 0.0000 0.1200 0.0000 0.4326 THE HIGH HYGROSCOPICITY OF SODIUM DITHIONITE ADDED TO THE CRYSTAL FOR FE REDUCTION LEADS TO THE INTRODUCTION OF EXCHANGEABLE H AND D ATOM POSITIONS DESPITE EFFORTS TO AVOID THE PRESENCE OF HYDROGEN ATOMS. 0.2264 0.1861 0.1881 1.381 27.465 505 10500 4.8 91.97 0.27 1 0 22.14 0.60 0.90 ML FLAT BULK SOLVENT MODEL 40.158 0.600 1.381 27.465 104 530 5 0 421 0.005 1120 0.865 1873 13.090 257 0.065 64 0.006 186 0.4166 0.3596 1.5202 123 2306 87.00 0.2568 0.2203 1.7401 114 2486 92.00 0.2071 0.1485 2.1922 139 2538 94.00 0.1935 0.1656 27.4702 129 2665 94.00 11.4 1.38 27.42 4AR4 10521 1.3 0.07 0.084 1 12.1 3.7 93.1 refinement PHENIX data reduction RETREAT data scaling RETREAT Neutron crystallographic structure of the reduced form perdeuterated Pyrococcus furiosus rubredoxin to 1.38 Angstrom resolution. 1 N N 2 N N 3 N N 3 N N 4 N N 4 N N 4 N N 4 N N 5 N N A PRO 19 A PRO 20 HELX_P A GLY 22 A GLY 23 5 1 4 A LYS 28 A LYS 29 HELX_P A LEU 32 A LEU 33 5 2 5 metalc 2.194 A CYS 5 A SG CYS 6 1_555 A FE 1054 B FE FE 1_555 metalc 2.452 A CYS 8 A SG CYS 9 1_555 A FE 1054 B FE FE 1_555 metalc 2.280 A CYS 38 A SG CYS 39 1_555 A FE 1054 B FE FE 1_555 metalc 2.251 A CYS 41 A SG CYS 42 1_555 A FE 1054 B FE FE 1_555 ELECTRON TRANSPORT ELECTRON TRANSPORT, PERDEUTERATED, MONOCHROMATIC NEUTRON CRYSTALLOGRAPHY, HYDRONIUM, PROTONATION STATE RUBR_PYRFU UNP 1 1 P24297 MAKWVCKICGYIYDEDAGDPDNGISPGTKFEELPDDWVCPICGAPKSEFEKLED 1 54 4AR4 0 53 P24297 A 1 1 54 3 anti-parallel anti-parallel A ILE 11 A ILE 12 A ASP 13 A ASP 14 A LYS 2 A LYS 3 A CYS 5 A CYS 6 A PHE 48 A PHE 49 A LYS 50 A LYS 51 BINDING SITE FOR RESIDUE FE A 1054 A FE 1054 Software 4 BINDING SITE FOR RESIDUE D3O A 1057 A D3O 1057 Software 3 BINDING SITE FOR RESIDUE D3O A 1058 A D3O 1058 Software 2 BINDING SITE FOR RESIDUE D3O A 1060 A D3O 1060 Software 2 A CYS 5 A CYS 6 4 1_555 A CYS 8 A CYS 9 4 1_555 A CYS 38 A CYS 39 4 1_555 A CYS 41 A CYS 42 4 1_555 A ALA 1 A ALA 2 3 1_555 A LYS 2 A LYS 3 3 1_555 A LEU 51 A LEU 52 3 1_555 A SER 24 A SER 25 2 1_555 A PRO 25 A PRO 26 2 1_555 A ALA 16 A ALA 17 2 1_555 A DOD 2036 I DOD 2 1_555 19 P 21 21 21