HEADER TRANSFERASE 02-DEC-02 1NBI TITLE STRUCTURE OF R175K MUTATED GLYCINE N-METHYLTRANSFERASE COMPLEXED WITH TITLE 2 S-ADENOSYLMETHIONINE, R175K:SAM. COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCINE N-METHYLTRANSFERASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: FOLATE-BINDING PROTEIN, GNMT; COMPND 5 EC: 2.1.1.20; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 ORGAN: LIVER; SOURCE 6 GENE: GNMT; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS METHYLTRANSFERASE, GLYCINE N-METHYLTRANSFERASE, CATALYTIC MECHANISM, KEYWDS 2 DYNAMICAL CATALYSIS, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.TAKATA,F.TAKUSAGAWA REVDAT 6 14-FEB-24 1NBI 1 REMARK REVDAT 5 27-OCT-21 1NBI 1 REMARK SEQADV REVDAT 4 11-OCT-17 1NBI 1 REMARK REVDAT 3 24-FEB-09 1NBI 1 VERSN REVDAT 2 29-JUL-03 1NBI 1 JRNL REVDAT 1 04-MAR-03 1NBI 0 JRNL AUTH Y.TAKATA,Y.HUANG,J.KOMOTO,T.YAMADA,K.KONISHI,H.OGAWA,T.GOMI, JRNL AUTH 2 M.FUJIOKA,F.TAKUSAGAWA JRNL TITL CATALYTIC MECHANISM OF GLYCINE N-METHYLTRANSFERASE JRNL REF BIOCHEMISTRY V. 42 8394 2003 JRNL REFN ISSN 0006-2960 JRNL PMID 12859184 JRNL DOI 10.1021/BI034245A REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 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 : 25540 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) : 0.165 REMARK 3 FREE R VALUE : 0.295 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2554 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 : 8632 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 108 REMARK 3 SOLVENT ATOMS : 244 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) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.250 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 27.60 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 1NBI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-DEC-02. REMARK 100 THE DEPOSITION ID IS D_1000017741. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 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 : NULL REMARK 200 OPTICS : CONFOCAL OPTICS 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 : 25997 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.0 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.0 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 (%): 53.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3400, PH 5.6, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 113.56500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 170.34750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 56.78250 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 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 2 REMARK 465 SER A 3 REMARK 465 VAL A 4 REMARK 465 TYR A 5 REMARK 465 ARG A 6 REMARK 465 THR A 7 REMARK 465 ARG A 8 REMARK 465 SER A 9 REMARK 465 LEU A 10 REMARK 465 GLY A 11 REMARK 465 VAL A 12 REMARK 465 ALA A 13 REMARK 465 ALA A 14 REMARK 465 GLU A 15 REMARK 465 GLY A 16 REMARK 465 ILE A 17 REMARK 465 VAL B 1 REMARK 465 ASP B 2 REMARK 465 SER B 3 REMARK 465 VAL B 4 REMARK 465 TYR B 5 REMARK 465 ARG B 6 REMARK 465 THR B 7 REMARK 465 ARG B 8 REMARK 465 SER B 9 REMARK 465 LEU B 10 REMARK 465 GLY B 11 REMARK 465 VAL B 12 REMARK 465 ALA B 13 REMARK 465 ALA B 14 REMARK 465 GLU B 15 REMARK 465 GLY B 16 REMARK 465 ILE B 17 REMARK 465 VAL C 1 REMARK 465 ASP C 2 REMARK 465 SER C 3 REMARK 465 VAL C 4 REMARK 465 TYR C 5 REMARK 465 ARG C 6 REMARK 465 THR C 7 REMARK 465 ARG C 8 REMARK 465 SER C 9 REMARK 465 LEU C 10 REMARK 465 GLY C 11 REMARK 465 VAL C 12 REMARK 465 ALA C 13 REMARK 465 ALA C 14 REMARK 465 GLU C 15 REMARK 465 GLY C 16 REMARK 465 ILE C 17 REMARK 465 VAL D 1 REMARK 465 ASP D 2 REMARK 465 SER D 3 REMARK 465 VAL D 4 REMARK 465 TYR D 5 REMARK 465 ARG D 6 REMARK 465 THR D 7 REMARK 465 ARG D 8 REMARK 465 SER D 9 REMARK 465 LEU D 10 REMARK 465 GLY D 11 REMARK 465 VAL D 12 REMARK 465 ALA D 13 REMARK 465 ALA D 14 REMARK 465 GLU D 15 REMARK 465 GLY D 16 REMARK 465 ILE D 17 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O GLU D 43 N TYR D 44 1.37 REMARK 500 O GLU C 43 N TYR C 44 1.45 REMARK 500 O HOH B 5117 O HOH B 5234 1.79 REMARK 500 O HOH C 5090 O HOH C 5233 1.95 REMARK 500 O HOH D 5054 O HOH D 5161 2.01 REMARK 500 O HOH C 5052 O HOH C 5210 2.07 REMARK 500 O ASP C 201 O ASP C 219 2.07 REMARK 500 O ASP D 201 O ASP D 219 2.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU C 43 C TYR C 44 N -0.611 REMARK 500 ALA C 186 C PRO C 187 N -0.153 REMARK 500 GLU D 43 C TYR D 44 N -0.661 REMARK 500 ALA D 186 C PRO D 187 N -0.152 REMARK 500 REMARK 500 REMARK: NULL 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 GLU C 43 CA - C - N ANGL. DEV. = 29.5 DEGREES REMARK 500 GLU C 43 O - C - N ANGL. DEV. = -30.9 DEGREES REMARK 500 TYR C 44 C - N - CA ANGL. DEV. = 55.7 DEGREES REMARK 500 GLU D 43 CA - C - N ANGL. DEV. = 34.0 DEGREES REMARK 500 GLU D 43 O - C - N ANGL. DEV. = -36.1 DEGREES REMARK 500 TYR D 44 C - N - CA ANGL. DEV. = 50.3 DEGREES REMARK 500 ALA D 186 O - C - N ANGL. DEV. = -11.9 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 44 0.37 50.18 REMARK 500 ASP A 145 40.05 -90.85 REMARK 500 SER A 146 -37.83 -37.17 REMARK 500 SER A 151 -71.48 -38.64 REMARK 500 THR A 199 84.61 -66.42 REMARK 500 ASP A 269 52.65 -111.37 REMARK 500 PHE A 270 43.74 75.73 REMARK 500 TYR B 44 2.08 51.51 REMARK 500 ASP B 145 41.71 -83.96 REMARK 500 SER B 146 -38.05 -39.56 REMARK 500 THR B 199 90.10 -64.13 REMARK 500 PRO B 225 138.73 -39.65 REMARK 500 ASP B 269 53.57 -110.55 REMARK 500 PHE B 270 39.27 76.84 REMARK 500 TYR C 44 12.67 -35.17 REMARK 500 VAL C 69 -71.33 -37.37 REMARK 500 ARG C 101 33.15 -96.59 REMARK 500 ALA C 141 -4.60 -58.31 REMARK 500 ASP C 145 40.60 -96.70 REMARK 500 SER C 146 -32.03 -36.70 REMARK 500 GLN C 150 28.81 -66.00 REMARK 500 LYS C 175 170.84 -58.41 REMARK 500 PRO C 244 91.82 -67.35 REMARK 500 PHE C 270 30.33 83.89 REMARK 500 ARG D 101 33.35 -95.32 REMARK 500 ALA D 141 -3.92 -59.69 REMARK 500 ASP D 145 39.35 -95.95 REMARK 500 SER D 146 -34.25 -35.45 REMARK 500 GLN D 150 32.60 -66.56 REMARK 500 ARG D 229 -179.93 -69.98 REMARK 500 PRO D 244 96.44 -66.01 REMARK 500 ASP D 269 50.93 -118.84 REMARK 500 PHE D 270 28.69 84.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLU C 43 TYR C 44 -98.52 REMARK 500 GLU D 43 TYR D 44 -49.82 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 ALA C 186 -12.07 REMARK 500 ALA D 186 -13.36 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 SAM A 293 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAM B 1293 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAM C 2293 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAM D 3293 DBREF 1NBI A 1 292 UNP P13255 GNMT_RAT 1 292 DBREF 1NBI B 1 292 UNP P13255 GNMT_RAT 1 292 DBREF 1NBI C 1 292 UNP P13255 GNMT_RAT 1 292 DBREF 1NBI D 1 292 UNP P13255 GNMT_RAT 1 292 SEQADV 1NBI LYS A 175 UNP P13255 ARG 175 ENGINEERED MUTATION SEQADV 1NBI LYS B 175 UNP P13255 ARG 175 ENGINEERED MUTATION SEQADV 1NBI LYS C 175 UNP P13255 ARG 175 ENGINEERED MUTATION SEQADV 1NBI LYS D 175 UNP P13255 ARG 175 ENGINEERED MUTATION 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 LYS 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 LYS 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 LYS 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 LYS 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 SAM A 293 27 HET SAM B1293 27 HET SAM C2293 27 HET SAM D3293 27 HETNAM SAM S-ADENOSYLMETHIONINE FORMUL 5 SAM 4(C15 H22 N6 O5 S) FORMUL 9 HOH *244(H2 O) HELIX 1 1 GLY A 24 GLY A 35 1 12 HELIX 2 2 ASP A 36 HIS A 55 1 20 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 SER A 162 1 13 HELIX 10 10 ASN A 176 THR A 183 1 8 HELIX 11 11 CYS A 246 PHE A 258 1 13 HELIX 12 12 GLU B 25 GLY B 35 1 11 HELIX 13 13 ASP B 36 HIS B 55 1 20 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 THR B 183 1 8 HELIX 22 22 CYS B 246 PHE B 258 1 13 HELIX 23 23 GLY C 24 GLY C 35 1 12 HELIX 24 24 ASP C 36 GLU C 43 1 8 HELIX 25 25 TYR C 44 HIS C 55 1 12 HELIX 26 26 GLY C 68 GLU C 77 1 10 HELIX 27 27 SER C 87 ARG C 101 1 15 HELIX 28 28 GLU C 104 LYS C 109 1 6 HELIX 29 29 ASN C 116 LEU C 118 5 3 HELIX 30 30 THR C 119 VAL C 124 1 6 HELIX 31 31 SER C 139 LEU C 143 5 5 HELIX 32 32 GLN C 150 SER C 162 1 13 HELIX 33 33 ASN C 176 GLY C 184 1 9 HELIX 34 34 CYS C 246 PHE C 258 1 13 HELIX 35 35 GLY D 24 GLY D 35 1 12 HELIX 36 36 ASP D 36 GLU D 43 1 8 HELIX 37 37 TYR D 44 HIS D 55 1 12 HELIX 38 38 GLY D 68 GLU D 77 1 10 HELIX 39 39 SER D 87 ARG D 101 1 15 HELIX 40 40 GLU D 104 LYS D 109 1 6 HELIX 41 41 ASN D 116 LEU D 118 5 3 HELIX 42 42 THR D 119 VAL D 124 1 6 HELIX 43 43 SER D 139 LEU D 143 5 5 HELIX 44 44 GLN D 150 SER D 162 1 13 HELIX 45 45 ASN D 176 GLY D 184 1 9 HELIX 46 46 CYS D 246 PHE D 258 1 13 SHEET 1 A 7 VAL A 111 GLU A 114 0 SHEET 2 A 7 SER A 80 ASP A 85 1 N SER A 83 O VAL A 111 SHEET 3 A 7 ARG A 59 ASP A 62 1 N ASP A 62 O VAL A 84 SHEET 4 A 7 PHE A 130 CYS A 135 1 O ILE A 134 N LEU A 61 SHEET 5 A 7 VAL A 164 LYS A 175 1 O ARG A 165 N PHE A 130 SHEET 6 A 7 TYR A 283 LYS A 290 -1 O HIS A 286 N ILE A 172 SHEET 7 A 7 CYS A 262 VAL A 266 -1 N SER A 265 O VAL A 287 SHEET 1 B 6 SER A 236 TYR A 242 0 SHEET 2 B 6 LYS A 212 VAL A 222 -1 N VAL A 222 O SER A 236 SHEET 3 B 6 THR A 199 VAL A 209 -1 N LEU A 207 O MET A 215 SHEET 4 B 6 THR D 204 VAL D 209 -1 O THR D 208 N VAL A 206 SHEET 5 B 6 LYS D 212 VAL D 222 -1 O MET D 215 N LEU D 207 SHEET 6 B 6 SER D 236 TYR D 242 -1 O TYR D 242 N VAL D 216 SHEET 1 C 7 VAL B 111 GLU B 114 0 SHEET 2 C 7 SER B 80 ASP B 85 1 N SER B 83 O VAL B 111 SHEET 3 C 7 ARG B 59 ASP B 62 1 N VAL B 60 O SER B 80 SHEET 4 C 7 PHE B 130 CYS B 135 1 O ILE B 134 N LEU B 61 SHEET 5 C 7 VAL B 164 LYS B 175 1 O ARG B 165 N PHE B 130 SHEET 6 C 7 TYR B 283 LYS B 290 -1 O HIS B 286 N ILE B 172 SHEET 7 C 7 CYS B 262 LEU B 267 -1 N SER B 265 O VAL B 287 SHEET 1 D 6 SER B 236 TYR B 242 0 SHEET 2 D 6 LYS B 212 VAL B 222 -1 N VAL B 222 O SER B 236 SHEET 3 D 6 THR B 199 VAL B 209 -1 N SER B 205 O THR B 217 SHEET 4 D 6 THR C 204 VAL C 209 -1 O THR C 208 N VAL B 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 LEU C 240 N LEU C 218 SHEET 1 E 7 VAL C 111 GLU C 114 0 SHEET 2 E 7 SER C 80 ASP C 85 1 N SER C 83 O VAL C 111 SHEET 3 E 7 ARG C 59 ASP C 62 1 N VAL C 60 O THR C 82 SHEET 4 E 7 PHE C 130 CYS C 135 1 O ALA C 132 N LEU C 61 SHEET 5 E 7 VAL C 164 LYS C 175 1 O VAL C 171 N CYS C 135 SHEET 6 E 7 TYR C 283 LYS C 289 -1 O HIS C 286 N ILE C 172 SHEET 7 E 7 SER C 265 LEU C 267 -1 N SER C 265 O VAL C 287 SHEET 1 F 7 VAL D 111 GLU D 114 0 SHEET 2 F 7 SER D 80 ASP D 85 1 N SER D 83 O VAL D 111 SHEET 3 F 7 ARG D 59 ASP D 62 1 N VAL D 60 O SER D 80 SHEET 4 F 7 PHE D 130 CYS D 135 1 O ALA D 132 N LEU D 61 SHEET 5 F 7 VAL D 164 LYS D 175 1 O VAL D 171 N CYS D 135 SHEET 6 F 7 TYR D 283 LYS D 289 -1 O HIS D 286 N ILE D 172 SHEET 7 F 7 SER D 265 LEU D 267 -1 N SER D 265 O VAL D 287 SITE 1 AC1 18 TYR A 21 TRP A 30 ILE A 34 ARG A 40 SITE 2 AC1 18 ALA A 64 GLY A 66 VAL A 69 ASP A 85 SITE 3 AC1 18 ALA A 86 SER A 87 MET A 90 ALA A 115 SITE 4 AC1 18 ASN A 116 TRP A 117 LEU A 136 SER A 139 SITE 5 AC1 18 HIS A 142 TYR A 194 SITE 1 AC2 19 TYR B 21 TRP B 30 ILE B 34 ARG B 40 SITE 2 AC2 19 ALA B 64 GLY B 66 VAL B 69 ASP B 85 SITE 3 AC2 19 ALA B 86 SER B 87 MET B 90 ALA B 115 SITE 4 AC2 19 ASN B 116 TRP B 117 LEU B 136 SER B 139 SITE 5 AC2 19 HIS B 142 TYR B 194 HOH B5048 SITE 1 AC3 17 TYR C 21 TRP C 30 ILE C 34 ARG C 40 SITE 2 AC3 17 ALA C 64 THR C 67 ASP C 85 ALA C 86 SITE 3 AC3 17 SER C 87 MET C 90 ALA C 115 ASN C 116 SITE 4 AC3 17 TRP C 117 LEU C 136 GLY C 137 SER C 139 SITE 5 AC3 17 HIS C 142 SITE 1 AC4 16 TRP D 30 ILE D 34 ARG D 40 ALA D 64 SITE 2 AC4 16 THR D 67 ASP D 85 ALA D 86 SER D 87 SITE 3 AC4 16 MET D 90 ALA D 115 ASN D 116 TRP D 117 SITE 4 AC4 16 LEU D 136 SER D 139 HIS D 142 TYR D 194 CRYST1 77.870 77.870 227.130 90.00 90.00 90.00 P 43 16 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 0.012842 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012842 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004403 0.00000