HEADER TRANSFERASE 07-FEB-23 8G3H TITLE STRUCTURE OF COBALAMIN-DEPENDENT METHIONINE SYNTHASE (METH) IN A TITLE 2 RESTING STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHIONINE SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 5-METHYLTETRAHYDROFOLATE--HOMOCYSTEINE METHYLTRANSFERASE; COMPND 5 EC: 2.1.1.13; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS FILIFORMIS; SOURCE 3 ORGANISM_TAXID: 276; SOURCE 4 GENE: THFILI_06775; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET-28C+ KEYWDS METHYLTRANSFERASE, TRANSFERASE, AMINO-ACID BIOSYNTHESIS, METHIONINE KEYWDS 2 BIOSYNTHESIS EXPDTA ELECTRON MICROSCOPY AUTHOR M.B.WATKINS,N.ANDO REVDAT 2 19-JUN-24 8G3H 1 REMARK REVDAT 1 28-JUN-23 8G3H 0 JRNL AUTH M.B.WATKINS,H.WANG,A.BURNIM,N.ANDO JRNL TITL CONFORMATIONAL SWITCHING AND FLEXIBILITY IN JRNL TITL 2 COBALAMIN-DEPENDENT METHIONINE SYNTHASE STUDIED BY JRNL TITL 3 SMALL-ANGLE X-RAY SCATTERING AND CRYOELECTRON MICROSCOPY. JRNL REF PROC.NATL.ACAD.SCI.USA V. 120 31120 2023 JRNL REFN ESSN 1091-6490 JRNL PMID 37339208 JRNL DOI 10.1073/PNAS.2302531120 REMARK 2 REMARK 2 RESOLUTION. 3.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, LEGINON, CRYOSPARC, UCSF REMARK 3 CHIMERA, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC, ISOLDE, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : INITIAL MODEL USED WAS THE 3 N-TERMINAL REMARK 3 DOMAINS OF ALPHAFOLD DATABASE MODEL A0A1Q9SZ17. EACH DOMAIN WAS REMARK 3 FIT INDIVIDUALLY BY RIGID-BODY FITTING IN CHIMERA. THE COBALAMIN REMARK 3 LIGAND WAS INITIALLY FIT BY ALIGNMENT OF THE 1BMT CRYSTAL REMARK 3 STRUCTURE TO THE APPROPRIATE BINDING REGION. REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 3.600 REMARK 3 NUMBER OF PARTICLES : 257706 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8G3H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1000272144. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : 2D ARRAY REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : COBALAMIN-DEPENDENT METHIONINE REMARK 245 SYNTHASE HOLOPROTEIN REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.26 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.60 REMARK 245 SAMPLE DETAILS : COBALAMIN-DEPENDENT METHIONINE REMARK 245 SYNTHASE (METH) IN COMPLEX WITH B12 AND ZINC REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 12768 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 6500.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 81000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 VAL A 2 REMARK 465 GLU A 3 REMARK 465 VAL A 4 REMARK 465 HIS A 5 REMARK 465 THR A 6 REMARK 465 CYS A 7 REMARK 465 SER A 8 REMARK 465 PRO A 9 REMARK 465 GLY A 10 REMARK 465 CYS A 11 REMARK 465 ARG A 12 REMARK 465 HIS A 13 REMARK 465 HIS A 14 REMARK 465 LEU A 15 REMARK 465 GLY A 16 REMARK 465 GLY A 17 REMARK 465 ALA A 18 REMARK 465 GLY A 19 REMARK 465 TRP A 20 REMARK 465 GLY A 21 REMARK 465 ASP A 22 REMARK 465 ALA A 23 REMARK 465 PRO A 24 REMARK 465 LEU A 25 REMARK 465 LEU A 26 REMARK 465 ARG A 27 REMARK 465 LEU A 28 REMARK 465 GLY A 29 REMARK 465 TYR A 30 REMARK 465 ASN A 31 REMARK 465 LYS A 32 REMARK 465 GLU A 33 REMARK 465 ALA A 34 REMARK 465 ARG A 35 REMARK 465 ALA A 36 REMARK 465 LEU A 878 REMARK 465 ARG A 879 REMARK 465 ARG A 880 REMARK 465 ALA A 881 REMARK 465 ARG A 882 REMARK 465 THR A 883 REMARK 465 THR A 884 REMARK 465 ARG A 885 REMARK 465 LYS A 886 REMARK 465 GLU A 887 REMARK 465 ALA A 888 REMARK 465 PRO A 889 REMARK 465 ALA A 890 REMARK 465 PRO A 891 REMARK 465 ARG A 892 REMARK 465 SER A 893 REMARK 465 LYS A 894 REMARK 465 PRO A 895 REMARK 465 VAL A 896 REMARK 465 SER A 897 REMARK 465 PRO A 898 REMARK 465 ALA A 899 REMARK 465 PRO A 900 REMARK 465 ASP A 901 REMARK 465 LEU A 902 REMARK 465 PRO A 903 REMARK 465 ARG A 904 REMARK 465 PRO A 905 REMARK 465 PRO A 906 REMARK 465 PHE A 907 REMARK 465 PHE A 908 REMARK 465 GLY A 909 REMARK 465 VAL A 910 REMARK 465 ARG A 911 REMARK 465 VAL A 912 REMARK 465 GLU A 913 REMARK 465 GLU A 914 REMARK 465 GLY A 915 REMARK 465 LEU A 916 REMARK 465 ASP A 917 REMARK 465 LEU A 918 REMARK 465 ALA A 919 REMARK 465 THR A 920 REMARK 465 ILE A 921 REMARK 465 ALA A 922 REMARK 465 HIS A 923 REMARK 465 TYR A 924 REMARK 465 VAL A 925 REMARK 465 ASN A 926 REMARK 465 ARG A 927 REMARK 465 LEU A 928 REMARK 465 ALA A 929 REMARK 465 LEU A 930 REMARK 465 TYR A 931 REMARK 465 ARG A 932 REMARK 465 GLY A 933 REMARK 465 GLN A 934 REMARK 465 TRP A 935 REMARK 465 GLY A 936 REMARK 465 PHE A 937 REMARK 465 SER A 938 REMARK 465 ARG A 939 REMARK 465 GLY A 940 REMARK 465 GLY A 941 REMARK 465 LEU A 942 REMARK 465 SER A 943 REMARK 465 ARG A 944 REMARK 465 GLU A 945 REMARK 465 GLU A 946 REMARK 465 TRP A 947 REMARK 465 GLU A 948 REMARK 465 ALA A 949 REMARK 465 TYR A 950 REMARK 465 VAL A 951 REMARK 465 LYS A 952 REMARK 465 ARG A 953 REMARK 465 GLU A 954 REMARK 465 ALA A 955 REMARK 465 ASP A 956 REMARK 465 PRO A 957 REMARK 465 VAL A 958 REMARK 465 PHE A 959 REMARK 465 ARG A 960 REMARK 465 ARG A 961 REMARK 465 LEU A 962 REMARK 465 LEU A 963 REMARK 465 ALA A 964 REMARK 465 GLU A 965 REMARK 465 ALA A 966 REMARK 465 MET A 967 REMARK 465 ALA A 968 REMARK 465 GLU A 969 REMARK 465 GLY A 970 REMARK 465 TRP A 971 REMARK 465 LEU A 972 REMARK 465 ARG A 973 REMARK 465 PRO A 974 REMARK 465 ARG A 975 REMARK 465 VAL A 976 REMARK 465 LEU A 977 REMARK 465 TYR A 978 REMARK 465 GLY A 979 REMARK 465 PHE A 980 REMARK 465 PHE A 981 REMARK 465 PRO A 982 REMARK 465 VAL A 983 REMARK 465 ALA A 984 REMARK 465 ARG A 985 REMARK 465 GLU A 986 REMARK 465 GLY A 987 REMARK 465 GLU A 988 REMARK 465 GLU A 989 REMARK 465 LEU A 990 REMARK 465 TRP A 991 REMARK 465 VAL A 992 REMARK 465 TYR A 993 REMARK 465 SER A 994 REMARK 465 PRO A 995 REMARK 465 GLU A 996 REMARK 465 GLY A 997 REMARK 465 GLU A 998 REMARK 465 LEU A 999 REMARK 465 LEU A 1000 REMARK 465 GLU A 1001 REMARK 465 LYS A 1002 REMARK 465 LEU A 1003 REMARK 465 ARG A 1004 REMARK 465 PHE A 1005 REMARK 465 PRO A 1006 REMARK 465 ARG A 1007 REMARK 465 GLN A 1008 REMARK 465 ARG A 1009 REMARK 465 GLY A 1010 REMARK 465 GLY A 1011 REMARK 465 GLY A 1012 REMARK 465 ILE A 1013 REMARK 465 SER A 1014 REMARK 465 LEU A 1015 REMARK 465 VAL A 1016 REMARK 465 ASP A 1017 REMARK 465 TYR A 1018 REMARK 465 PHE A 1019 REMARK 465 ARG A 1020 REMARK 465 PRO A 1021 REMARK 465 ARG A 1022 REMARK 465 PHE A 1023 REMARK 465 ALA A 1024 REMARK 465 GLU A 1025 REMARK 465 PRO A 1026 REMARK 465 LEU A 1027 REMARK 465 SER A 1028 REMARK 465 ASP A 1029 REMARK 465 GLU A 1030 REMARK 465 ALA A 1031 REMARK 465 ASP A 1032 REMARK 465 TRP A 1033 REMARK 465 LEU A 1034 REMARK 465 PRO A 1035 REMARK 465 GLY A 1036 REMARK 465 TYR A 1037 REMARK 465 GLU A 1038 REMARK 465 GLU A 1039 REMARK 465 GLY A 1040 REMARK 465 ALA A 1041 REMARK 465 ARG A 1042 REMARK 465 ASP A 1043 REMARK 465 VAL A 1044 REMARK 465 LEU A 1045 REMARK 465 GLY A 1046 REMARK 465 VAL A 1047 REMARK 465 GLN A 1048 REMARK 465 LEU A 1049 REMARK 465 VAL A 1050 REMARK 465 THR A 1051 REMARK 465 MET A 1052 REMARK 465 GLY A 1053 REMARK 465 GLU A 1054 REMARK 465 GLU A 1055 REMARK 465 PRO A 1056 REMARK 465 LYS A 1057 REMARK 465 ARG A 1058 REMARK 465 LYS A 1059 REMARK 465 ALA A 1060 REMARK 465 GLU A 1061 REMARK 465 ALA A 1062 REMARK 465 LEU A 1063 REMARK 465 TYR A 1064 REMARK 465 ARG A 1065 REMARK 465 GLU A 1066 REMARK 465 GLY A 1067 REMARK 465 ARG A 1068 REMARK 465 TYR A 1069 REMARK 465 GLN A 1070 REMARK 465 ASP A 1071 REMARK 465 TYR A 1072 REMARK 465 LEU A 1073 REMARK 465 PHE A 1074 REMARK 465 VAL A 1075 REMARK 465 HIS A 1076 REMARK 465 GLY A 1077 REMARK 465 PHE A 1078 REMARK 465 ALA A 1079 REMARK 465 VAL A 1080 REMARK 465 GLU A 1081 REMARK 465 MET A 1082 REMARK 465 THR A 1083 REMARK 465 GLU A 1084 REMARK 465 ALA A 1085 REMARK 465 LEU A 1086 REMARK 465 ALA A 1087 REMARK 465 GLU A 1088 REMARK 465 TYR A 1089 REMARK 465 TRP A 1090 REMARK 465 HIS A 1091 REMARK 465 LYS A 1092 REMARK 465 ARG A 1093 REMARK 465 MET A 1094 REMARK 465 ARG A 1095 REMARK 465 GLN A 1096 REMARK 465 MET A 1097 REMARK 465 TRP A 1098 REMARK 465 GLY A 1099 REMARK 465 ILE A 1100 REMARK 465 ALA A 1101 REMARK 465 GLY A 1102 REMARK 465 GLN A 1103 REMARK 465 ASP A 1104 REMARK 465 ALA A 1105 REMARK 465 PRO A 1106 REMARK 465 GLU A 1107 REMARK 465 ILE A 1108 REMARK 465 ARG A 1109 REMARK 465 ARG A 1110 REMARK 465 LEU A 1111 REMARK 465 PHE A 1112 REMARK 465 GLN A 1113 REMARK 465 GLN A 1114 REMARK 465 GLU A 1115 REMARK 465 TYR A 1116 REMARK 465 ARG A 1117 REMARK 465 GLY A 1118 REMARK 465 ALA A 1119 REMARK 465 ARG A 1120 REMARK 465 TYR A 1121 REMARK 465 SER A 1122 REMARK 465 PHE A 1123 REMARK 465 GLY A 1124 REMARK 465 TYR A 1125 REMARK 465 PRO A 1126 REMARK 465 ALA A 1127 REMARK 465 CYS A 1128 REMARK 465 PRO A 1129 REMARK 465 ASP A 1130 REMARK 465 LEU A 1131 REMARK 465 ALA A 1132 REMARK 465 ASP A 1133 REMARK 465 GLN A 1134 REMARK 465 ALA A 1135 REMARK 465 LYS A 1136 REMARK 465 LEU A 1137 REMARK 465 ASP A 1138 REMARK 465 ARG A 1139 REMARK 465 LEU A 1140 REMARK 465 MET A 1141 REMARK 465 ASP A 1142 REMARK 465 PHE A 1143 REMARK 465 SER A 1144 REMARK 465 ARG A 1145 REMARK 465 ILE A 1146 REMARK 465 GLY A 1147 REMARK 465 VAL A 1148 REMARK 465 ARG A 1149 REMARK 465 LEU A 1150 REMARK 465 THR A 1151 REMARK 465 GLU A 1152 REMARK 465 ASN A 1153 REMARK 465 TYR A 1154 REMARK 465 GLN A 1155 REMARK 465 LEU A 1156 REMARK 465 ASP A 1157 REMARK 465 PRO A 1158 REMARK 465 GLU A 1159 REMARK 465 HIS A 1160 REMARK 465 SER A 1161 REMARK 465 THR A 1162 REMARK 465 SER A 1163 REMARK 465 ALA A 1164 REMARK 465 LEU A 1165 REMARK 465 VAL A 1166 REMARK 465 VAL A 1167 REMARK 465 HIS A 1168 REMARK 465 HIS A 1169 REMARK 465 PRO A 1170 REMARK 465 GLU A 1171 REMARK 465 ALA A 1172 REMARK 465 ARG A 1173 REMARK 465 TYR A 1174 REMARK 465 PHE A 1175 REMARK 465 SER A 1176 REMARK 465 VAL A 1177 REMARK 465 ASP A 1178 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 37 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 473 CG CD OE1 OE2 REMARK 470 LYS A 596 CG CD CE NZ REMARK 470 GLU A 646 CG CD OE1 OE2 REMARK 470 LYS A 655 CG CD CE NZ REMARK 470 GLU A 656 CG CD OE1 OE2 REMARK 470 ARG A 689 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 740 CG CD OE1 OE2 REMARK 470 LYS A 741 CG CD CE NZ REMARK 470 LYS A 742 CG CD CE NZ REMARK 470 TYR A 775 CG CD1 CD2 CE1 CE2 CZ OH REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 VAL A 81 N - CA - C ANGL. DEV. = -16.6 DEGREES REMARK 500 ARG A 84 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 178 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 200 NE - CZ - NH2 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG A 293 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES REMARK 500 GLY A 321 N - CA - C ANGL. DEV. = -19.6 DEGREES REMARK 500 ARG A 331 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES REMARK 500 LYS A 483 CB - CA - C ANGL. DEV. = -13.1 DEGREES REMARK 500 ARG A 512 NE - CZ - NH2 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 584 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 631 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 666 NE - CZ - NH2 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 668 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES REMARK 500 ALA A 855 CB - CA - C ANGL. DEV. = 27.8 DEGREES REMARK 500 ALA A 855 N - CA - C ANGL. DEV. = -27.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 TYR A 75 47.23 -88.15 REMARK 500 VAL A 81 -46.65 -137.86 REMARK 500 SER A 109 23.55 -153.28 REMARK 500 LEU A 190 35.74 -85.58 REMARK 500 PRO A 218 63.60 -68.62 REMARK 500 CYS A 256 26.89 49.34 REMARK 500 ARG A 268 -70.77 -72.16 REMARK 500 ASN A 283 37.17 -86.99 REMARK 500 TYR A 296 -165.74 -123.58 REMARK 500 CYS A 322 -66.07 -122.20 REMARK 500 THR A 366 129.77 -171.37 REMARK 500 PRO A 447 -5.18 -57.65 REMARK 500 PRO A 458 -178.25 -66.73 REMARK 500 ALA A 461 -169.57 -121.84 REMARK 500 ASN A 464 48.17 -96.07 REMARK 500 LEU A 468 40.89 34.72 REMARK 500 ALA A 488 94.99 -165.04 REMARK 500 ALA A 500 120.70 -39.65 REMARK 500 MET A 513 -73.08 -93.84 REMARK 500 ARG A 561 15.34 -144.96 REMARK 500 LEU A 562 65.76 -119.90 REMARK 500 LEU A 651 50.59 -93.20 REMARK 500 ALA A 652 -157.73 -143.80 REMARK 500 GLU A 656 -68.22 -134.69 REMARK 500 MET A 739 45.75 -80.13 REMARK 500 ASP A 760 27.29 -151.67 REMARK 500 LYS A 783 19.76 -142.68 REMARK 500 VAL A 842 -38.86 -131.06 REMARK 500 GLU A 851 40.24 -149.46 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 PRO A 287 -10.44 REMARK 500 MET A 513 11.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 256 SG REMARK 620 2 CYS A 323 SG 101.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 B12 A1202 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 759 NE2 REMARK 620 2 B12 A1202 N21 105.6 REMARK 620 3 B12 A1202 N22 79.0 88.8 REMARK 620 4 B12 A1202 N23 81.5 172.9 92.1 REMARK 620 5 B12 A1202 N24 101.6 89.0 177.8 90.1 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-29699 RELATED DB: EMDB REMARK 900 STRUCTURE OF COBALAMIN-DEPENDENT METHIONINE SYNTHASE (METH) IN A REMARK 900 RESTING STATE DBREF1 8G3H A 1 1178 UNP A0A0A2XCD7_THEFI DBREF2 8G3H A A0A0A2XCD7 1 1178 SEQRES 1 A 1178 MET VAL GLU VAL HIS THR CYS SER PRO GLY CYS ARG HIS SEQRES 2 A 1178 HIS LEU GLY GLY ALA GLY TRP GLY ASP ALA PRO LEU LEU SEQRES 3 A 1178 ARG LEU GLY TYR ASN LYS GLU ALA ARG ALA ARG ARG PHE SEQRES 4 A 1178 PRO TYR LEU ARG ALA LEU SER GLN ARG VAL LEU VAL PHE SEQRES 5 A 1178 ASP GLY ALA MET GLY THR GLU LEU GLN LYS ARG ASP LEU SEQRES 6 A 1178 THR PRO GLU ASP TYR GLY GLU GLU ALA TYR TYR GLY CYS SEQRES 7 A 1178 PRO GLU VAL LEU ASN ARG THR ARG PRO ASP VAL VAL ARG SEQRES 8 A 1178 GLU ILE HIS LEU SER TYR LEU GLU ALA GLY ALA GLU VAL SEQRES 9 A 1178 ILE GLU THR ASN SER PHE GLY ALA LEU ARG HIS VAL LEU SEQRES 10 A 1178 ALA GLU TYR GLY LEU GLY GLU GLU ALA GLU GLU LEU ALA SEQRES 11 A 1178 TYR ARG ALA ALA ARG ILE ALA LYS GLU ALA ALA GLU PRO SEQRES 12 A 1178 TYR GLY ALA PHE VAL ALA GLY ALA LEU GLY PRO GLY THR SEQRES 13 A 1178 LYS LEU VAL SER LEU GLY GLN ILE SER TRP GLU GLU LEU SEQRES 14 A 1178 PHE SER ALA TYR LYS GLU ALA VAL ARG GLY LEU VAL ARG SEQRES 15 A 1178 GLY GLY VAL ASP LEU ILE LEU LEU GLU THR ALA GLN ASP SEQRES 16 A 1178 ILE LEU GLN VAL ARG CYS ALA VAL LEU ALA ALA ARG GLU SEQRES 17 A 1178 ALA MET ALA GLU LEU GLY VAL GLU LEU PRO LEU GLN VAL SEQRES 18 A 1178 GLN VAL THR PHE GLU ALA THR GLY THR MET LEU VAL GLY SEQRES 19 A 1178 THR ASP GLU GLN ALA ALA LEU ALA ALA LEU GLU SER LEU SEQRES 20 A 1178 PRO ILE ASP VAL VAL GLY MET ASN CYS ALA THR GLY PRO SEQRES 21 A 1178 ASP LEU MET ASP ALA LYS ILE ARG TYR PHE ALA GLN GLU SEQRES 22 A 1178 SER THR ARG PHE VAL ALA CYS LEU PRO ASN ALA GLY LEU SEQRES 23 A 1178 PRO ARG ASN GLU GLY GLY ARG VAL VAL TYR ASP LEU THR SEQRES 24 A 1178 PRO GLU GLU LEU ALA ARG TRP HIS LEU LYS PHE VAL THR SEQRES 25 A 1178 GLU TYR GLY VAL ASN ALA VAL GLY GLY CYS CYS GLY THR SEQRES 26 A 1178 GLY PRO GLU HIS ILE ARG LYS VAL ALA GLU ALA VAL GLY SEQRES 27 A 1178 GLY ARG PRO SER PRO VAL HIS LYS THR ALA PHE PRO PRO SEQRES 28 A 1178 GLN VAL ALA SER LEU TYR GLN ALA VAL PRO LEU ARG GLN SEQRES 29 A 1178 GLU THR SER LEU LEU LEU VAL GLY GLU ARG LEU ASN ALA SEQRES 30 A 1178 THR GLY SER LYS ARG PHE ARG GLU LEU LEU PHE ALA GLY SEQRES 31 A 1178 ASP LEU GLU GLY ILE LEU ALA LEU ALA GLN GLU GLN VAL SEQRES 32 A 1178 ALA GLU GLY ALA HIS VAL LEU ASP LEU SER VAL ALA TRP SEQRES 33 A 1178 THR GLY ARG ASP GLU LEU GLU ASP MET LYS ARG VAL LEU SEQRES 34 A 1178 SER LYS LEU ALA THR GLY VAL THR VAL PRO PHE MET VAL SEQRES 35 A 1178 ASP SER THR SER PRO GLU VAL MET GLU GLU ALA LEU LYS SEQRES 36 A 1178 ARG LEU PRO GLY ARG ALA ILE LEU ASN SER ALA ASN LEU SEQRES 37 A 1178 GLU ASP GLY LEU GLU LYS PHE ASP ARG VAL ALA SER LEU SEQRES 38 A 1178 ALA LYS ALA HIS GLY ALA ALA LEU VAL ALA LEU ALA ILE SEQRES 39 A 1178 ASP GLU GLU GLY MET ALA LYS THR ARG VAL LYS LYS VAL SEQRES 40 A 1178 GLU VAL ALA LEU ARG MET TYR GLU ARG LEU THR GLU HIS SEQRES 41 A 1178 HIS GLY LEU ARG PRO GLU ASP LEU LEU PHE ASP LEU LEU SEQRES 42 A 1178 THR PHE PRO ILE THR GLN GLY ASP GLU GLU THR ARG PRO SEQRES 43 A 1178 LEU ALA ARG GLU THR LEU LEU ALA LEU GLU GLU LEU ARG SEQRES 44 A 1178 GLU ARG LEU PRO GLY VAL GLY PHE VAL LEU GLY VAL SER SEQRES 45 A 1178 ASN VAL SER PHE GLY LEU LYS PRO LYS ALA ARG ARG VAL SEQRES 46 A 1178 LEU ASN SER VAL PHE LEU ASP GLU ALA ARG LYS LYS GLY SEQRES 47 A 1178 LEU THR ALA ALA ILE VAL ASP ALA GLY LYS ILE LEU PRO SEQRES 48 A 1178 ILE SER GLN ILE PRO GLU GLU ALA TYR ALA LEU ALA LEU SEQRES 49 A 1178 ASP LEU ILE TYR ASP ARG ARG GLU GLY GLN ASP PRO LEU SEQRES 50 A 1178 PHE ALA PHE ILE ARG PHE PHE GLU GLU HIS LYS GLU VAL SEQRES 51 A 1178 LEU ALA GLU ASP LYS GLU ALA PHE GLN ALA LEU PRO VAL SEQRES 52 A 1178 GLU GLU ARG LEU ARG ARG ARG VAL LEU GLU GLY LYS ARG SEQRES 53 A 1178 VAL GLY LEU GLU GLU ASP LEU ALA GLU ALA LEU GLY ARG SEQRES 54 A 1178 MET ARG PRO LEU GLU ILE ILE ASN GLY PRO LEU LEU GLU SEQRES 55 A 1178 ALA MET LYS GLU VAL GLY GLU LEU PHE GLY ALA GLY LYS SEQRES 56 A 1178 MET GLN LEU PRO PHE VAL LEU GLN ALA ALA GLU VAL MET SEQRES 57 A 1178 LYS GLN ALA VAL ALA TYR LEU GLU PRO HIS MET GLU LYS SEQRES 58 A 1178 LYS GLY GLU GLY LYS GLY LYS LEU VAL LEU ALA THR VAL SEQRES 59 A 1178 LYS GLY ASP VAL HIS ASP ILE GLY LYS ASN LEU VAL ASP SEQRES 60 A 1178 ILE ILE LEU THR ASN ASN GLY TYR THR VAL TYR ASN LEU SEQRES 61 A 1178 GLY ILE LYS VAL PRO ILE GLU GLU MET LEU LYS ALA VAL SEQRES 62 A 1178 ASP GLU VAL LYS PRO HIS ALA LEU GLY MET SER GLY LEU SEQRES 63 A 1178 LEU VAL LYS SER THR GLN VAL MET LYS GLU ASN LEU GLU SEQRES 64 A 1178 TYR MET ARG ALA ARG GLY TYR THR LEU PRO VAL ILE LEU SEQRES 65 A 1178 GLY GLY ALA ALA LEU THR ARG ALA TYR VAL GLU GLU LEU SEQRES 66 A 1178 ARG SER ILE TYR PRO GLU VAL TYR TYR ALA GLU ASP ALA SEQRES 67 A 1178 PHE GLU GLY LEU ALA LEU MET GLU GLU LEU THR GLY HIS SEQRES 68 A 1178 ARG PRO LYS ASP LEU THR LEU ARG ARG ALA ARG THR THR SEQRES 69 A 1178 ARG LYS GLU ALA PRO ALA PRO ARG SER LYS PRO VAL SER SEQRES 70 A 1178 PRO ALA PRO ASP LEU PRO ARG PRO PRO PHE PHE GLY VAL SEQRES 71 A 1178 ARG VAL GLU GLU GLY LEU ASP LEU ALA THR ILE ALA HIS SEQRES 72 A 1178 TYR VAL ASN ARG LEU ALA LEU TYR ARG GLY GLN TRP GLY SEQRES 73 A 1178 PHE SER ARG GLY GLY LEU SER ARG GLU GLU TRP GLU ALA SEQRES 74 A 1178 TYR VAL LYS ARG GLU ALA ASP PRO VAL PHE ARG ARG LEU SEQRES 75 A 1178 LEU ALA GLU ALA MET ALA GLU GLY TRP LEU ARG PRO ARG SEQRES 76 A 1178 VAL LEU TYR GLY PHE PHE PRO VAL ALA ARG GLU GLY GLU SEQRES 77 A 1178 GLU LEU TRP VAL TYR SER PRO GLU GLY GLU LEU LEU GLU SEQRES 78 A 1178 LYS LEU ARG PHE PRO ARG GLN ARG GLY GLY GLY ILE SER SEQRES 79 A 1178 LEU VAL ASP TYR PHE ARG PRO ARG PHE ALA GLU PRO LEU SEQRES 80 A 1178 SER ASP GLU ALA ASP TRP LEU PRO GLY TYR GLU GLU GLY SEQRES 81 A 1178 ALA ARG ASP VAL LEU GLY VAL GLN LEU VAL THR MET GLY SEQRES 82 A 1178 GLU GLU PRO LYS ARG LYS ALA GLU ALA LEU TYR ARG GLU SEQRES 83 A 1178 GLY ARG TYR GLN ASP TYR LEU PHE VAL HIS GLY PHE ALA SEQRES 84 A 1178 VAL GLU MET THR GLU ALA LEU ALA GLU TYR TRP HIS LYS SEQRES 85 A 1178 ARG MET ARG GLN MET TRP GLY ILE ALA GLY GLN ASP ALA SEQRES 86 A 1178 PRO GLU ILE ARG ARG LEU PHE GLN GLN GLU TYR ARG GLY SEQRES 87 A 1178 ALA ARG TYR SER PHE GLY TYR PRO ALA CYS PRO ASP LEU SEQRES 88 A 1178 ALA ASP GLN ALA LYS LEU ASP ARG LEU MET ASP PHE SER SEQRES 89 A 1178 ARG ILE GLY VAL ARG LEU THR GLU ASN TYR GLN LEU ASP SEQRES 90 A 1178 PRO GLU HIS SER THR SER ALA LEU VAL VAL HIS HIS PRO SEQRES 91 A 1178 GLU ALA ARG TYR PHE SER VAL ASP HET ZN A1201 1 HET B12 A1202 91 HETNAM ZN ZINC ION HETNAM B12 COBALAMIN FORMUL 2 ZN ZN 2+ FORMUL 3 B12 C62 H89 CO N13 O14 P 2+ HELIX 1 AA1 PHE A 39 ARG A 48 1 10 HELIX 2 AA2 MET A 56 GLN A 61 1 6 HELIX 3 AA3 THR A 66 GLY A 71 5 6 HELIX 4 AA4 VAL A 81 ARG A 86 1 6 HELIX 5 AA5 ARG A 86 ALA A 100 1 15 HELIX 6 AA6 LEU A 113 ALA A 118 1 6 HELIX 7 AA7 GLU A 119 GLY A 121 5 3 HELIX 8 AA8 GLU A 125 GLU A 142 1 18 HELIX 9 AA9 SER A 165 GLY A 183 1 19 HELIX 10 AB1 ASP A 195 GLU A 212 1 18 HELIX 11 AB2 ASP A 236 GLU A 245 1 10 HELIX 12 AB3 GLY A 259 GLN A 272 1 14 HELIX 13 AB4 THR A 299 GLU A 313 1 15 HELIX 14 AB5 GLY A 326 GLY A 338 1 13 HELIX 15 AB6 LYS A 381 LEU A 387 1 7 HELIX 16 AB7 ASP A 391 GLY A 406 1 16 HELIX 17 AB8 ASP A 420 VAL A 436 1 17 HELIX 18 AB9 SER A 446 LYS A 455 1 10 HELIX 19 AC1 ASP A 470 HIS A 485 1 16 HELIX 20 AC2 THR A 502 GLY A 522 1 21 HELIX 21 AC3 ARG A 524 ASP A 527 5 4 HELIX 22 AC4 PRO A 546 GLU A 560 1 15 HELIX 23 AC5 SER A 572 VAL A 574 5 3 HELIX 24 AC6 PRO A 580 ARG A 595 1 16 HELIX 25 AC7 ASP A 605 ILE A 609 5 5 HELIX 26 AC8 PRO A 616 ASP A 629 1 14 HELIX 27 AC9 ASP A 635 HIS A 647 1 13 HELIX 28 AD1 PRO A 662 GLY A 674 1 13 HELIX 29 AD2 GLY A 678 MET A 690 1 13 HELIX 30 AD3 ARG A 691 GLY A 698 1 8 HELIX 31 AD4 GLY A 698 ALA A 713 1 16 HELIX 32 AD5 GLN A 717 GLU A 736 1 20 HELIX 33 AD6 ASP A 760 ASN A 772 1 13 HELIX 34 AD7 PRO A 785 LYS A 797 1 13 HELIX 35 AD8 LEU A 807 ARG A 824 1 18 HELIX 36 AD9 THR A 838 ILE A 848 5 11 HELIX 37 AE1 ASP A 857 THR A 869 1 13 SHEET 1 AA1 2 LEU A 50 VAL A 51 0 SHEET 2 AA1 2 ALA A 318 VAL A 319 1 O VAL A 319 N LEU A 50 SHEET 1 AA2 4 VAL A 104 GLU A 106 0 SHEET 2 AA2 4 PHE A 147 ALA A 151 1 O PHE A 147 N ILE A 105 SHEET 3 AA2 4 LEU A 187 ALA A 193 1 O LEU A 189 N GLY A 150 SHEET 4 AA2 4 GLN A 220 VAL A 223 1 O GLN A 220 N ILE A 188 SHEET 1 AA3 2 VAL A 251 GLY A 253 0 SHEET 2 AA3 2 PHE A 277 ALA A 279 1 O PHE A 277 N VAL A 252 SHEET 1 AA4 2 ARG A 288 GLU A 290 0 SHEET 2 AA4 2 ARG A 293 VAL A 295 -1 O ARG A 293 N GLU A 290 SHEET 1 AA5 2 GLN A 352 ALA A 354 0 SHEET 2 AA5 2 ALA A 359 PRO A 361 -1 O VAL A 360 N VAL A 353 SHEET 1 AA6 7 PHE A 440 VAL A 442 0 SHEET 2 AA6 7 VAL A 409 SER A 413 1 N LEU A 410 O MET A 441 SHEET 3 AA6 7 LEU A 369 ASN A 376 1 N GLY A 372 O ASP A 411 SHEET 4 AA6 7 ALA A 601 VAL A 604 1 O ALA A 602 N VAL A 371 SHEET 5 AA6 7 GLY A 566 GLY A 570 1 N PHE A 567 O ALA A 601 SHEET 6 AA6 7 LEU A 529 ASP A 531 1 N PHE A 530 O VAL A 568 SHEET 7 AA6 7 ALA A 491 LEU A 492 1 N ALA A 491 O ASP A 531 SHEET 1 AA7 4 THR A 776 ASN A 779 0 SHEET 2 AA7 4 LYS A 748 LEU A 751 1 N LEU A 749 O THR A 776 SHEET 3 AA7 4 ALA A 800 GLY A 802 1 O GLY A 802 N VAL A 750 SHEET 4 AA7 4 VAL A 830 ILE A 831 1 O ILE A 831 N LEU A 801 LINK SG CYS A 256 ZN ZN A1201 1555 1555 2.31 LINK SG CYS A 323 ZN ZN A1201 1555 1555 2.37 LINK NE2 HIS A 759 CO B12 A1202 1555 1555 2.71 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000