HEADER TRANSFERASE 02-APR-18 6G6R TITLE HUMAN METHIONINE ADENOSYLTRANSFERASE II WITH SAME 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; COMPND 6 EC: 2.5.1.6; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MAT2A, AMS2, MATA2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4 KEYWDS TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.PANMANEE,S.V.ANTONYUK,S.S.HASNAIN REVDAT 3 17-JAN-24 6G6R 1 REMARK LINK REVDAT 2 12-JUN-19 6G6R 1 JRNL REVDAT 1 10-APR-19 6G6R 0 JRNL AUTH J.PANMANEE,J.BRADLEY-CLARKE,J.M.MATO,P.M.O'NEILL, JRNL AUTH 2 S.V.ANTONYUK,S.S.HASNAIN JRNL TITL CONTROL AND REGULATION OF S-ADENOSYLMETHIONINE BIOSYNTHESIS JRNL TITL 2 BY THE REGULATORY BETA SUBUNIT AND QUINOLONE-BASED JRNL TITL 3 COMPOUNDS. JRNL REF FEBS J. V. 286 2135 2019 JRNL REFN ISSN 1742-464X JRNL PMID 30776190 JRNL DOI 10.1111/FEBS.14790 REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0189 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 73.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 76413 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) : 0.139 REMARK 3 R VALUE (WORKING SET) : 0.137 REMARK 3 FREE R VALUE : 0.162 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4047 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) : 1.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.39 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5484 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.67 REMARK 3 BIN R VALUE (WORKING SET) : 0.2780 REMARK 3 BIN FREE R VALUE SET COUNT : 288 REMARK 3 BIN FREE R VALUE : 0.3110 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2942 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 74 REMARK 3 SOLVENT ATOMS : 408 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.21000 REMARK 3 B22 (A**2) : -0.36000 REMARK 3 B33 (A**2) : -0.85000 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): 0.046 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.048 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.038 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.003 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.981 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.973 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3258 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3096 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4424 ; 1.690 ; 1.987 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7212 ; 1.000 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 428 ; 6.392 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 139 ;36.590 ;24.029 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 572 ;12.083 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;18.811 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 495 ; 0.111 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3618 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 642 ; 0.002 ; 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): 1586 ; 0.931 ; 1.172 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1586 ; 0.931 ; 1.172 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1997 ; 1.454 ; 1.758 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1998 ; 1.454 ; 1.758 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1672 ; 1.410 ; 1.403 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1672 ; 1.410 ; 1.403 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2406 ; 2.162 ; 2.015 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3773 ; 4.626 ;15.793 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3649 ; 3.868 ;14.797 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL 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 REMARK 4 REMARK 4 6G6R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-APR-18. REMARK 100 THE DEPOSITION ID IS D_1200007432. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUN-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 80461 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 73.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.57500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 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: 5A1I REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG600 0.1M HEPES PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 33.81500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 58.34500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 33.81500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 58.34500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 33.81500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 47.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 58.34500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 33.81500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 47.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 58.34500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 21290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 46450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -158.0 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 A 756 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 808 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 465 GLU A 15 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 GLU A 85 CD OE1 OE2 REMARK 470 GLU A 238 CG CD OE1 OE2 REMARK 470 ARG A 343 CD NE CZ NH1 NH2 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 ARG A 199 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 313 NE - CZ - NH2 ANGL. DEV. = -3.2 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 62 117.65 -36.46 REMARK 500 THR A 270 -105.55 -119.30 REMARK 500 REMARK 500 REMARK: NULL REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 HOH A 509 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 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 31 OD2 REMARK 620 2 PPK A 401 O2G 93.3 REMARK 620 3 PPK A 401 O1B 176.0 90.2 REMARK 620 4 PPK A 401 O1A 85.7 91.3 92.3 REMARK 620 5 HOH A 538 O 87.1 177.7 89.3 86.5 REMARK 620 6 HOH A 552 O 91.5 98.0 89.9 170.4 84.3 REMARK 620 N 1 2 3 4 5 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 GLU A 57 OE2 REMARK 620 2 ASP A 258 OD1 34.4 REMARK 620 3 ALA A 259 O 30.5 5.8 REMARK 620 4 PPK A 401 O1B 36.8 10.0 15.0 REMARK 620 5 HOH A 509 O 43.8 10.5 16.2 9.1 REMARK 620 6 HOH A 538 O 27.9 8.3 9.2 9.6 16.0 REMARK 620 7 HOH A 552 O 33.6 6.8 11.1 4.2 10.6 5.8 REMARK 620 8 HOH A 553 O 43.6 10.5 13.1 17.1 10.6 18.8 15.9 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PPK A 401 O3G REMARK 620 2 PPK A 401 O4A 87.2 REMARK 620 3 HOH A 533 O 93.9 174.1 REMARK 620 4 HOH A 536 O 83.4 95.9 90.0 REMARK 620 5 HOH A 573 O 107.5 85.9 88.2 169.1 REMARK 620 6 HOH A 624 O 170.4 90.1 89.7 87.7 81.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 405 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 665 O REMARK 620 2 HOH A 751 O 156.4 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SAM A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 A 409 DBREF 6G6R 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 PPK A 401 13 HET MG A 402 1 HET MG A 403 1 HET K A 404 1 HET K A 405 1 HET SAM A 406 27 HET EDO A 407 4 HET PG4 A 408 13 HET PG4 A 409 13 HETNAM PPK (DIPHOSPHONO)AMINOPHOSPHONIC ACID HETNAM MG MAGNESIUM ION HETNAM K POTASSIUM ION HETNAM SAM S-ADENOSYLMETHIONINE HETNAM EDO 1,2-ETHANEDIOL HETNAM PG4 TETRAETHYLENE GLYCOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 PPK H6 N O9 P3 FORMUL 3 MG 2(MG 2+) FORMUL 5 K 2(K 1+) FORMUL 7 SAM C15 H22 N6 O5 S FORMUL 8 EDO C2 H6 O2 FORMUL 9 PG4 2(C8 H18 O5) FORMUL 11 HOH *408(H2 O) HELIX 1 AA1 HIS A 29 ASP A 49 1 21 HELIX 2 AA2 ASP A 78 GLY A 91 1 14 HELIX 3 AA3 SER A 95 GLY A 98 5 4 HELIX 4 AA4 SER A 114 HIS A 122 1 9 HELIX 5 AA5 ASN A 126 ILE A 130 5 5 HELIX 6 AA6 PRO A 151 ASN A 170 1 20 HELIX 7 AA7 CYS A 214 LYS A 225 1 12 HELIX 8 AA8 VAL A 226 VAL A 231 1 6 HELIX 9 AA9 PRO A 232 LEU A 236 5 5 HELIX 10 AB1 GLY A 253 GLY A 257 5 5 HELIX 11 AB2 LYS A 289 GLY A 308 1 20 HELIX 12 AB3 SER A 341 PHE A 353 1 13 HELIX 13 AB4 ARG A 356 LEU A 364 1 9 HELIX 14 AB5 TYR A 371 ALA A 375 5 5 HELIX 15 AB6 PHE A 385 VAL A 389 5 5 SHEET 1 AA1 4 PHE A 18 VAL A 25 0 SHEET 2 AA1 4 LEU A 176 ASP A 191 -1 O TYR A 188 N PHE A 18 SHEET 3 AA1 4 ALA A 194 HIS A 209 -1 O ILE A 198 N GLN A 187 SHEET 4 AA1 4 ILE A 241 LEU A 244 1 O HIS A 243 N ILE A 203 SHEET 1 AA2 4 ASN A 105 GLU A 111 0 SHEET 2 AA2 4 MET A 64 THR A 72 1 N LEU A 67 O ALA A 109 SHEET 3 AA2 4 LYS A 53 LYS A 61 -1 N LYS A 53 O THR A 72 SHEET 4 AA2 4 GLY A 260 LEU A 261 -1 O GLY A 260 N ALA A 60 SHEET 1 AA3 2 ASP A 93 ASP A 94 0 SHEET 2 AA3 2 PHE A 99 ASP A 100 -1 O PHE A 99 N ASP A 94 SHEET 1 AA4 3 GLY A 136 THR A 143 0 SHEET 2 AA4 3 ARG A 313 TYR A 320 -1 O VAL A 316 N GLY A 140 SHEET 3 AA4 3 SER A 329 PHE A 333 -1 O PHE A 333 N LEU A 315 LINK OD2 ASP A 31 MG A MG A 402 1555 1555 2.08 LINK OE2 GLU A 57 K A K A 404 1555 2555 2.71 LINK OD1 ASP A 258 K A K A 404 1555 1555 2.73 LINK O ALA A 259 K A K A 404 1555 1555 2.80 LINK O2GAPPK A 401 MG A MG A 402 1555 1555 1.97 LINK O1BAPPK A 401 MG A MG A 402 1555 1555 2.04 LINK O1AAPPK A 401 MG A MG A 402 1555 1555 1.98 LINK O3GAPPK A 401 MG A MG A 403 1555 1555 2.16 LINK O4AAPPK A 401 MG A MG A 403 1555 1555 1.97 LINK O1BAPPK A 401 K A K A 404 1555 1555 2.69 LINK MG A MG A 402 O HOH A 538 1555 1555 2.17 LINK MG A MG A 402 O HOH A 552 1555 1555 2.14 LINK MG A MG A 403 O HOH A 533 1555 2555 1.97 LINK MG A MG A 403 O HOH A 536 1555 1555 2.13 LINK MG A MG A 403 O AHOH A 573 1555 2555 2.18 LINK MG A MG A 403 O HOH A 624 1555 1555 2.24 LINK K A K A 404 O AHOH A 509 1555 1555 3.30 LINK K A K A 404 O HOH A 538 1555 1555 3.21 LINK K A K A 404 O HOH A 552 1555 1555 3.22 LINK K A K A 404 O HOH A 553 1555 2555 3.05 LINK K A K A 405 O AHOH A 665 1555 1555 2.87 LINK K A K A 405 O HOH A 751 1555 1555 2.73 SITE 1 AC1 23 HIS A 29 ASP A 31 ASP A 134 LYS A 181 SITE 2 AC1 23 ARG A 264 LYS A 265 GLY A 280 ALA A 281 SITE 3 AC1 23 LYS A 285 ASP A 291 MG A 402 MG A 403 SITE 4 AC1 23 K A 404 SAM A 406 HOH A 506 HOH A 509 SITE 5 AC1 23 HOH A 533 HOH A 536 HOH A 538 HOH A 541 SITE 6 AC1 23 HOH A 552 HOH A 573 HOH A 624 SITE 1 AC2 5 ASP A 31 LYS A 265 PPK A 401 HOH A 538 SITE 2 AC2 5 HOH A 552 SITE 1 AC3 5 PPK A 401 HOH A 533 HOH A 536 HOH A 573 SITE 2 AC3 5 HOH A 624 SITE 1 AC4 5 GLU A 57 ASP A 258 ALA A 259 PPK A 401 SITE 2 AC4 5 HOH A 553 SITE 1 AC5 6 MET A 138 PHE A 139 HIS A 277 GLY A 278 SITE 2 AC5 6 HOH A 665 HOH A 751 SITE 1 AC6 23 HIS A 29 PRO A 30 ALA A 55 GLU A 70 SITE 2 AC6 23 GLN A 113 ASP A 116 ILE A 117 GLY A 133 SITE 3 AC6 23 ASP A 134 ASP A 179 LYS A 181 SER A 247 SITE 4 AC6 23 ARG A 249 PHE A 250 ASP A 258 LYS A 289 SITE 5 AC6 23 PPK A 401 HOH A 509 HOH A 565 HOH A 579 SITE 6 AC6 23 HOH A 618 HOH A 622 HOH A 716 SITE 1 AC7 4 HOH A 587 HOH A 621 HOH A 641 HOH A 730 SITE 1 AC8 7 GLN A 36 HIS A 89 GLN A 372 ARG A 373 SITE 2 AC8 7 TYR A 377 HOH A 613 HOH A 737 SITE 1 AC9 5 PHE A 18 GLN A 190 ARG A 313 PHE A 333 SITE 2 AC9 5 TYR A 335 CRYST1 67.630 94.000 116.690 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 0.014786 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010638 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008570 0.00000