HEADER TRANSFERASE 15-SEP-06 2IDJ TITLE CRYSTAL STRUCTURE OF RAT GLYCINE N-METHYLTRANSFERASE APOPROTEIN, TITLE 2 MONOCLINIC FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCINE N-METHYLTRANSFERASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: FOLATE-BINDING PROTEIN; COMPND 5 EC: 2.1.1.20; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 STRAIN: SPRAGUE-DAWLEY; SOURCE 6 GENE: GNMT; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PET17-B; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PR6 KEYWDS GLYCINE N-METHYLTRANSFERASE, RAT, APOPROTEIN., TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Z.LUKA,S.PAKHOMOVA,L.V.LOUKACHEVITCH,M.EGLI,M.E.NEWCOMER,C.WAGNER REVDAT 5 30-AUG-23 2IDJ 1 REMARK LINK REVDAT 4 18-OCT-17 2IDJ 1 REMARK REVDAT 3 24-FEB-09 2IDJ 1 VERSN REVDAT 2 01-MAY-07 2IDJ 1 JRNL REVDAT 1 19-DEC-06 2IDJ 0 JRNL AUTH Z.LUKA,S.PAKHOMOVA,L.V.LOUKACHEVITCH,M.EGLI,M.E.NEWCOMER, JRNL AUTH 2 C.WAGNER JRNL TITL 5-METHYLTETRAHYDROFOLATE IS BOUND IN INTERSUBUNIT AREAS OF JRNL TITL 2 RAT LIVER FOLATE-BINDING PROTEIN GLYCINE JRNL TITL 3 N-METHYLTRANSFERASE. JRNL REF J.BIOL.CHEM. V. 282 4069 2007 JRNL REFN ISSN 0021-9258 JRNL PMID 17158459 JRNL DOI 10.1074/JBC.M610384200 REMARK 2 REMARK 2 RESOLUTION. 2.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.11 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) (%) : 94.1 REMARK 3 NUMBER OF REFLECTIONS : 50393 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2525 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) : 2.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.50 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3110 REMARK 3 BIN FREE R VALUE : 0.3930 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 349 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.021 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 8782 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 115 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.69000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : -0.74000 REMARK 3 B13 (A**2) : -5.95000 REMARK 3 B23 (A**2) : -3.89000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.31 REMARK 3 ESD FROM SIGMAA (A) : 0.29 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.40 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.41 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.690 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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: NULL REMARK 4 REMARK 4 2IDJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-SEP-06. REMARK 100 THE DEPOSITION ID IS D_1000039448. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-OCT-05 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53782 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.66000 REMARK 200 FOR THE DATA SET : 25.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.45600 REMARK 200 FOR SHELL : 2.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1BHJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.1 M CA ACETATE, 0.025 REMARK 280 M TRIS, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 42.61150 REMARK 290 SMTRY3 2 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 13020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 46610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -76.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 VAL A 1 REMARK 465 ASP A 197 REMARK 465 LEU A 198 REMARK 465 THR A 199 REMARK 465 VAL A 224 REMARK 465 PRO A 225 REMARK 465 GLY A 226 REMARK 465 ALA A 227 REMARK 465 GLY A 228 REMARK 465 ARG A 229 REMARK 465 ASP A 230 REMARK 465 GLY A 231 REMARK 465 ALA A 232 REMARK 465 PRO A 233 REMARK 465 GLY A 234 REMARK 465 GLY B 228 REMARK 465 ARG B 229 REMARK 465 ASP B 230 REMARK 465 GLY B 231 REMARK 465 ALA B 232 REMARK 465 PRO B 233 REMARK 465 GLY B 234 REMARK 465 VAL C 1 REMARK 465 VAL C 224 REMARK 465 PRO C 225 REMARK 465 GLY C 226 REMARK 465 ALA C 227 REMARK 465 GLY C 228 REMARK 465 ARG C 229 REMARK 465 ASP C 230 REMARK 465 GLY C 231 REMARK 465 ALA C 232 REMARK 465 PRO C 233 REMARK 465 GLY C 234 REMARK 465 GLY D 228 REMARK 465 ARG D 229 REMARK 465 ASP D 230 REMARK 465 GLY D 231 REMARK 465 ALA D 232 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 TYR A 5 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASP A 23 CG OD1 OD2 REMARK 470 GLU A 25 CG CD OE1 OE2 REMARK 470 ARG A 38 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 45 CG CD CE NZ REMARK 470 ASP A 128 CG OD1 OD2 REMARK 470 LYS A 190 CG CD CE NZ REMARK 470 GLN A 223 CG CD OE1 NE2 REMARK 470 ARG B 38 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 128 CG OD1 OD2 REMARK 470 GLN B 223 CG CD OE1 NE2 REMARK 470 PRO B 225 CG CD REMARK 470 TYR C 5 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU C 25 CG CD OE1 OE2 REMARK 470 ASP C 128 CG OD1 OD2 REMARK 470 PRO C 188 CG CD REMARK 470 LYS C 190 CG CD CE NZ REMARK 470 TYR C 194 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS C 195 CG CD CE NZ REMARK 470 SER C 196 OG REMARK 470 ASP C 197 CG OD1 OD2 REMARK 470 LEU C 198 CG CD1 CD2 REMARK 470 GLN C 223 CG CD OE1 NE2 REMARK 470 ARG C 261 CG CD NE CZ NH1 NH2 REMARK 470 VAL D 1 CG1 CG2 REMARK 470 ARG D 38 CG CD NE CZ NH1 NH2 REMARK 470 GLN D 223 CG CD OE1 NE2 REMARK 470 PRO D 225 CG CD REMARK 470 PRO D 233 CG CD 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 SER A 3 -159.88 -105.87 REMARK 500 ASP A 36 39.86 -95.40 REMARK 500 THR A 37 -4.48 -147.07 REMARK 500 GLN A 54 9.37 -59.68 REMARK 500 THR A 119 22.16 -146.66 REMARK 500 ALA A 141 -9.84 -59.73 REMARK 500 PRO A 187 160.33 -40.76 REMARK 500 PRO A 188 168.12 -46.98 REMARK 500 LYS A 195 70.58 -103.12 REMARK 500 ASN A 210 42.01 72.47 REMARK 500 MET A 215 142.66 -172.74 REMARK 500 PHE A 270 -28.05 87.03 REMARK 500 GLN A 277 144.72 -25.13 REMARK 500 THR A 291 -78.35 -111.23 REMARK 500 SER B 3 138.01 -173.39 REMARK 500 GLN B 20 -83.82 -1.88 REMARK 500 ARG B 38 13.18 -63.78 REMARK 500 ALA B 126 -124.69 -105.27 REMARK 500 ASP B 145 77.65 -112.96 REMARK 500 LYS B 190 -60.73 -152.14 REMARK 500 ASN B 191 98.87 32.22 REMARK 500 PRO B 225 103.33 -57.21 REMARK 500 PHE B 270 -11.02 75.08 REMARK 500 SER C 3 -161.66 -114.03 REMARK 500 TYR C 21 -1.01 69.29 REMARK 500 ASP C 36 39.74 -91.65 REMARK 500 THR C 37 -1.28 -146.72 REMARK 500 ARG C 38 21.47 -78.06 REMARK 500 GLN C 54 1.03 -60.02 REMARK 500 THR C 119 25.21 -144.56 REMARK 500 ILE C 192 -16.08 -157.77 REMARK 500 PRO C 244 84.85 -67.47 REMARK 500 PHE C 270 -27.96 83.83 REMARK 500 GLN C 277 144.11 -30.10 REMARK 500 THR C 291 -77.22 -108.86 REMARK 500 SER D 3 137.39 -174.23 REMARK 500 GLN D 20 -85.13 -2.31 REMARK 500 ARG D 38 12.42 -66.82 REMARK 500 HIS D 58 -50.18 -122.24 REMARK 500 ALA D 126 -126.99 -107.09 REMARK 500 ASP D 145 77.72 -117.98 REMARK 500 LYS D 190 -57.74 -155.54 REMARK 500 ASN D 191 97.82 30.18 REMARK 500 PRO D 225 105.56 -58.59 REMARK 500 PHE D 270 -1.52 76.16 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 CA B 293 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN B 211 OD1 REMARK 620 2 HOH B 297 O 74.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA C 293 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU C 15 OE1 REMARK 620 2 GLU C 15 OE2 45.3 REMARK 620 3 HOH D 320 O 138.1 92.8 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 293 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA C 293 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BHJ RELATED DB: PDB REMARK 900 THE SAME PROTEIN, ORTHORHOMBIC FORM REMARK 900 RELATED ID: 1NBH RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH SAM AND ACETATE REMARK 900 RELATED ID: 1NBI RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH SAM REMARK 900 RELATED ID: 1R74 RELATED DB: PDB REMARK 900 HUMAN GNMT REMARK 900 RELATED ID: 1R8X RELATED DB: PDB REMARK 900 TETRAGONAL FORM OF MOUSE GNMT REMARK 900 RELATED ID: 2IDK RELATED DB: PDB DBREF 2IDJ A 1 292 UNP P13255 GNMT_RAT 1 292 DBREF 2IDJ B 1 292 UNP P13255 GNMT_RAT 1 292 DBREF 2IDJ C 1 292 UNP P13255 GNMT_RAT 1 292 DBREF 2IDJ D 1 292 UNP P13255 GNMT_RAT 1 292 SEQRES 1 A 292 VAL ASP SER VAL TYR ARG THR ARG SER LEU GLY VAL ALA SEQRES 2 A 292 ALA GLU GLY ILE PRO ASP GLN TYR ALA ASP GLY GLU ALA SEQRES 3 A 292 ALA ARG VAL TRP GLN LEU TYR ILE GLY ASP THR ARG SER SEQRES 4 A 292 ARG THR ALA GLU TYR LYS ALA TRP LEU LEU GLY LEU LEU SEQRES 5 A 292 ARG GLN HIS GLY CYS HIS ARG VAL LEU ASP VAL ALA CYS SEQRES 6 A 292 GLY THR GLY VAL ASP SER ILE MET LEU VAL GLU GLU GLY SEQRES 7 A 292 PHE SER VAL THR SER VAL ASP ALA SER ASP LYS MET LEU SEQRES 8 A 292 LYS TYR ALA LEU LYS GLU ARG TRP ASN ARG ARG LYS GLU SEQRES 9 A 292 PRO ALA PHE ASP LYS TRP VAL ILE GLU GLU ALA ASN TRP SEQRES 10 A 292 LEU THR LEU ASP LYS ASP VAL PRO ALA GLY ASP GLY PHE SEQRES 11 A 292 ASP ALA VAL ILE CYS LEU GLY ASN SER PHE ALA HIS LEU SEQRES 12 A 292 PRO ASP SER LYS GLY ASP GLN SER GLU HIS ARG LEU ALA SEQRES 13 A 292 LEU LYS ASN ILE ALA SER MET VAL ARG PRO GLY GLY LEU SEQRES 14 A 292 LEU VAL ILE ASP HIS ARG ASN TYR ASP TYR ILE LEU SER SEQRES 15 A 292 THR GLY CYS ALA PRO PRO GLY LYS ASN ILE TYR TYR LYS SEQRES 16 A 292 SER ASP LEU THR LYS ASP ILE THR THR SER VAL LEU THR SEQRES 17 A 292 VAL ASN ASN LYS ALA HIS MET VAL THR LEU ASP TYR THR SEQRES 18 A 292 VAL GLN VAL PRO GLY ALA GLY ARG ASP GLY ALA PRO GLY SEQRES 19 A 292 PHE SER LYS PHE ARG LEU SER TYR TYR PRO HIS CYS LEU SEQRES 20 A 292 ALA SER PHE THR GLU LEU VAL GLN GLU ALA PHE GLY GLY SEQRES 21 A 292 ARG CYS GLN HIS SER VAL LEU GLY ASP PHE LYS PRO TYR SEQRES 22 A 292 ARG PRO GLY GLN ALA TYR VAL PRO CYS TYR PHE ILE HIS SEQRES 23 A 292 VAL LEU LYS LYS THR GLY SEQRES 1 B 292 VAL ASP SER VAL TYR ARG THR ARG SER LEU GLY VAL ALA SEQRES 2 B 292 ALA GLU GLY ILE PRO ASP GLN TYR ALA ASP GLY GLU ALA SEQRES 3 B 292 ALA ARG VAL TRP GLN LEU TYR ILE GLY ASP THR ARG SER SEQRES 4 B 292 ARG THR ALA GLU TYR LYS ALA TRP LEU LEU GLY LEU LEU SEQRES 5 B 292 ARG GLN HIS GLY CYS HIS ARG VAL LEU ASP VAL ALA CYS SEQRES 6 B 292 GLY THR GLY VAL ASP SER ILE MET LEU VAL GLU GLU GLY SEQRES 7 B 292 PHE SER VAL THR SER VAL ASP ALA SER ASP LYS MET LEU SEQRES 8 B 292 LYS TYR ALA LEU LYS GLU ARG TRP ASN ARG ARG LYS GLU SEQRES 9 B 292 PRO ALA PHE ASP LYS TRP VAL ILE GLU GLU ALA ASN TRP SEQRES 10 B 292 LEU THR LEU ASP LYS ASP VAL PRO ALA GLY ASP GLY PHE SEQRES 11 B 292 ASP ALA VAL ILE CYS LEU GLY ASN SER PHE ALA HIS LEU SEQRES 12 B 292 PRO ASP SER LYS GLY ASP GLN SER GLU HIS ARG LEU ALA SEQRES 13 B 292 LEU LYS ASN ILE ALA SER MET VAL ARG PRO GLY GLY LEU SEQRES 14 B 292 LEU VAL ILE ASP HIS ARG ASN TYR ASP TYR ILE LEU SER SEQRES 15 B 292 THR GLY CYS ALA PRO PRO GLY LYS ASN ILE TYR TYR LYS SEQRES 16 B 292 SER ASP LEU THR LYS ASP ILE THR THR SER VAL LEU THR SEQRES 17 B 292 VAL ASN ASN LYS ALA HIS MET VAL THR LEU ASP TYR THR SEQRES 18 B 292 VAL GLN VAL PRO GLY ALA GLY ARG ASP GLY ALA PRO GLY SEQRES 19 B 292 PHE SER LYS PHE ARG LEU SER TYR TYR PRO HIS CYS LEU SEQRES 20 B 292 ALA SER PHE THR GLU LEU VAL GLN GLU ALA PHE GLY GLY SEQRES 21 B 292 ARG CYS GLN HIS SER VAL LEU GLY ASP PHE LYS PRO TYR SEQRES 22 B 292 ARG PRO GLY GLN ALA TYR VAL PRO CYS TYR PHE ILE HIS SEQRES 23 B 292 VAL LEU LYS LYS THR GLY SEQRES 1 C 292 VAL ASP SER VAL TYR ARG THR ARG SER LEU GLY VAL ALA SEQRES 2 C 292 ALA GLU GLY ILE PRO ASP GLN TYR ALA ASP GLY GLU ALA SEQRES 3 C 292 ALA ARG VAL TRP GLN LEU TYR ILE GLY ASP THR ARG SER SEQRES 4 C 292 ARG THR ALA GLU TYR LYS ALA TRP LEU LEU GLY LEU LEU SEQRES 5 C 292 ARG GLN HIS GLY CYS HIS ARG VAL LEU ASP VAL ALA CYS SEQRES 6 C 292 GLY THR GLY VAL ASP SER ILE MET LEU VAL GLU GLU GLY SEQRES 7 C 292 PHE SER VAL THR SER VAL ASP ALA SER ASP LYS MET LEU SEQRES 8 C 292 LYS TYR ALA LEU LYS GLU ARG TRP ASN ARG ARG LYS GLU SEQRES 9 C 292 PRO ALA PHE ASP LYS TRP VAL ILE GLU GLU ALA ASN TRP SEQRES 10 C 292 LEU THR LEU ASP LYS ASP VAL PRO ALA GLY ASP GLY PHE SEQRES 11 C 292 ASP ALA VAL ILE CYS LEU GLY ASN SER PHE ALA HIS LEU SEQRES 12 C 292 PRO ASP SER LYS GLY ASP GLN SER GLU HIS ARG LEU ALA SEQRES 13 C 292 LEU LYS ASN ILE ALA SER MET VAL ARG PRO GLY GLY LEU SEQRES 14 C 292 LEU VAL ILE ASP HIS ARG ASN TYR ASP TYR ILE LEU SER SEQRES 15 C 292 THR GLY CYS ALA PRO PRO GLY LYS ASN ILE TYR TYR LYS SEQRES 16 C 292 SER ASP LEU THR LYS ASP ILE THR THR SER VAL LEU THR SEQRES 17 C 292 VAL ASN ASN LYS ALA HIS MET VAL THR LEU ASP TYR THR SEQRES 18 C 292 VAL GLN VAL PRO GLY ALA GLY ARG ASP GLY ALA PRO GLY SEQRES 19 C 292 PHE SER LYS PHE ARG LEU SER TYR TYR PRO HIS CYS LEU SEQRES 20 C 292 ALA SER PHE THR GLU LEU VAL GLN GLU ALA PHE GLY GLY SEQRES 21 C 292 ARG CYS GLN HIS SER VAL LEU GLY ASP PHE LYS PRO TYR SEQRES 22 C 292 ARG PRO GLY GLN ALA TYR VAL PRO CYS TYR PHE ILE HIS SEQRES 23 C 292 VAL LEU LYS LYS THR GLY SEQRES 1 D 292 VAL ASP SER VAL TYR ARG THR ARG SER LEU GLY VAL ALA SEQRES 2 D 292 ALA GLU GLY ILE PRO ASP GLN TYR ALA ASP GLY GLU ALA SEQRES 3 D 292 ALA ARG VAL TRP GLN LEU TYR ILE GLY ASP THR ARG SER SEQRES 4 D 292 ARG THR ALA GLU TYR LYS ALA TRP LEU LEU GLY LEU LEU SEQRES 5 D 292 ARG GLN HIS GLY CYS HIS ARG VAL LEU ASP VAL ALA CYS SEQRES 6 D 292 GLY THR GLY VAL ASP SER ILE MET LEU VAL GLU GLU GLY SEQRES 7 D 292 PHE SER VAL THR SER VAL ASP ALA SER ASP LYS MET LEU SEQRES 8 D 292 LYS TYR ALA LEU LYS GLU ARG TRP ASN ARG ARG LYS GLU SEQRES 9 D 292 PRO ALA PHE ASP LYS TRP VAL ILE GLU GLU ALA ASN TRP SEQRES 10 D 292 LEU THR LEU ASP LYS ASP VAL PRO ALA GLY ASP GLY PHE SEQRES 11 D 292 ASP ALA VAL ILE CYS LEU GLY ASN SER PHE ALA HIS LEU SEQRES 12 D 292 PRO ASP SER LYS GLY ASP GLN SER GLU HIS ARG LEU ALA SEQRES 13 D 292 LEU LYS ASN ILE ALA SER MET VAL ARG PRO GLY GLY LEU SEQRES 14 D 292 LEU VAL ILE ASP HIS ARG ASN TYR ASP TYR ILE LEU SER SEQRES 15 D 292 THR GLY CYS ALA PRO PRO GLY LYS ASN ILE TYR TYR LYS SEQRES 16 D 292 SER ASP LEU THR LYS ASP ILE THR THR SER VAL LEU THR SEQRES 17 D 292 VAL ASN ASN LYS ALA HIS MET VAL THR LEU ASP TYR THR SEQRES 18 D 292 VAL GLN VAL PRO GLY ALA GLY ARG ASP GLY ALA PRO GLY SEQRES 19 D 292 PHE SER LYS PHE ARG LEU SER TYR TYR PRO HIS CYS LEU SEQRES 20 D 292 ALA SER PHE THR GLU LEU VAL GLN GLU ALA PHE GLY GLY SEQRES 21 D 292 ARG CYS GLN HIS SER VAL LEU GLY ASP PHE LYS PRO TYR SEQRES 22 D 292 ARG PRO GLY GLN ALA TYR VAL PRO CYS TYR PHE ILE HIS SEQRES 23 D 292 VAL LEU LYS LYS THR GLY HET CA B 293 1 HET CA C 293 1 HETNAM CA CALCIUM ION FORMUL 5 CA 2(CA 2+) FORMUL 7 HOH *115(H2 O) HELIX 1 1 GLY A 24 ASP A 36 1 13 HELIX 2 2 THR A 41 GLN A 54 1 14 HELIX 3 3 GLY A 68 GLU A 77 1 10 HELIX 4 4 SER A 87 ARG A 101 1 15 HELIX 5 5 GLU A 104 LYS A 109 1 6 HELIX 6 6 ASN A 116 LEU A 118 5 3 HELIX 7 7 THR A 119 VAL A 124 1 6 HELIX 8 8 SER A 139 LEU A 143 5 5 HELIX 9 9 GLN A 150 MET A 163 1 14 HELIX 10 10 ASN A 176 GLY A 184 1 9 HELIX 11 11 CYS A 246 GLU A 256 1 11 HELIX 12 12 GLY B 24 ASP B 36 1 13 HELIX 13 13 THR B 41 HIS B 55 1 15 HELIX 14 14 GLY B 68 GLU B 77 1 10 HELIX 15 15 SER B 87 ARG B 101 1 15 HELIX 16 16 GLU B 104 LYS B 109 1 6 HELIX 17 17 ASN B 116 LEU B 118 5 3 HELIX 18 18 THR B 119 VAL B 124 1 6 HELIX 19 19 SER B 139 LEU B 143 5 5 HELIX 20 20 GLN B 150 SER B 162 1 13 HELIX 21 21 ASN B 176 GLY B 184 1 9 HELIX 22 22 CYS B 246 ALA B 257 1 12 HELIX 23 23 GLY C 24 ASP C 36 1 13 HELIX 24 24 THR C 41 GLN C 54 1 14 HELIX 25 25 GLY C 68 GLU C 77 1 10 HELIX 26 26 SER C 87 ARG C 101 1 15 HELIX 27 27 GLU C 104 LYS C 109 1 6 HELIX 28 28 ASN C 116 LEU C 118 5 3 HELIX 29 29 THR C 119 VAL C 124 1 6 HELIX 30 30 SER C 139 LEU C 143 5 5 HELIX 31 31 GLN C 150 SER C 162 1 13 HELIX 32 32 ASN C 176 GLY C 184 1 9 HELIX 33 33 CYS C 246 ALA C 257 1 12 HELIX 34 34 GLY D 24 ASP D 36 1 13 HELIX 35 35 THR D 41 HIS D 55 1 15 HELIX 36 36 GLY D 68 GLU D 77 1 10 HELIX 37 37 SER D 87 ARG D 101 1 15 HELIX 38 38 GLU D 104 LYS D 109 1 6 HELIX 39 39 ASN D 116 LEU D 118 5 3 HELIX 40 40 THR D 119 VAL D 124 1 6 HELIX 41 41 SER D 139 LEU D 143 5 5 HELIX 42 42 GLN D 150 SER D 162 1 13 HELIX 43 43 ASN D 176 GLY D 184 1 9 HELIX 44 44 CYS D 246 ALA D 257 1 12 SHEET 1 A 2 VAL A 4 ARG A 6 0 SHEET 2 A 2 VAL C 4 ARG C 6 -1 O TYR C 5 N TYR A 5 SHEET 1 B 7 VAL A 111 GLU A 114 0 SHEET 2 B 7 SER A 80 ASP A 85 1 N SER A 83 O VAL A 111 SHEET 3 B 7 ARG A 59 ASP A 62 1 N ASP A 62 O VAL A 84 SHEET 4 B 7 PHE A 130 CYS A 135 1 O ILE A 134 N LEU A 61 SHEET 5 B 7 VAL A 164 ARG A 175 1 O VAL A 171 N CYS A 135 SHEET 6 B 7 TYR A 283 LYS A 290 -1 O HIS A 286 N ILE A 172 SHEET 7 B 7 CYS A 262 GLN A 263 -1 N GLN A 263 O LYS A 289 SHEET 1 C 8 VAL A 111 GLU A 114 0 SHEET 2 C 8 SER A 80 ASP A 85 1 N SER A 83 O VAL A 111 SHEET 3 C 8 ARG A 59 ASP A 62 1 N ASP A 62 O VAL A 84 SHEET 4 C 8 PHE A 130 CYS A 135 1 O ILE A 134 N LEU A 61 SHEET 5 C 8 VAL A 164 ARG A 175 1 O VAL A 171 N CYS A 135 SHEET 6 C 8 TYR A 283 LYS A 290 -1 O HIS A 286 N ILE A 172 SHEET 7 C 8 VAL A 266 GLY A 268 -1 N LEU A 267 O ILE A 285 SHEET 8 C 8 LYS A 271 PRO A 272 -1 O LYS A 271 N GLY A 268 SHEET 1 D 6 SER A 236 TYR A 242 0 SHEET 2 D 6 LYS A 212 VAL A 222 -1 N VAL A 216 O TYR A 242 SHEET 3 D 6 ASP A 201 VAL A 209 -1 N SER A 205 O THR A 217 SHEET 4 D 6 ASP C 201 VAL C 209 -1 O THR C 208 N VAL A 206 SHEET 5 D 6 LYS C 212 VAL C 222 -1 O MET C 215 N LEU C 207 SHEET 6 D 6 SER C 236 TYR C 242 -1 O TYR C 242 N VAL C 216 SHEET 1 E 2 VAL B 4 TYR B 5 0 SHEET 2 E 2 TYR D 5 ARG D 6 -1 O TYR D 5 N TYR B 5 SHEET 1 F 8 VAL B 111 GLU B 114 0 SHEET 2 F 8 SER B 80 ASP B 85 1 N SER B 83 O VAL B 111 SHEET 3 F 8 ARG B 59 ASP B 62 1 N VAL B 60 O SER B 80 SHEET 4 F 8 PHE B 130 CYS B 135 1 O ILE B 134 N LEU B 61 SHEET 5 F 8 VAL B 164 ARG B 175 1 O VAL B 171 N VAL B 133 SHEET 6 F 8 TYR B 283 LYS B 290 -1 O HIS B 286 N ILE B 172 SHEET 7 F 8 CYS B 262 GLY B 268 -1 N LEU B 267 O ILE B 285 SHEET 8 F 8 LYS B 271 PRO B 272 -1 O LYS B 271 N GLY B 268 SHEET 1 G 6 SER B 236 TYR B 242 0 SHEET 2 G 6 LYS B 212 VAL B 222 -1 N LEU B 218 O LEU B 240 SHEET 3 G 6 LYS B 200 VAL B 209 -1 N LEU B 207 O MET B 215 SHEET 4 G 6 LYS D 200 VAL D 209 -1 O VAL D 206 N THR B 208 SHEET 5 G 6 LYS D 212 VAL D 224 -1 O HIS D 214 N LEU D 207 SHEET 6 G 6 GLY D 234 TYR D 242 -1 O LEU D 240 N LEU D 218 SHEET 1 H 7 VAL C 111 GLU C 114 0 SHEET 2 H 7 SER C 80 ASP C 85 1 N SER C 83 O VAL C 111 SHEET 3 H 7 ARG C 59 ASP C 62 1 N VAL C 60 O SER C 80 SHEET 4 H 7 PHE C 130 CYS C 135 1 O ILE C 134 N LEU C 61 SHEET 5 H 7 VAL C 164 ARG C 175 1 O VAL C 171 N CYS C 135 SHEET 6 H 7 TYR C 283 LYS C 290 -1 O HIS C 286 N ILE C 172 SHEET 7 H 7 CYS C 262 GLN C 263 -1 N GLN C 263 O LYS C 289 SHEET 1 I 8 VAL C 111 GLU C 114 0 SHEET 2 I 8 SER C 80 ASP C 85 1 N SER C 83 O VAL C 111 SHEET 3 I 8 ARG C 59 ASP C 62 1 N VAL C 60 O SER C 80 SHEET 4 I 8 PHE C 130 CYS C 135 1 O ILE C 134 N LEU C 61 SHEET 5 I 8 VAL C 164 ARG C 175 1 O VAL C 171 N CYS C 135 SHEET 6 I 8 TYR C 283 LYS C 290 -1 O HIS C 286 N ILE C 172 SHEET 7 I 8 VAL C 266 GLY C 268 -1 N LEU C 267 O ILE C 285 SHEET 8 I 8 LYS C 271 PRO C 272 -1 O LYS C 271 N GLY C 268 SHEET 1 J 8 VAL D 111 GLU D 114 0 SHEET 2 J 8 SER D 80 ASP D 85 1 N SER D 83 O VAL D 111 SHEET 3 J 8 ARG D 59 ASP D 62 1 N VAL D 60 O SER D 80 SHEET 4 J 8 PHE D 130 CYS D 135 1 O ALA D 132 N LEU D 61 SHEET 5 J 8 VAL D 164 ARG D 175 1 O VAL D 171 N CYS D 135 SHEET 6 J 8 TYR D 283 LYS D 290 -1 O LYS D 290 N GLY D 168 SHEET 7 J 8 CYS D 262 GLY D 268 -1 N LEU D 267 O ILE D 285 SHEET 8 J 8 LYS D 271 PRO D 272 -1 O LYS D 271 N GLY D 268 LINK OD1 ASN B 211 CA CA B 293 1555 1555 2.31 LINK CA CA B 293 O HOH B 297 1555 1555 2.77 LINK OE1 GLU C 15 CA CA C 293 1555 1555 2.96 LINK OE2 GLU C 15 CA CA C 293 1555 1555 2.71 LINK CA CA C 293 O HOH D 320 1555 1555 3.14 SITE 1 AC1 2 ASN B 211 HOH B 297 SITE 1 AC2 1 GLU C 15 CRYST1 57.869 85.223 131.861 90.00 91.40 90.00 P 1 21 1 8 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 0.017280 0.000000 0.000422 0.00000 SCALE2 0.000000 0.011734 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007586 0.00000