PDB Short entry for 1XCJ HEADER TRANSFERASE 02-SEP-04 1XCJ TITLE GUANIDINOACETATE METHYLTRANSFERASE CONTAINING S-ADENOSYLHOMOCYSTEINE TITLE 2 AND GUANIDINOACETATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GUANIDINOACETATE N-METHYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.1.1.2; COMPND 5 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 TISSUE: LIVER; SOURCE 6 GENE: GAMT; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: JM109; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PUCGAT9-1 KEYWDS GUANIDINOACETATE METHYLTRANSFERASE, METHYLTRANSFERASE, S- KEYWDS 2 ADENOSYLHOMOCYSTEINE, GUANIDINOACETATE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.KOMOTO,T.YAMADA,Y.TAKATA,F.TAKUSAGAWA REVDAT 4 14-FEB-24 1XCJ 1 REMARK REVDAT 3 11-OCT-17 1XCJ 1 REMARK REVDAT 2 24-FEB-09 1XCJ 1 VERSN REVDAT 1 07-DEC-04 1XCJ 0 JRNL AUTH J.KOMOTO,T.YAMADA,Y.TAKATA,K.KONISHI,H.OGAWA,T.GOMI, JRNL AUTH 2 M.FUJIOKA,F.TAKUSAGAWA JRNL TITL CATALYTIC MECHANISM OF GUANIDINOACETATE METHYLTRANSFERASE: JRNL TITL 2 CRYSTAL STRUCTURES OF GUANIDINOACETATE METHYLTRANSFERASE JRNL TITL 3 TERNARY COMPLEXES. JRNL REF BIOCHEMISTRY V. 43 14385 2004 JRNL REFN ISSN 0006-2960 JRNL PMID 15533043 JRNL DOI 10.1021/BI0486785 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.843 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 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 : 12785 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1310 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 : 1816 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 60 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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: NULL REMARK 4 REMARK 4 1XCJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-SEP-04. REMARK 100 THE DEPOSITION ID IS D_1000030203. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-04 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NONE REMARK 200 OPTICS : CONFOCAL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12785 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.03800 REMARK 200 R SYM (I) : 0.03800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.0 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8% PEG8000, PH 6.8, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 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 SER A 1 REMARK 465 SER A 2 REMARK 465 SER A 3 REMARK 465 ALA A 4 REMARK 465 ALA A 5 REMARK 465 SER A 6 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 THR A 135 -164.63 -109.43 REMARK 500 PRO A 225 25.73 -79.63 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 SAH A 236 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NMG A 237 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XCL RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE THE AUTHOR STATES THAT RESIDUE 119 IS INDEED A VAL REMARK 999 INSTEAD OF GLU. THERE IS AN ERROR IN THE ORIGINAL PUBLISHED REMARK 999 SEQUENCE (PROC. NATL. ACAD. SCI. USA 85, 694-698 (1988)). DBREF 1XCJ A 1 235 UNP P10868 GAMT_RAT 1 235 SEQADV 1XCJ VAL A 119 UNP P10868 GLU 119 SEE REMARK 999 SEQRES 1 A 235 SER SER SER ALA ALA SER PRO LEU PHE ALA PRO GLY GLU SEQRES 2 A 235 ASP CYS GLY PRO ALA TRP ARG ALA ALA PRO ALA ALA TYR SEQRES 3 A 235 ASP THR SER ASP THR HIS LEU GLN ILE LEU GLY LYS PRO SEQRES 4 A 235 VAL MET GLU ARG TRP GLU THR PRO TYR MET HIS SER LEU SEQRES 5 A 235 ALA ALA ALA ALA ALA SER ARG GLY GLY ARG VAL LEU GLU SEQRES 6 A 235 VAL GLY PHE GLY MET ALA ILE ALA ALA SER ARG VAL GLN SEQRES 7 A 235 GLN ALA PRO ILE LYS GLU HIS TRP ILE ILE GLU CYS ASN SEQRES 8 A 235 ASP GLY VAL PHE GLN ARG LEU GLN ASN TRP ALA LEU LYS SEQRES 9 A 235 GLN PRO HIS LYS VAL VAL PRO LEU LYS GLY LEU TRP GLU SEQRES 10 A 235 GLU VAL ALA PRO THR LEU PRO ASP GLY HIS PHE ASP GLY SEQRES 11 A 235 ILE LEU TYR ASP THR TYR PRO LEU SER GLU GLU THR TRP SEQRES 12 A 235 HIS THR HIS GLN PHE ASN PHE ILE LYS THR HIS ALA PHE SEQRES 13 A 235 ARG LEU LEU LYS PRO GLY GLY ILE LEU THR TYR CYS ASN SEQRES 14 A 235 LEU THR SER TRP GLY GLU LEU MET LYS SER LYS TYR THR SEQRES 15 A 235 ASP ILE THR ALA MET PHE GLU GLU THR GLN VAL PRO ALA SEQRES 16 A 235 LEU LEU GLU ALA GLY PHE GLN ARG GLU ASN ILE CYS THR SEQRES 17 A 235 GLU VAL MET ALA LEU VAL PRO PRO ALA ASP CYS ARG TYR SEQRES 18 A 235 TYR ALA PHE PRO GLN MET ILE THR PRO LEU VAL THR LYS SEQRES 19 A 235 HIS HET SAH A 236 26 HET NMG A 237 8 HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM NMG GUANIDINO ACETATE HETSYN NMG N-[AMINO(IMINO)METHYL]GLYCINE FORMUL 2 SAH C14 H20 N6 O5 S FORMUL 3 NMG C3 H7 N3 O2 FORMUL 4 HOH *60(H2 O) HELIX 1 1 CYS A 15 ARG A 20 1 6 HELIX 2 2 GLU A 45 ALA A 57 1 13 HELIX 3 3 ALA A 71 ALA A 80 1 10 HELIX 4 4 ASN A 91 LEU A 103 1 13 HELIX 5 5 LEU A 115 ALA A 120 1 6 HELIX 6 6 PRO A 121 LEU A 123 5 3 HELIX 7 7 SER A 139 TRP A 143 5 5 HELIX 8 8 THR A 145 HIS A 154 1 10 HELIX 9 9 HIS A 154 LEU A 158 1 5 HELIX 10 10 ASN A 169 LYS A 180 1 12 HELIX 11 11 ASP A 183 GLN A 192 1 10 HELIX 12 12 GLN A 192 GLY A 200 1 9 HELIX 13 13 GLN A 202 GLU A 204 5 3 SHEET 1 A 3 ALA A 25 TYR A 26 0 SHEET 2 A 3 HIS A 32 ILE A 35 -1 O GLN A 34 N ALA A 25 SHEET 3 A 3 LYS A 38 GLU A 42 -1 O MET A 41 N LEU A 33 SHEET 1 B 7 LYS A 108 LYS A 113 0 SHEET 2 B 7 GLU A 84 GLU A 89 1 N ILE A 87 O LEU A 112 SHEET 3 B 7 ARG A 62 VAL A 66 1 N VAL A 63 O GLU A 84 SHEET 4 B 7 PHE A 128 TYR A 133 1 O LEU A 132 N VAL A 66 SHEET 5 B 7 LEU A 159 TYR A 167 1 O LYS A 160 N PHE A 128 SHEET 6 B 7 GLN A 226 THR A 233 -1 O VAL A 232 N LEU A 165 SHEET 7 B 7 ILE A 206 ALA A 212 -1 N CYS A 207 O LEU A 231 SITE 1 AC1 24 TRP A 19 VAL A 40 MET A 41 MET A 49 SITE 2 AC1 24 GLY A 67 PHE A 68 GLY A 69 MET A 70 SITE 3 AC1 24 ALA A 71 ILE A 72 ALA A 73 GLU A 89 SITE 4 AC1 24 CYS A 90 ASN A 91 VAL A 94 GLY A 114 SITE 5 AC1 24 LEU A 115 TRP A 116 GLU A 117 ASP A 134 SITE 6 AC1 24 THR A 135 TYR A 136 LEU A 138 HOH A1002 SITE 1 AC2 11 VAL A 40 MET A 41 GLU A 45 ASP A 134 SITE 2 AC2 11 THR A 135 CYS A 168 ASN A 169 LEU A 170 SITE 3 AC2 11 THR A 171 HOH A1009 HOH A1052 CRYST1 36.188 41.403 42.320 104.25 112.67 104.45 P 1 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 0.027633 0.007121 0.015449 0.00000 SCALE2 0.000000 0.024942 0.010345 0.00000 SCALE3 0.000000 0.000000 0.027723 0.00000