1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Maglio, O. Nastri, F. Pavone, V. Lombardi, A. DeGrado, W.F. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic C2 H4 O 44.053 ACETYL GROUP 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 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 H2 N 16.023 AMINO GROUP non-polymer C5 H9 N O2 115.130 y PROLINE 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 Proc.Natl.Acad.Sci.USA PNASA6 0040 0027-8424 100 3772 3777 10.1073/pnas.0730771100 12655072 Preorganization of molecular binding sites in designed diiron proteins 2003 US Proc.Natl.Acad.Sci.USA PNASA6 0040 0027-8424 97 6298 6305 10.1073/pnas.97.12.6298 Retrostructural Analysis of Metalloproteins. Application to the Design of a Minimal Model for Diiron Proteins 2000 UK CURR.OPIN.STRUCT.BIOL. COSBEF 0801 0959-440X 9 500 508 10.1016/S0959-440X(99)80071-2 Tertiary Templates for the Design of Diiron Protein 1999 US J.Am.Chem.Soc. JACSAT 0004 0002-7863 123 12749 12757 10.1021/ja010506x Toward the De Novo Design of a Catalytically Active Helix Bundle: a Substrate-Accessible Carboxylate-Bridged Dinuclear Metal Center 2001 GE Angew.Chem.Int.Ed.Engl. ACIEAY 0179 0570-0833 42 417 420 10.1002/anie.200390127 Sliding Helix and Change of Coordination Geometry in a Model di-Mn(II) Protein 2003 10.2210/pdb1nvo/pdb pdb_00001nvo 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 SINGLE WAVELENGTH M 1 1.0 5870.894 Homodimeric Alpha2 Four-Helix Bundle 2 syn polymer no yes (ACE)DYLRELLKLELQLIKQYREALEYVKLPVLAKILEDEEKHIEWLETILG(NH2) XDYLRELLKLELQLIKQYREALEYVKLPVLAKILEDEEKHIEWLETILGX A,B 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 database_2 pdbx_nmr_software pdbx_nmr_spectrometer pdbx_struct_assembly pdbx_struct_oper_list struct_conn struct_site repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2003-03-25 1 1 2008-04-29 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _pdbx_nmr_spectrometer.model _struct_conn.pdbx_leaving_atom_flag _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id 1EC5 is the crystal structure of DF1-di-Zn(II) derivative 1JMB is the crystal structure of a DF1 mutant (L13A-DF1) in the di-Mn(II) form (S.G. C 2 2 21) 1JM0 is a different crystalline form (S. G. P212121) of 1JMB 1LT1 is the crystal structure of L13G-DF1 in the di-Mn(II) form RCSB Y RCSB 2003-02-04 REL REL Chemically Synthesized sample This structure was determined using standard 2D homonuclear techniques structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy 40 14 2D TOCSY 2D NOESY DQF-COSY 4.0 Ambient 298 K Torsion Angle Dynamics, Simulated Annealing, Energy Restrained Minimization 1 closest to the average 1.0 mM protein concentration; 90% H2O, 10% DMSO 90% H2O, 10% DMSO Delaglio et al. processing NMRPipe Guentert et al. structure solution DYANA 1.5 Case et al. refinement Amber 7.0 600 Bruker AVANCE ACE 0 n 1 ACE 0 A ASP 1 n 2 ASP 1 A TYR 2 n 3 TYR 2 A LEU 3 n 4 LEU 3 A ARG 4 n 5 ARG 4 A GLU 5 n 6 GLU 5 A LEU 6 n 7 LEU 6 A LEU 7 n 8 LEU 7 A LYS 8 n 9 LYS 8 A LEU 9 n 10 LEU 9 A GLU 10 n 11 GLU 10 A LEU 11 n 12 LEU 11 A GLN 12 n 13 GLN 12 A LEU 13 n 14 LEU 13 A ILE 14 n 15 ILE 14 A LYS 15 n 16 LYS 15 A GLN 16 n 17 GLN 16 A TYR 17 n 18 TYR 17 A ARG 18 n 19 ARG 18 A GLU 19 n 20 GLU 19 A ALA 20 n 21 ALA 20 A LEU 21 n 22 LEU 21 A GLU 22 n 23 GLU 22 A TYR 23 n 24 TYR 23 A VAL 24 n 25 VAL 24 A LYS 25 n 26 LYS 25 A LEU 26 n 27 LEU 26 A PRO 27 n 28 PRO 27 A VAL 28 n 29 VAL 28 A LEU 29 n 30 LEU 29 A ALA 30 n 31 ALA 30 A LYS 31 n 32 LYS 31 A ILE 32 n 33 ILE 32 A LEU 33 n 34 LEU 33 A GLU 34 n 35 GLU 34 A ASP 35 n 36 ASP 35 A GLU 36 n 37 GLU 36 A GLU 37 n 38 GLU 37 A LYS 38 n 39 LYS 38 A HIS 39 n 40 HIS 39 A ILE 40 n 41 ILE 40 A GLU 41 n 42 GLU 41 A TRP 42 n 43 TRP 42 A LEU 43 n 44 LEU 43 A GLU 44 n 45 GLU 44 A THR 45 n 46 THR 45 A ILE 46 n 47 ILE 46 A LEU 47 n 48 LEU 47 A GLY 48 n 49 GLY 48 A NH2 49 n 50 NH2 49 A ACE 0 n 1 ACE 0 B ASP 1 n 2 ASP 1 B TYR 2 n 3 TYR 2 B LEU 3 n 4 LEU 3 B ARG 4 n 5 ARG 4 B GLU 5 n 6 GLU 5 B LEU 6 n 7 LEU 6 B LEU 7 n 8 LEU 7 B LYS 8 n 9 LYS 8 B LEU 9 n 10 LEU 9 B GLU 10 n 11 GLU 10 B LEU 11 n 12 LEU 11 B GLN 12 n 13 GLN 12 B LEU 13 n 14 LEU 13 B ILE 14 n 15 ILE 14 B LYS 15 n 16 LYS 15 B GLN 16 n 17 GLN 16 B TYR 17 n 18 TYR 17 B ARG 18 n 19 ARG 18 B GLU 19 n 20 GLU 19 B ALA 20 n 21 ALA 20 B LEU 21 n 22 LEU 21 B GLU 22 n 23 GLU 22 B TYR 23 n 24 TYR 23 B VAL 24 n 25 VAL 24 B LYS 25 n 26 LYS 25 B LEU 26 n 27 LEU 26 B PRO 27 n 28 PRO 27 B VAL 28 n 29 VAL 28 B LEU 29 n 30 LEU 29 B ALA 30 n 31 ALA 30 B LYS 31 n 32 LYS 31 B ILE 32 n 33 ILE 32 B LEU 33 n 34 LEU 33 B GLU 34 n 35 GLU 34 B ASP 35 n 36 ASP 35 B GLU 36 n 37 GLU 36 B GLU 37 n 38 GLU 37 B LYS 38 n 39 LYS 38 B HIS 39 n 40 HIS 39 B ILE 40 n 41 ILE 40 B GLU 41 n 42 GLU 41 B TRP 42 n 43 TRP 42 B LEU 43 n 44 LEU 43 B GLU 44 n 45 GLU 44 B THR 45 n 46 THR 45 B ILE 46 n 47 ILE 46 B LEU 47 n 48 LEU 47 B GLY 48 n 49 GLY 48 B NH2 49 n 50 NH2 49 B author_defined_assembly 2 dimeric 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 A TYR 2 0.088 SIDE CHAIN 1 B TYR 2 0.072 SIDE CHAIN 1 B TYR 17 0.087 SIDE CHAIN 2 B TYR 2 0.105 SIDE CHAIN 3 A TYR 2 0.182 SIDE CHAIN 3 A TYR 17 0.085 SIDE CHAIN 3 B TYR 2 0.066 SIDE CHAIN 4 A TYR 2 0.083 SIDE CHAIN 4 B TYR 2 0.071 SIDE CHAIN 4 B TYR 17 0.085 SIDE CHAIN 5 A TYR 17 0.071 SIDE CHAIN 6 B TYR 2 0.079 SIDE CHAIN 7 A TYR 17 0.128 SIDE CHAIN 8 B TYR 2 0.087 SIDE CHAIN 9 B TYR 2 0.090 SIDE CHAIN 10 A TYR 2 0.068 SIDE CHAIN 10 A TYR 23 0.078 SIDE CHAIN 11 A TYR 17 0.094 SIDE CHAIN 12 A TYR 17 0.144 SIDE CHAIN 12 B TYR 2 0.135 SIDE CHAIN 13 A TYR 2 0.105 SIDE CHAIN 13 A TYR 17 0.069 SIDE CHAIN 13 B ARG 4 0.087 SIDE CHAIN 13 B TYR 17 0.073 SIDE CHAIN 14 B TYR 17 0.065 SIDE CHAIN 1 -4.29 0.60 121.00 116.71 A A A CB CG CD2 TYR TYR TYR 2 2 2 N 6 -3.62 0.60 121.00 117.38 A A A CB CG CD2 TYR TYR TYR 2 2 2 N 8 -3.76 0.60 121.00 117.24 A A A CB CG CD2 TYR TYR TYR 2 2 2 N 1 A LEU 7 -131.33 -43.46 1 A GLU 44 -75.92 27.56 1 A THR 45 -148.30 -51.01 1 A LEU 47 72.53 -54.14 1 B LEU 7 -145.59 -61.79 2 A TYR 2 -19.10 -55.35 2 A LEU 6 -95.19 37.51 2 A LEU 7 -144.51 -57.83 2 A ILE 46 -26.25 -58.31 2 A LEU 47 -170.71 134.02 2 B TYR 2 -26.81 -69.76 2 B LEU 7 -151.39 -66.45 2 B GLU 44 -76.86 35.75 2 B THR 45 -150.22 -48.27 2 B ILE 46 36.21 66.22 3 A LEU 7 -130.99 -51.95 3 A ILE 46 35.67 67.55 3 A LEU 47 57.87 16.20 3 B GLU 5 -137.44 -50.24 4 A GLU 5 -102.59 -63.33 4 A LEU 6 -83.67 33.97 4 A LEU 7 -143.66 -55.47 4 B GLU 5 -102.28 -74.07 4 B LEU 47 64.63 -138.47 5 A LEU 7 -135.67 -47.78 5 A LYS 25 61.69 63.99 5 A THR 45 -152.71 -46.43 5 A LEU 47 62.87 79.80 5 B LEU 7 -133.60 -62.66 5 B GLU 44 -75.47 27.30 5 B THR 45 -150.16 -45.46 5 B ILE 46 39.80 49.20 6 A LEU 7 -160.58 -58.09 6 B GLU 5 -127.28 -69.46 6 B LEU 7 -140.20 -53.77 6 B LYS 25 62.40 71.11 6 B ILE 46 -27.28 111.03 7 A TYR 2 -20.01 -57.58 7 A GLU 5 -98.23 -66.13 7 B GLU 5 -112.65 -160.77 7 B LEU 7 -177.62 -59.59 7 B GLU 44 -77.79 36.94 7 B THR 45 -156.65 -49.11 7 B ILE 46 43.69 -136.55 8 A LEU 3 -164.12 66.61 8 A ARG 4 -153.89 -7.65 8 A LEU 7 -129.18 -51.95 8 B GLU 5 -125.73 -76.88 8 B LEU 6 -68.02 6.78 8 B LEU 7 -127.49 -56.31 8 B THR 45 -143.96 -46.28 9 A LEU 7 -160.76 -52.93 9 A PRO 27 -76.06 39.29 9 A GLU 44 -76.58 30.51 9 A THR 45 -154.59 -44.23 9 B GLU 5 -120.55 -69.39 9 B LEU 7 -122.95 -53.65 9 B LEU 21 -96.62 -65.06 9 B VAL 24 -88.69 -92.56 9 B LYS 25 173.38 26.85 9 B GLU 44 -81.93 35.36 9 B THR 45 -148.21 -47.08 9 B ILE 46 37.88 63.13 10 A TYR 2 -10.46 -53.38 10 A LEU 7 -136.00 -50.92 10 A GLU 44 -76.99 38.93 10 A THR 45 -162.86 -28.04 10 A ILE 46 -55.55 98.15 10 A LEU 47 65.68 164.27 10 B LEU 7 -104.02 -65.73 10 B GLU 44 -75.43 28.62 10 B THR 45 -151.08 -49.82 11 A TYR 2 -22.36 -49.38 11 A LEU 3 -130.39 -30.40 11 A LEU 7 -153.04 -70.36 11 B TYR 2 -26.90 -67.00 11 B LEU 7 -148.43 -62.20 11 B GLU 44 -71.26 26.60 11 B THR 45 -154.06 -45.09 12 A LEU 3 -88.95 40.42 12 A LEU 6 -69.51 2.83 12 A GLU 44 -75.80 22.02 12 A THR 45 -146.17 -54.15 12 A ILE 46 57.20 157.65 12 B GLU 5 -89.81 -71.11 12 B GLU 44 -78.42 29.29 12 B THR 45 -153.37 -42.29 13 A ILE 46 -43.59 101.64 13 A LEU 47 -166.13 -53.70 13 B LEU 7 -135.45 -63.15 13 B LYS 25 56.98 71.13 14 A LEU 7 -152.27 -58.04 14 A LEU 47 66.37 -70.08 14 B LEU 6 -84.92 38.30 14 B LEU 7 -153.92 -72.19 14 B GLU 44 -74.07 25.75 14 B THR 45 -147.90 -45.69 14 B LEU 47 -69.39 86.04 Solution structure of a four-helix bundle model, apo-DF1 1 N N 1 N N A LEU 7 A LEU 8 HELX_P A LYS 25 A LYS 26 1 1 19 A LEU 26 A LEU 27 HELX_P A GLU 44 A GLU 45 1 2 19 B ASP 1 B ASP 2 HELX_P B LEU 7 B LEU 8 1 3 7 B LEU 7 B LEU 8 HELX_P B TYR 23 B TYR 24 1 4 17 B LEU 26 B LEU 27 HELX_P B ILE 46 B ILE 47 1 5 21 covale 1.337 both A ACE 0 A C ACE 1 1_555 A ASP 1 A N ASP 2 1_555 covale 1.334 both A GLY 48 A C GLY 49 1_555 A NH2 49 A N NH2 50 1_555 covale 1.336 both B ACE 0 B C ACE 1 1_555 B ASP 1 B N ASP 2 1_555 covale 1.334 both B GLY 48 B C GLY 49 1_555 B NH2 49 B N NH2 50 1_555 UNKNOWN FUNCTION De Novo Protein Design, Alpha-Helical Bundle, Diiron Protein Model, UNKNOWN FUNCTION 1NVO PDB 1 1NVO 0 49 1NVO 0 49 1NVO A 1 1 50 0 49 1NVO 0 49 1NVO B 1 1 50 BINDING SITE FOR RESIDUE NH2 A 49 A NH2 49 Software 1 BINDING SITE FOR RESIDUE NH2 B 49 B NH2 49 Software 1 A GLY 48 A GLY 49 1 1_555 B GLY 48 B GLY 49 1 1_555