HEADER TRANSFERASE 30-APR-15 5A1I TITLE THE STRUCTURE OF HUMAN MAT2A IN COMPLEX WITH SAM, ADENOSINE, TITLE 2 METHIONINE AND PPNP. COMPND MOL_ID: 1; COMPND 2 MOLECULE: S-ADENOSYLMETHIONINE SYNTHASE ISOFORM TYPE-2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ADOMET SYNTHASE 2, METHIONINE ADENOSYLTRANSFERASE 2, MAT 2, COMPND 5 METHIONINE ADENOSYLTRANSFERASE II, MAT-II, METHIONINE COMPND 6 ADENOSYLTRANSFERASE 2A; COMPND 7 EC: 2.5.1.6; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4 KEYWDS TRANSFERASE, METHIONINE ADENOSYLTRANSFERASE, CELL GROWTH, LIVER KEYWDS 2 CANCER, METHYLATION EXPDTA X-RAY DIFFRACTION AUTHOR B.MURRAY,S.V.ANTONYUK,A.MARINA,S.C.LU,J.M.MATO,S.S.HASNAIN,A.L.ROJAS REVDAT 4 10-JAN-24 5A1I 1 REMARK LINK REVDAT 3 06-DEC-17 5A1I 1 TITLE REVDAT 2 01-NOV-17 5A1I 1 TITLE REVDAT 1 09-MAR-16 5A1I 0 JRNL AUTH B.MURRAY,S.V.ANTONYUK,A.MARINA,S.C.LU,J.M.MATO,S.S.HASNAIN, JRNL AUTH 2 A.L.ROJAS JRNL TITL CRYSTALLOGRAPHY CAPTURES CATALYTIC STEPS IN HUMAN METHIONINE JRNL TITL 2 ADENOSYLTRANSFERASE ENZYMES. JRNL REF PROC.NATL.ACAD.SCI.USA V. 113 2104 2016 JRNL REFN ISSN 0027-8424 JRNL PMID 26858410 JRNL DOI 10.1073/PNAS.1510959113 REMARK 2 REMARK 2 RESOLUTION. 1.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0131 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 73.37 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 144726 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 + TEST SET) : 0.105 REMARK 3 R VALUE (WORKING SET) : 0.104 REMARK 3 FREE R VALUE : 0.124 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 7510 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.12 REMARK 3 REFLECTION IN BIN (WORKING SET) : 9708 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.04 REMARK 3 BIN R VALUE (WORKING SET) : 0.1980 REMARK 3 BIN FREE R VALUE SET COUNT : 514 REMARK 3 BIN FREE R VALUE : 0.2050 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2963 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 96 REMARK 3 SOLVENT ATOMS : 515 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.04 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.46000 REMARK 3 B22 (A**2) : 0.12000 REMARK 3 B33 (A**2) : -1.58000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.022 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.023 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.016 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.749 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.987 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.981 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3527 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3433 ; 0.005 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4837 ; 1.797 ; 1.994 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7965 ; 1.035 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 473 ; 6.632 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 157 ;36.970 ;23.758 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 633 ;11.930 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;18.214 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 529 ; 0.120 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4085 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 799 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1709 ; 0.863 ; 1.009 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1708 ; 0.863 ; 1.009 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2180 ; 1.145 ; 1.525 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2181 ; 1.145 ; 1.526 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1818 ; 1.773 ; 1.266 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1818 ; 1.775 ; 1.266 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2631 ; 2.096 ; 1.809 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4624 ; 4.369 ;10.610 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4266 ; 2.553 ; 9.228 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 6958 ; 2.308 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 111 ;37.162 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 7301 ;12.244 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. U VALUES REFINED INDIVIDUALLY REMARK 4 REMARK 4 5A1I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-APR-15. REMARK 100 THE DEPOSITION ID IS D_1290063719. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-APR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92 REMARK 200 MONOCHROMATOR : SI111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 176512 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 73.370 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 12.30 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 24.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.70 REMARK 200 R MERGE FOR SHELL (I) : 0.09000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2P02 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.5, 30 % PEG 600 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 33.98600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.03700 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 58.60800 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 33.98600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.03700 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 58.60800 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 33.98600 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 47.03700 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 58.60800 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 33.98600 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 47.03700 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 58.60800 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: 23410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 46740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -153.8 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1088 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1336 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1591 LIES ON A SPECIAL POSITION. 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 ASN A 2 REMARK 465 GLY A 3 REMARK 465 GLN A 4 REMARK 465 LEU A 5 REMARK 465 ASN A 6 REMARK 465 GLY A 7 REMARK 465 PHE A 8 REMARK 465 HIS A 9 REMARK 465 GLU A 10 REMARK 465 ALA A 11 REMARK 465 PHE A 12 REMARK 465 ILE A 13 REMARK 465 GLU A 14 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 A 111 CD GLU A 111 OE2 -0.068 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 SER A 95 CB - CA - C ANGL. DEV. = -11.9 DEGREES REMARK 500 ARG A 177 NE - CZ - NH1 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 199 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 199 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 PHE A 250 CB - CG - CD1 ANGL. DEV. = 4.6 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 THR A 62 119.67 -39.51 REMARK 500 THR A 270 -105.62 -121.83 REMARK 500 ARG A 292 -60.72 -90.07 REMARK 500 ASP A 383 -0.13 78.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1379 DISTANCE = 6.49 ANGSTROMS REMARK 525 HOH A1381 DISTANCE = 11.78 ANGSTROMS REMARK 525 HOH A1385 DISTANCE = 6.39 ANGSTROMS REMARK 525 HOH A1390 DISTANCE = 5.94 ANGSTROMS REMARK 525 HOH A1393 DISTANCE = 6.96 ANGSTROMS REMARK 525 HOH A1397 DISTANCE = 6.05 ANGSTROMS REMARK 525 HOH A1400 DISTANCE = 6.73 ANGSTROMS REMARK 525 HOH A1401 DISTANCE = 6.46 ANGSTROMS REMARK 525 HOH A1402 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH A1473 DISTANCE = 6.91 ANGSTROMS REMARK 525 HOH A1495 DISTANCE = 7.91 ANGSTROMS REMARK 525 HOH A1511 DISTANCE = 8.15 ANGSTROMS REMARK 525 HOH A1523 DISTANCE = 9.38 ANGSTROMS REMARK 525 HOH A1528 DISTANCE = 6.72 ANGSTROMS REMARK 525 HOH A1564 DISTANCE = 6.38 ANGSTROMS REMARK 525 HOH A1583 DISTANCE = 6.94 ANGSTROMS 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 MG A 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 31 OD2 REMARK 620 2 PPK A 400 O2G 93.2 REMARK 620 3 PPK A 400 O1B 176.1 88.9 REMARK 620 4 PPK A 400 O1A 84.5 91.5 92.2 REMARK 620 5 HOH A1047 O 88.7 178.0 89.3 89.4 REMARK 620 6 HOH A1278 O 91.8 95.8 91.2 171.9 83.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 403 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 259 O REMARK 620 2 PPK A 400 O1B 112.8 REMARK 620 3 HOH A1047 O 55.4 58.8 REMARK 620 4 HOH A1278 O 72.0 58.2 52.2 REMARK 620 5 HOH A1362 O 159.4 76.0 124.9 126.2 REMARK 620 6 HOH A1441 O 101.1 145.5 150.4 144.3 70.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PPK A 400 O1G REMARK 620 2 PPK A 400 O2A 86.3 REMARK 620 3 HOH A1057 O 171.6 90.6 REMARK 620 4 HOH A1279 O 105.3 88.9 82.5 REMARK 620 5 HOH A1330 O 84.0 94.2 88.5 170.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 404 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A1062 O REMARK 620 2 HOH A1067 O 126.1 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PPK A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAM A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 412 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5A19 RELATED DB: PDB REMARK 900 THE STRUCTURE OF MAT2A IN COMPLEX WITH PPNP. REMARK 900 RELATED ID: 5A1G RELATED DB: PDB REMARK 900 THE STRUCTURE OF HUMAN MAT2A IN COMPLEX WITH S- ADENOSYLETHIONINE REMARK 900 AND PPNP. DBREF 5A1I A 1 395 UNP P31153 METK2_HUMAN 1 395 SEQRES 1 A 395 MET ASN GLY GLN LEU ASN GLY PHE HIS GLU ALA PHE ILE SEQRES 2 A 395 GLU GLU GLY THR PHE LEU PHE THR SER GLU SER VAL GLY SEQRES 3 A 395 GLU GLY HIS PRO ASP LYS ILE CYS ASP GLN ILE SER ASP SEQRES 4 A 395 ALA VAL LEU ASP ALA HIS LEU GLN GLN ASP PRO ASP ALA SEQRES 5 A 395 LYS VAL ALA CYS GLU THR VAL ALA LYS THR GLY MET ILE SEQRES 6 A 395 LEU LEU ALA GLY GLU ILE THR SER ARG ALA ALA VAL ASP SEQRES 7 A 395 TYR GLN LYS VAL VAL ARG GLU ALA VAL LYS HIS ILE GLY SEQRES 8 A 395 TYR ASP ASP SER SER LYS GLY PHE ASP TYR LYS THR CYS SEQRES 9 A 395 ASN VAL LEU VAL ALA LEU GLU GLN GLN SER PRO ASP ILE SEQRES 10 A 395 ALA GLN GLY VAL HIS LEU ASP ARG ASN GLU GLU ASP ILE SEQRES 11 A 395 GLY ALA GLY ASP GLN GLY LEU MET PHE GLY TYR ALA THR SEQRES 12 A 395 ASP GLU THR GLU GLU CYS MET PRO LEU THR ILE VAL LEU SEQRES 13 A 395 ALA HIS LYS LEU ASN ALA LYS LEU ALA GLU LEU ARG ARG SEQRES 14 A 395 ASN GLY THR LEU PRO TRP LEU ARG PRO ASP SER LYS THR SEQRES 15 A 395 GLN VAL THR VAL GLN TYR MET GLN ASP ARG GLY ALA VAL SEQRES 16 A 395 LEU PRO ILE ARG VAL HIS THR ILE VAL ILE SER VAL GLN SEQRES 17 A 395 HIS ASP GLU GLU VAL CYS LEU ASP GLU MET ARG ASP ALA SEQRES 18 A 395 LEU LYS GLU LYS VAL ILE LYS ALA VAL VAL PRO ALA LYS SEQRES 19 A 395 TYR LEU ASP GLU ASP THR ILE TYR HIS LEU GLN PRO SER SEQRES 20 A 395 GLY ARG PHE VAL ILE GLY GLY PRO GLN GLY ASP ALA GLY SEQRES 21 A 395 LEU THR GLY ARG LYS ILE ILE VAL ASP THR TYR GLY GLY SEQRES 22 A 395 TRP GLY ALA HIS GLY GLY GLY ALA PHE SER GLY LYS ASP SEQRES 23 A 395 TYR THR LYS VAL ASP ARG SER ALA ALA TYR ALA ALA ARG SEQRES 24 A 395 TRP VAL ALA LYS SER LEU VAL LYS GLY GLY LEU CYS ARG SEQRES 25 A 395 ARG VAL LEU VAL GLN VAL SER TYR ALA ILE GLY VAL SER SEQRES 26 A 395 HIS PRO LEU SER ILE SER ILE PHE HIS TYR GLY THR SER SEQRES 27 A 395 GLN LYS SER GLU ARG GLU LEU LEU GLU ILE VAL LYS LYS SEQRES 28 A 395 ASN PHE ASP LEU ARG PRO GLY VAL ILE VAL ARG ASP LEU SEQRES 29 A 395 ASP LEU LYS LYS PRO ILE TYR GLN ARG THR ALA ALA TYR SEQRES 30 A 395 GLY HIS PHE GLY ARG ASP SER PHE PRO TRP GLU VAL PRO SEQRES 31 A 395 LYS LYS LEU LYS TYR HET MET A 406 9 HET PPK A 400 13 HET MG A 401 1 HET MG A 402 1 HET K A 403 1 HET K A 404 1 HET SAM A 405 27 HET ADN A 407 19 HET PEG A 408 7 HET EDO A 411 4 HET PG4 A 412 13 HETNAM MET METHIONINE HETNAM PPK (DIPHOSPHONO)AMINOPHOSPHONIC ACID HETNAM MG MAGNESIUM ION HETNAM K POTASSIUM ION HETNAM SAM S-ADENOSYLMETHIONINE HETNAM ADN ADENOSINE HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM EDO 1,2-ETHANEDIOL HETNAM PG4 TETRAETHYLENE GLYCOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 MET C5 H11 N O2 S FORMUL 3 PPK H6 N O9 P3 FORMUL 4 MG 2(MG 2+) FORMUL 6 K 2(K 1+) FORMUL 8 SAM C15 H22 N6 O5 S FORMUL 9 ADN C10 H13 N5 O4 FORMUL 10 PEG C4 H10 O3 FORMUL 11 EDO C2 H6 O2 FORMUL 12 PG4 C8 H18 O5 FORMUL 13 HOH *515(H2 O) HELIX 1 1 HIS A 29 ASP A 49 1 21 HELIX 2 2 ASP A 78 GLY A 91 1 14 HELIX 3 3 SER A 95 GLY A 98 5 4 HELIX 4 4 SER A 114 HIS A 122 1 9 HELIX 5 5 ASN A 126 ILE A 130 5 5 HELIX 6 6 PRO A 151 ASN A 170 1 20 HELIX 7 7 CYS A 214 VAL A 226 1 13 HELIX 8 8 VAL A 226 VAL A 231 1 6 HELIX 9 9 PRO A 232 LEU A 236 5 5 HELIX 10 10 GLY A 253 GLY A 257 5 5 HELIX 11 11 LYS A 289 GLY A 308 1 20 HELIX 12 12 SER A 341 PHE A 353 1 13 HELIX 13 13 ARG A 356 LEU A 364 1 9 HELIX 14 14 ILE A 370 ALA A 375 5 6 HELIX 15 15 PHE A 385 VAL A 389 5 5 SHEET 1 AA 4 THR A 17 VAL A 25 0 SHEET 2 AA 4 LEU A 176 ASP A 191 -1 O THR A 182 N SER A 24 SHEET 3 AA 4 ALA A 194 HIS A 209 -1 O ALA A 194 N ASP A 191 SHEET 4 AA 4 ILE A 241 LEU A 244 1 O ILE A 241 N ILE A 203 SHEET 1 AB 4 ASN A 105 GLU A 111 0 SHEET 2 AB 4 MET A 64 THR A 72 1 O ILE A 65 N LEU A 107 SHEET 3 AB 4 LYS A 53 LYS A 61 -1 O LYS A 53 N THR A 72 SHEET 4 AB 4 GLY A 260 LEU A 261 -1 O GLY A 260 N ALA A 60 SHEET 1 AC 2 ASP A 93 ASP A 94 0 SHEET 2 AC 2 PHE A 99 ASP A 100 -1 O PHE A 99 N ASP A 94 SHEET 1 AD 3 GLY A 136 THR A 143 0 SHEET 2 AD 3 ARG A 313 TYR A 320 -1 O VAL A 314 N ALA A 142 SHEET 3 AD 3 SER A 329 PHE A 333 -1 O SER A 329 N SER A 319 LINK OD2 ASP A 31 MG A MG A 401 1555 1555 2.08 LINK O ALA A 259 K A K A 403 1555 1555 2.81 LINK O2GAPPK A 400 MG A MG A 401 1555 1555 1.96 LINK O1BAPPK A 400 MG A MG A 401 1555 1555 2.04 LINK O1AAPPK A 400 MG A MG A 401 1555 1555 2.01 LINK O1GAPPK A 400 MG A MG A 402 1555 1555 2.19 LINK O2AAPPK A 400 MG A MG A 402 1555 1555 1.94 LINK O1BAPPK A 400 K A K A 403 1555 1555 2.77 LINK MG A MG A 401 O AHOH A1047 1555 1555 2.14 LINK MG A MG A 401 O AHOH A1278 1555 1555 2.13 LINK MG A MG A 402 O HOH A1057 1555 1555 2.32 LINK MG A MG A 402 O AHOH A1279 1555 1555 2.16 LINK MG A MG A 402 O AHOH A1330 1555 1555 2.06 LINK K A K A 403 O AHOH A1047 1555 1555 3.17 LINK K A K A 403 O AHOH A1278 1555 1555 3.28 LINK K A K A 403 O AHOH A1362 1555 1555 3.20 LINK K A K A 403 O HOH A1441 1555 1555 2.77 LINK K A K A 404 O AHOH A1062 1555 1555 3.15 LINK K A K A 404 O AHOH A1067 1555 1555 2.74 SITE 1 AC1 21 HIS A 29 ASP A 31 ASP A 134 LYS A 181 SITE 2 AC1 21 ARG A 264 LYS A 265 ALA A 281 LYS A 285 SITE 3 AC1 21 ASP A 291 MG A 401 MG A 402 K A 403 SITE 4 AC1 21 SAM A 405 HOH A1047 HOH A1057 HOH A1109 SITE 5 AC1 21 HOH A1278 HOH A1279 HOH A1330 HOH A1362 SITE 6 AC1 21 HOH A1395 SITE 1 AC2 5 ASP A 31 LYS A 265 PPK A 400 HOH A1047 SITE 2 AC2 5 HOH A1278 SITE 1 AC3 4 PPK A 400 HOH A1057 HOH A1279 HOH A1330 SITE 1 AC4 5 GLU A 57 ASP A 258 ALA A 259 PPK A 400 SITE 2 AC4 5 HOH A1441 SITE 1 AC5 5 MET A 138 PHE A 139 HIS A 277 GLY A 278 SITE 2 AC5 5 HOH A1067 SITE 1 AC6 22 HIS A 29 PRO A 30 ALA A 55 GLU A 70 SITE 2 AC6 22 GLN A 113 ASP A 116 ILE A 117 ASP A 134 SITE 3 AC6 22 ASP A 179 LYS A 181 SER A 247 ARG A 249 SITE 4 AC6 22 PHE A 250 ASP A 258 LYS A 289 PPK A 400 SITE 5 AC6 22 HOH A1021 HOH A1037 HOH A1084 HOH A1362 SITE 6 AC6 22 HOH A1442 HOH A1443 SITE 1 AC7 5 LYS A 350 LYS A 351 ASN A 352 PHE A 353 SITE 2 AC7 5 HOH A1197 SITE 1 AC8 6 GLN A 190 GLY A 193 ARG A 313 PHE A 333 SITE 2 AC8 6 TYR A 335 HOH A1591 CRYST1 67.972 94.074 117.216 90.00 90.00 90.00 I 2 2 2 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 0.014712 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010630 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008531 0.00000