HEADER TRANSFERASE 19-DEC-17 6FBO TITLE HUMAN METHIONINE ADENOSYLTRANSFERASE II MUTANT (S114A) IN I222 CRYSTAL TITLE 2 FORM 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; COMPND 8 MUTATION: 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 6FBO 1 LINK REVDAT 2 14-AUG-19 6FBO 1 JRNL REVDAT 1 30-JAN-19 6FBO 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. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 58.28 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 32796 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) : 0.152 REMARK 3 R VALUE (WORKING SET) : 0.151 REMARK 3 FREE R VALUE : 0.174 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1697 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2417 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.84 REMARK 3 BIN R VALUE (WORKING SET) : 0.2550 REMARK 3 BIN FREE R VALUE SET COUNT : 113 REMARK 3 BIN FREE R VALUE : 0.2430 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2958 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 79 REMARK 3 SOLVENT ATOMS : 218 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.78 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.48000 REMARK 3 B22 (A**2) : -0.87000 REMARK 3 B33 (A**2) : -2.61000 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): 0.113 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.101 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3137 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2960 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4244 ; 1.671 ; 1.982 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6863 ; 3.655 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 394 ; 6.413 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 135 ;39.130 ;23.852 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 533 ;13.112 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;19.655 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 467 ; 0.103 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3479 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 625 ; 0.009 ; 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): 1552 ; 1.524 ; 1.968 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1551 ; 1.522 ; 1.967 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1948 ; 2.293 ; 2.946 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1949 ; 2.293 ; 2.947 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1585 ; 2.437 ; 2.346 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1585 ; 2.436 ; 2.346 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2295 ; 3.824 ; 3.366 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 15469 ; 5.664 ;39.318 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 15374 ; 5.627 ;39.298 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 6FBO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1200007420. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUL-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) : 0.97 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34507 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 58.280 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.17000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 0.76600 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: MOLREP REMARK 200 STARTING MODEL: 5A1I REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG600 0.1M HEPES PH.7.0, PH 7.0, REMARK 280 VAPOR 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 33.31050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.34100 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 58.27500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 33.31050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.34100 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 58.27500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 33.31050 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 47.34100 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 58.27500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 33.31050 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 47.34100 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 58.27500 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: 27300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 45110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -76.0 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 632 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 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 15 CG CD OE1 OE2 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 62 112.97 -35.66 REMARK 500 PHE A 250 64.83 -152.53 REMARK 500 THR A 270 -100.55 -121.87 REMARK 500 ASP A 383 10.42 80.11 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 MG A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 31 OD2 REMARK 620 2 PPK A 401 O2G 88.8 REMARK 620 3 PPK A 401 O1B 177.5 93.2 REMARK 620 4 PPK A 401 O1A 86.2 90.7 92.3 REMARK 620 5 HOH A 504 O 93.3 177.7 84.7 88.4 REMARK 620 6 HOH A 513 O 89.8 94.4 91.5 173.4 86.6 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 38.0 REMARK 620 3 ALA A 259 O 33.8 5.8 REMARK 620 4 PPK A 401 O1B 40.5 9.6 14.6 REMARK 620 5 HOH A 501 O 46.8 9.9 15.6 8.4 REMARK 620 6 HOH A 504 O 32.0 7.7 8.6 9.2 14.9 REMARK 620 7 HOH A 513 O 37.3 6.9 11.1 3.9 10.1 5.5 REMARK 620 8 HOH A 523 O 46.5 9.7 12.7 16.0 9.9 17.4 15.2 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 89.6 REMARK 620 3 HOH A 524 O 106.5 86.5 REMARK 620 4 HOH A 548 O 81.2 95.0 172.1 REMARK 620 5 HOH A 561 O 168.6 87.1 84.2 88.2 REMARK 620 N 1 2 3 4 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 591 O REMARK 620 2 HOH A 594 O 44.1 REMARK 620 3 HOH A 662 O 123.8 157.3 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 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 ADN A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 413 DBREF 6FBO A 1 395 UNP P31153 METK2_HUMAN 1 395 SEQADV 6FBO ALA A 114 UNP P31153 SER 114 ENGINEERED MUTATION 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 ALA 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 ADN A 406 19 HET PG4 A 407 13 HET PEG A 408 7 HET PEG A 409 7 HET EDO A 410 4 HET EDO A 411 4 HET EDO A 412 4 HET EDO A 413 4 HETNAM PPK (DIPHOSPHONO)AMINOPHOSPHONIC ACID HETNAM MG MAGNESIUM ION HETNAM K POTASSIUM ION HETNAM ADN ADENOSINE HETNAM PG4 TETRAETHYLENE GLYCOL HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM EDO 1,2-ETHANEDIOL 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 ADN C10 H13 N5 O4 FORMUL 8 PG4 C8 H18 O5 FORMUL 9 PEG 2(C4 H10 O3) FORMUL 11 EDO 4(C2 H6 O2) FORMUL 15 HOH *218(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 ALA 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 ILE A 370 ALA A 375 1 6 HELIX 15 AB6 PHE A 385 VAL A 389 5 5 SHEET 1 AA1 4 THR A 17 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 LEU A 196 N MET A 189 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 GLU A 57 O ALA A 68 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 2.10 LINK OE2 GLU A 57 K A K A 404 1555 2555 2.67 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 2.83 LINK O2GAPPK A 401 MG A MG A 402 1555 1555 2.05 LINK O1BAPPK A 401 MG A MG A 402 1555 1555 2.07 LINK O1AAPPK A 401 MG A MG A 402 1555 1555 1.99 LINK O3GAPPK A 401 MG A MG A 403 1555 1555 2.10 LINK O4AAPPK A 401 MG A MG A 403 1555 1555 2.07 LINK O1BAPPK A 401 K A K A 404 1555 1555 2.60 LINK MG A MG A 402 O AHOH A 504 1555 1555 2.17 LINK MG A MG A 402 O HOH A 513 1555 1555 2.17 LINK MG A MG A 403 O AHOH A 524 1555 2555 2.16 LINK MG A MG A 403 O AHOH A 548 1555 1555 2.19 LINK MG A MG A 403 O HOH A 561 1555 1555 2.31 LINK K A K A 404 O HOH A 501 1555 1555 2.90 LINK K A K A 404 O AHOH A 504 1555 1555 3.07 LINK K A K A 404 O HOH A 513 1555 1555 3.24 LINK K A K A 404 O HOH A 523 1555 2555 2.83 LINK K A K A 405 O HOH A 591 1555 1555 3.39 LINK K A K A 405 O AHOH A 594 1555 1555 3.43 LINK K A K A 405 O AHOH A 662 1555 1555 2.72 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 ADN A 406 HOH A 501 HOH A 504 SITE 5 AC1 23 HOH A 513 HOH A 524 HOH A 534 HOH A 545 SITE 6 AC1 23 HOH A 548 HOH A 549 HOH A 561 SITE 1 AC2 6 ASP A 31 LYS A 265 PPK A 401 K A 404 SITE 2 AC2 6 HOH A 504 HOH A 513 SITE 1 AC3 5 PPK A 401 HOH A 524 HOH A 534 HOH A 548 SITE 2 AC3 5 HOH A 561 SITE 1 AC4 8 GLU A 57 ASP A 258 ALA A 259 PPK A 401 SITE 2 AC4 8 MG A 402 HOH A 501 HOH A 504 HOH A 523 SITE 1 AC5 5 MET A 138 PHE A 139 HIS A 277 GLY A 278 SITE 2 AC5 5 HOH A 662 SITE 1 AC6 14 HIS A 29 PRO A 30 ASP A 116 ILE A 117 SITE 2 AC6 14 ASP A 134 ASP A 179 LYS A 181 SER A 247 SITE 3 AC6 14 ARG A 249 PHE A 250 ASP A 258 PPK A 401 SITE 4 AC6 14 HOH A 530 HOH A 665 SITE 1 AC7 4 GLN A 190 ARG A 313 PHE A 333 TYR A 335 SITE 1 AC8 5 HIS A 89 GLN A 372 ARG A 373 TYR A 377 SITE 2 AC8 5 HOH A 529 SITE 1 AC9 1 ALA A 162 SITE 1 AD1 3 PRO A 327 LEU A 328 LYS A 350 SITE 1 AD2 5 THR A 62 ARG A 84 LYS A 102 GLU A 111 SITE 2 AD2 5 GLN A 256 SITE 1 AD3 1 THR A 72 SITE 1 AD4 2 GLN A 47 GLN A 48 CRYST1 66.621 94.682 116.550 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 0.015010 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010562 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008580 0.00000