0.033333 0.000000 0.000000 0.000000 0.033333 0.000000 0.000000 0.000000 0.004566 0.00000 0.00000 0.00000 Rivera, M. White, S.P. Zhang, X. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 30.000 30.000 219.000 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 C34 H32 Fe N4 O4 616.487 PROTOPORPHYRIN IX CONTAINING FE HEME non-polymer 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 Biochemistry BICHAW 0033 0006-2960 35 16378 16390 10.1021/bi961895o 8973214 13C NMR spectroscopic and X-ray crystallographic study of the role played by mitochondrial cytochrome b5 heme propionates in the electrostatic binding to cytochrome c. 1996 10.2210/pdb1b5m/pdb pdb_00001b5m 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 298 1 AREA DETECTOR 1996-04-18 SIEMENS DIAMOND C(111) M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE RIGAKU FROM RAT OUTER MITOCHONDRIAL MEMBRANE 9605.570 CYTOCHROME B5 WATER SOLUBLE DOMAIN 1 man polymer 616.487 PROTOPORPHYRIN IX CONTAINING FE 1 syn non-polymer no no AVTYYRLEEVAKRNTAEETWMVIHGRVYDITRFLSEHPGGEEVLLEQAGADATESFEDVGHSPDAREMLKQYYIGDVHPN DLKP AVTYYRLEEVAKRNTAEETWMVIHGRVYDITRFLSEHPGGEEVLLEQAGADATESFEDVGHSPDAREMLKQYYIGDVHPN DLKP 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 Norway rat Rattus Escherichia Escherichia coli sample HEPATOCYTE BL21 OUTER MITOCHONDRIAL MEMBRANE 10116 LIVER MITOCHONDRION Rattus norvegicus PERIPLASMIC SPACE 469008 Escherichia coli BL21(DE3) BL21 (DE3) PLASMID PET 11A 1 2.56 52.02 vapor diffusion with slow evaporation 6.5 CRYSTALS WERE OBTAINED BY VAPOR DIFFUSION TOGETHER WITH SLOW EVAPORATION USING 20% PEG 8000 IN 0.1M SODIUM CACODYLATE (PH = 6.5 WITH 0.2 M MAGNESIUM ACETATE., vapor diffusion with slow evaporation database_2 pdbx_database_status pdbx_initial_refinement_model struct_conn struct_site repository Initial release Version format compliance Version format compliance Database references Derived calculations Other Refinement description 1 0 1997-03-12 1 1 2008-03-24 1 2 2011-07-13 1 3 2023-08-02 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.process_site _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_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Y BNL 1996-11-07 REL HEM PROTOPORPHYRIN IX CONTAINING FE 3B5C PDB ENTRY 3B5C PDB experimental model HEM 201 2 HEM HEM 201 A ALA 3 n 1 ALA 3 A VAL 4 n 2 VAL 4 A THR 5 n 3 THR 5 A TYR 6 n 4 TYR 6 A TYR 7 n 5 TYR 7 A ARG 8 n 6 ARG 8 A LEU 9 n 7 LEU 9 A GLU 10 n 8 GLU 10 A GLU 11 n 9 GLU 11 A VAL 12 n 10 VAL 12 A ALA 13 n 11 ALA 13 A LYS 14 n 12 LYS 14 A ARG 15 n 13 ARG 15 A ASN 16 n 14 ASN 16 A THR 17 n 15 THR 17 A ALA 18 n 16 ALA 18 A GLU 19 n 17 GLU 19 A GLU 20 n 18 GLU 20 A THR 21 n 19 THR 21 A TRP 22 n 20 TRP 22 A MET 23 n 21 MET 23 A VAL 24 n 22 VAL 24 A ILE 25 n 23 ILE 25 A HIS 26 n 24 HIS 26 A GLY 27 n 25 GLY 27 A ARG 28 n 26 ARG 28 A VAL 29 n 27 VAL 29 A TYR 30 n 28 TYR 30 A ASP 31 n 29 ASP 31 A ILE 32 n 30 ILE 32 A THR 33 n 31 THR 33 A ARG 34 n 32 ARG 34 A PHE 35 n 33 PHE 35 A LEU 36 n 34 LEU 36 A SER 37 n 35 SER 37 A GLU 38 n 36 GLU 38 A HIS 39 n 37 HIS 39 A PRO 40 n 38 PRO 40 A GLY 41 n 39 GLY 41 A GLY 42 n 40 GLY 42 A GLU 43 n 41 GLU 43 A GLU 44 n 42 GLU 44 A VAL 45 n 43 VAL 45 A LEU 46 n 44 LEU 46 A LEU 47 n 45 LEU 47 A GLU 48 n 46 GLU 48 A GLN 49 n 47 GLN 49 A ALA 50 n 48 ALA 50 A GLY 51 n 49 GLY 51 A ALA 52 n 50 ALA 52 A ASP 53 n 51 ASP 53 A ALA 54 n 52 ALA 54 A THR 55 n 53 THR 55 A GLU 56 n 54 GLU 56 A SER 57 n 55 SER 57 A PHE 58 n 56 PHE 58 A GLU 59 n 57 GLU 59 A ASP 60 n 58 ASP 60 A VAL 61 n 59 VAL 61 A GLY 62 n 60 GLY 62 A HIS 63 n 61 HIS 63 A SER 64 n 62 SER 64 A PRO 65 n 63 PRO 65 A ASP 66 n 64 ASP 66 A ALA 67 n 65 ALA 67 A ARG 68 n 66 ARG 68 A GLU 69 n 67 GLU 69 A MET 70 n 68 MET 70 A LEU 71 n 69 LEU 71 A LYS 72 n 70 LYS 72 A GLN 73 n 71 GLN 73 A TYR 74 n 72 TYR 74 A TYR 75 n 73 TYR 75 A ILE 76 n 74 ILE 76 A GLY 77 n 75 GLY 77 A ASP 78 n 76 ASP 78 A VAL 79 n 77 VAL 79 A HIS 80 n 78 HIS 80 A PRO 81 n 79 PRO 81 A ASN 82 n 80 ASN 82 A ASP 83 n 81 ASP 83 A LEU 84 n 82 LEU 84 A LYS 85 n 83 LYS 85 A PRO 86 n 84 PRO 86 A 0.2200000 author_defined_assembly 1 monomeric A HIS 39 A NE2 HIS 37 1_555 A HEM 201 B FE HEM 1_555 A HEM 201 B NA HEM 1_555 85.7 A HIS 39 A NE2 HIS 37 1_555 A HEM 201 B FE HEM 1_555 A HEM 201 B NB HEM 1_555 98.9 A HEM 201 B NA HEM 1_555 A HEM 201 B FE HEM 1_555 A HEM 201 B NB HEM 1_555 88.6 A HIS 39 A NE2 HIS 37 1_555 A HEM 201 B FE HEM 1_555 A HEM 201 B NC HEM 1_555 99.1 A HEM 201 B NA HEM 1_555 A HEM 201 B FE HEM 1_555 A HEM 201 B NC HEM 1_555 175.2 A HEM 201 B NB HEM 1_555 A HEM 201 B FE HEM 1_555 A HEM 201 B NC HEM 1_555 91.2 A HIS 39 A NE2 HIS 37 1_555 A HEM 201 B FE HEM 1_555 A HEM 201 B ND HEM 1_555 90.9 A HEM 201 B NA HEM 1_555 A HEM 201 B FE HEM 1_555 A HEM 201 B ND HEM 1_555 89.6 A HEM 201 B NB HEM 1_555 A HEM 201 B FE HEM 1_555 A HEM 201 B ND HEM 1_555 169.9 A HEM 201 B NC HEM 1_555 A HEM 201 B FE HEM 1_555 A HEM 201 B ND HEM 1_555 89.7 A HIS 39 A NE2 HIS 37 1_555 A HEM 201 B FE HEM 1_555 A HIS 63 A NE2 HIS 61 1_555 166.3 A HEM 201 B NA HEM 1_555 A HEM 201 B FE HEM 1_555 A HIS 63 A NE2 HIS 61 1_555 98.0 A HEM 201 B NB HEM 1_555 A HEM 201 B FE HEM 1_555 A HIS 63 A NE2 HIS 61 1_555 94.4 A HEM 201 B NC HEM 1_555 A HEM 201 B FE HEM 1_555 A HIS 63 A NE2 HIS 61 1_555 77.2 A HEM 201 B ND HEM 1_555 A HEM 201 B FE HEM 1_555 A HIS 63 A NE2 HIS 61 1_555 76.0 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 O MET 23 A O MET 21 A N TYR 30 A N TYR 28 A O VAL 29 A O VAL 27 A N GLY 77 A N GLY 75 1 A CA SER 57 PLANAR 1 3.81 0.50 120.30 124.11 A A A NE CZ NH1 ARG ARG ARG 15 15 15 N 1 3.48 0.50 120.30 123.78 A A A NE CZ NH1 ARG ARG ARG 28 28 28 N 1 -5.96 0.90 118.30 112.34 A A A CB CG OD2 ASP ASP ASP 31 31 31 N 1 12.80 1.90 110.10 122.90 A A A CB CA C SER SER SER 57 57 57 N 1 -5.56 0.90 118.30 112.74 A A A CB CG OD2 ASP ASP ASP 60 60 60 N 1 -5.93 0.90 118.30 112.37 A A A CB CG OD2 ASP ASP ASP 66 66 66 N 1 -4.00 0.60 121.00 117.00 A A A CB CG CD2 TYR TYR TYR 75 75 75 N 1 8.40 0.90 118.30 126.70 A A A CB CG OD1 ASP ASP ASP 83 83 83 N 1 -7.21 0.90 118.30 111.09 A A A CB CG OD2 ASP ASP ASP 83 83 83 N 1 -44.51 2.10 128.40 83.89 A A A C N CD LYS PRO PRO 85 86 86 Y 1 A A CD OE2 GLU GLU 19 19 0.067 0.011 1.252 1.319 N 1 A A CD OE2 GLU GLU 20 20 0.072 0.011 1.252 1.324 N 1 A A CD OE2 GLU GLU 43 43 0.071 0.011 1.252 1.323 N 1 A A CD OE2 GLU GLU 44 44 0.096 0.011 1.252 1.348 N 1 A A CD OE1 GLU GLU 59 59 0.070 0.011 1.252 1.322 N 1 A A CD OE2 GLU GLU 69 69 0.074 0.011 1.252 1.326 N 1 A ARG 15 -89.12 44.97 1 A THR 33 -29.56 -59.24 1 A LEU 36 -21.77 -51.53 1 A HIS 39 -51.99 106.06 0.2200000 2.7 20.0 3123 3123 3123 96. 1 TNT 0.0 MOLECULAR REPLACEMENT PDB ENTRY 3B5C TNT BSOL 99.7 0.79 2.7 20.0 0 719 43 0 676 0.016 744 0.8 2.9 1003 1.3 20 412 0. 0 0.007 23 2.0 0.012 104 5. 4.99 692 2. 0.023 25 10.0 36. 2.7 20.0 1B5M 3123 0.0 0.0490000 1 1.5 2.5 96. 2.7 3.05 1.0 0.0880000 4. 85. model building MRCHK refinement TNT 5E data reduction FRAMBO data reduction SADIE data scaling SAINT phasing MRCHK RAT OUTER MITOCHONDRIAL MEMBRANE CYTOCHROME B5 1 N N 2 N N A LEU 9 A LEU 7 HELX_P A LYS 14 A LYS 12 1 1 6 A GLU 44 A GLU 42 HELX_P A GLN 49 A GLN 47 1 2 6 A THR 55 A THR 53 HELX_P A VAL 61 A VAL 59 1 3 7 A PRO 65 A PRO 63 HELX_P A GLN 73 A GLN 71 1 4 9 metalc 1.918 A HIS 39 A NE2 HIS 37 1_555 A HEM 201 B FE HEM 1_555 metalc 1.820 A HIS 63 A NE2 HIS 61 1_555 A HEM 201 B FE HEM 1_555 ELECTRON TRANSPORT CYTOCHROME, ELECTRON TRANSPORT, HEME CYM5_RAT UNP 1 1 P04166 MATPEASGSGRNGQGSDPAVTYYRLEEVAKRNTAEETWMVIHGRVYDITRFLSEHPGGEEVLLEQAGADATESFEDVGHS PDAREMLKQYYIGDVHPNDLKPKDGDKDPSKNNSCQSSWAYWIVPIVGAILIGFLYRHFWADSKSS 19 102 1B5M 3 86 P04166 A 1 1 84 3 anti-parallel anti-parallel A TRP 22 A TRP 20 A ILE 25 A ILE 23 A ARG 28 A ARG 26 A ASP 31 A ASP 29 A TYR 75 A TYR 73 A ASP 78 A ASP 76 BINDING SITE FOR RESIDUE HEM A 201 A HEM 201 Software 16 A PHE 35 A PHE 33 16 1_555 A HIS 39 A HIS 37 16 1_555 A PRO 40 A PRO 38 16 1_555 A GLY 41 A GLY 39 16 1_555 A GLU 44 A GLU 42 16 5_355 A LEU 46 A LEU 44 16 1_555 A GLN 49 A GLN 47 16 1_555 A ALA 54 A ALA 52 16 1_555 A SER 57 A SER 55 16 1_555 A PHE 58 A PHE 56 16 1_555 A VAL 61 A VAL 59 16 1_555 A HIS 63 A HIS 61 16 1_555 A SER 64 A SER 62 16 1_555 A ALA 67 A ALA 65 16 1_555 A ARG 68 A ARG 66 16 5_345 A LEU 71 A LEU 69 16 1_555 96 P 43 21 2