HEADER METHYLTRANSFERASE 03-AUG-96 1MSK TITLE METHIONINE SYNTHASE (ACTIVATION DOMAIN) COMPND MOL_ID: 1; COMPND 2 MOLECULE: COBALAMIN-DEPENDENT METHIONINE SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ACTIVATION DOMAIN, RESIDUES 897 - 1227; COMPND 5 EC: 2.1.1.13; COMPND 6 OTHER_DETAILS: GENERATED BY TRYPSIN CLEAVAGE OF THE METHIONINE COMPND 7 SYNTHASE HOLOENZYME SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K-12, DH5AF'-P4B6.3 KEYWDS METHYLTRANSFERASE, TRANSFERASE, METHIONINE BIOSYNTHESIS, VITAMIN B12 EXPDTA X-RAY DIFFRACTION AUTHOR M.M.DIXON,S.HUANG,R.G.MATTHEWS,M.L.LUDWIG REVDAT 3 14-FEB-24 1MSK 1 REMARK REVDAT 2 24-FEB-09 1MSK 1 VERSN REVDAT 1 01-APR-97 1MSK 0 JRNL AUTH M.M.DIXON,S.HUANG,R.G.MATTHEWS,M.LUDWIG JRNL TITL THE STRUCTURE OF THE C-TERMINAL DOMAIN OF METHIONINE JRNL TITL 2 SYNTHASE: PRESENTING S-ADENOSYLMETHIONINE FOR REDUCTIVE JRNL TITL 3 METHYLATION OF B12. JRNL REF STRUCTURE V. 4 1263 1996 JRNL REFN ISSN 0969-2126 JRNL PMID 8939751 JRNL DOI 10.1016/S0969-2126(96)00135-9 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.L.DRENNAN,S.HUANG,J.T.DRUMMOND,R.G.MATTHEWS,M.L.LUDWIG REMARK 1 TITL HOW A PROTEIN BINDS B12: A 3.0 A X-RAY STRUCTURE OF REMARK 1 TITL 2 B12-BINDING DOMAINS OF METHIONINE SYNTHASE REMARK 1 REF SCIENCE V. 266 1669 1994 REMARK 1 REFN ISSN 0036-8075 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 28445 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2630 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 212 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.018 REMARK 3 BOND ANGLES (DEGREES) : 1.840 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.690 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 TWO LOOPS, CONSISTING OF RESIDUES 965 - 967 AND 1035 - REMARK 3 1036, ARE DISORDERED, WITH AVERAGE MAIN-CHAIN B-FACTORS > REMARK 3 50.0 A**2. THREE RESIDUES AT THE C-TERMINAL END, 1225 - REMARK 3 1227, ARE DISORDERED, WITH AVERAGE MAIN-CHAIN B-FACTORS > REMARK 3 50.0 A**2. REMARK 4 REMARK 4 1MSK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000175149. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : ADSC REMARK 200 DATA SCALING SOFTWARE : ADSC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28762 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.0 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.05320 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.2 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 19.43000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.41000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.18000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.41000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.43000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.18000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 400 REMARK 400 COMPOUND REMARK 400 THE ACTIVATION DOMAIN WAS GENERATED BY TRYPSIN CLEAVAGE OF REMARK 400 THE METHIONINE SYNTHASE HOLOENZYME. 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 LYS A 897 REMARK 465 LYS A 898 REMARK 465 PRO A 899 REMARK 465 ARG A 900 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 ASN A 912 42.06 -103.41 REMARK 500 VAL A 968 -52.07 -122.56 REMARK 500 ASN A1129 49.40 -87.86 REMARK 500 ALA A1193 -147.20 73.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAM A 1301 DBREF 1MSK A 897 1227 UNP P13009 METH_ECOLI 896 1226 SEQRES 1 A 331 LYS LYS PRO ARG THR PRO PRO VAL THR LEU GLU ALA ALA SEQRES 2 A 331 ARG ASP ASN ASP PHE ALA PHE ASP TRP GLN ALA TYR THR SEQRES 3 A 331 PRO PRO VAL ALA HIS ARG LEU GLY VAL GLN GLU VAL GLU SEQRES 4 A 331 ALA SER ILE GLU THR LEU ARG ASN TYR ILE ASP TRP THR SEQRES 5 A 331 PRO PHE PHE MET THR TRP SER LEU ALA GLY LYS TYR PRO SEQRES 6 A 331 ARG ILE LEU GLU ASP GLU VAL VAL GLY VAL GLU ALA GLN SEQRES 7 A 331 ARG LEU PHE LYS ASP ALA ASN ASP MET LEU ASP LYS LEU SEQRES 8 A 331 SER ALA GLU LYS THR LEU ASN PRO ARG GLY VAL VAL GLY SEQRES 9 A 331 LEU PHE PRO ALA ASN ARG VAL GLY ASP ASP ILE GLU ILE SEQRES 10 A 331 TYR ARG ASP GLU THR ARG THR HIS VAL ILE ASN VAL SER SEQRES 11 A 331 HIS HIS LEU ARG GLN GLN THR GLU LYS THR GLY PHE ALA SEQRES 12 A 331 ASN TYR CYS LEU ALA ASP PHE VAL ALA PRO LYS LEU SER SEQRES 13 A 331 GLY LYS ALA ASP TYR ILE GLY ALA PHE ALA VAL THR GLY SEQRES 14 A 331 GLY LEU GLU GLU ASP ALA LEU ALA ASP ALA PHE GLU ALA SEQRES 15 A 331 GLN HIS ASP ASP TYR ASN LYS ILE MET VAL LYS ALA LEU SEQRES 16 A 331 ALA ASP ARG LEU ALA GLU ALA PHE ALA GLU TYR LEU HIS SEQRES 17 A 331 GLU ARG VAL ARG LYS VAL TYR TRP GLY TYR ALA PRO ASN SEQRES 18 A 331 GLU ASN LEU SER ASN GLU GLU LEU ILE ARG GLU ASN TYR SEQRES 19 A 331 GLN GLY ILE ARG PRO ALA PRO GLY TYR PRO ALA CYS PRO SEQRES 20 A 331 GLU HIS THR GLU LYS ALA THR ILE TRP GLU LEU LEU GLU SEQRES 21 A 331 VAL GLU LYS HIS THR GLY MET LYS LEU THR GLU SER PHE SEQRES 22 A 331 ALA MET TRP PRO GLY ALA SER VAL SER GLY TRP TYR PHE SEQRES 23 A 331 SER HIS PRO ASP SER LYS TYR TYR ALA VAL ALA GLN ILE SEQRES 24 A 331 GLN ARG ASP GLN VAL GLU ASP TYR ALA ARG ARG LYS GLY SEQRES 25 A 331 MET SER VAL THR GLU VAL GLU ARG TRP LEU ALA PRO ASN SEQRES 26 A 331 LEU GLY TYR ASP ALA ASP HET ACT A1302 4 HET SAM A1301 27 HETNAM ACT ACETATE ION HETNAM SAM S-ADENOSYLMETHIONINE FORMUL 2 ACT C2 H3 O2 1- FORMUL 3 SAM C15 H22 N6 O5 S FORMUL 4 HOH *212(H2 O) HELIX 1 1 LEU A 906 ASN A 912 1 7 HELIX 2 2 ILE A 938 TYR A 944 1 7 HELIX 3 3 THR A 948 TRP A 954 1 7 HELIX 4 4 ARG A 962 GLU A 965 5 4 HELIX 5 5 GLY A 970 GLU A 990 1 21 HELIX 6 6 LEU A 1067 ALA A 1078 5 12 HELIX 7 7 ASP A 1082 LYS A 1109 1 28 HELIX 8 8 ASN A 1122 ILE A 1126 1 5 HELIX 9 9 HIS A 1145 LEU A 1154 5 10 HELIX 10 10 VAL A 1157 THR A 1161 1 5 HELIX 11 11 ARG A 1197 LYS A 1207 1 11 HELIX 12 12 VAL A 1211 ASN A 1221 1 11 SHEET 1 A 4 GLY A 930 GLU A 935 0 SHEET 2 A 4 ARG A 996 ALA A1004 -1 N LEU A1001 O GLY A 930 SHEET 3 A 4 ASP A1056 THR A1064 -1 N THR A1064 O ARG A 996 SHEET 4 A 4 SER A1176 TYR A1181 -1 N TYR A1181 O GLY A1059 SHEET 1 B 3 ALA A1004 VAL A1007 0 SHEET 2 B 3 ASP A1010 TYR A1014 -1 N GLU A1012 O ASN A1005 SHEET 3 B 3 VAL A1022 HIS A1027 -1 N SER A1026 O ILE A1011 CISPEP 1 TYR A 960 PRO A 961 0 1.44 CISPEP 2 TRP A 1172 PRO A 1173 0 -1.52 SITE 1 AC1 5 VAL A 934 LYS A1050 ARG A1106 TYR A1111 SITE 2 AC1 5 HOH A2053 SITE 1 AC2 16 ASP A 946 ARG A1094 GLU A1097 ARG A1134 SITE 2 AC2 16 PRO A1135 ALA A1136 TYR A1139 ALA A1141 SITE 3 AC2 16 TYR A1189 TYR A1190 HOH A2075 HOH A2076 SITE 4 AC2 16 HOH A2079 HOH A2129 HOH A2168 HOH A2193 CRYST1 38.860 62.360 140.820 90.00 90.00 90.00 P 21 21 21 4 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 0.025733 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016036 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007101 0.00000