HEADER TRANSFERASE 19-DEC-17 6FBN TITLE HUMAN METHIONINE ADENOSYLTRANSFERASE II MUTANT (Q113A) COMPND MOL_ID: 1; COMPND 2 MOLECULE: S-ADENOSYLMETHIONINE SYNTHASE ISOFORM TYPE-2; COMPND 3 CHAIN: A, B; 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 6FBN 1 LINK REVDAT 2 14-AUG-19 6FBN 1 JRNL REVDAT 1 30-JAN-19 6FBN 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. 2.70 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 103.93 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 19576 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) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 966 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) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1429 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.93 REMARK 3 BIN R VALUE (WORKING SET) : 0.2790 REMARK 3 BIN FREE R VALUE SET COUNT : 71 REMARK 3 BIN FREE R VALUE : 0.3010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5711 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 77 REMARK 3 SOLVENT ATOMS : 85 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 44.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.82 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.51000 REMARK 3 B22 (A**2) : -2.76000 REMARK 3 B33 (A**2) : -1.75000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.286 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.236 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.684 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5894 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5505 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7976 ; 1.548 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12745 ; 1.073 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 737 ; 6.580 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 253 ;35.953 ;23.953 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 983 ;16.365 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;19.615 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 891 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6539 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1172 ; 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): 2963 ; 2.069 ; 4.567 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2963 ; 2.069 ; 4.567 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3695 ; 3.356 ; 6.838 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3696 ; 3.355 ; 6.838 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2931 ; 2.188 ; 4.827 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2931 ; 2.185 ; 4.828 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4282 ; 3.563 ; 7.144 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 24153 ; 6.538 ;86.353 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 24154 ; 6.538 ;86.353 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 6FBN 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_1200007415. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-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 : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9282 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20580 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 103.930 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.14300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : 0.77600 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 (%): 44.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG600 0.1M HEPES PH7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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+1/2,-Z+1/2 REMARK 290 4555 -X,-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 51.96700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.89350 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.96700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 54.89350 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 MET B 1 REMARK 465 ASN B 2 REMARK 465 GLY B 3 REMARK 465 GLN B 4 REMARK 465 LEU B 5 REMARK 465 ASN B 6 REMARK 465 GLY B 7 REMARK 465 PHE B 8 REMARK 465 HIS B 9 REMARK 465 GLU B 10 REMARK 465 ALA B 11 REMARK 465 PHE B 12 REMARK 465 ILE B 13 REMARK 465 GLU B 14 REMARK 465 GLU B 15 REMARK 465 ILE B 117 REMARK 465 ALA B 118 REMARK 465 GLN B 119 REMARK 465 GLY B 120 REMARK 465 VAL B 121 REMARK 465 HIS B 122 REMARK 465 LEU B 123 REMARK 465 ASP B 124 REMARK 465 ARG B 125 REMARK 465 ASN B 126 REMARK 465 GLU B 127 REMARK 465 GLU B 128 REMARK 465 ASP B 129 REMARK 465 ILE B 130 REMARK 465 GLY B 131 REMARK 465 ALA B 132 REMARK 465 GLY B 133 REMARK 465 ALA B 321 REMARK 465 ILE B 322 REMARK 465 GLY B 323 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 LYS A 81 CG CD CE NZ REMARK 470 LEU A 215 CD1 REMARK 470 LYS A 228 CD CE NZ REMARK 470 GLU A 238 CG CD OE1 OE2 REMARK 470 ARG A 249 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 370 CG1 CD1 REMARK 470 ASP A 383 CG OD1 OD2 REMARK 470 LYS A 392 CD CE NZ REMARK 470 LYS A 394 CG CD CE NZ REMARK 470 GLU B 238 CG CD OE1 OE2 REMARK 470 LEU B 328 CG CD1 CD2 REMARK 470 ARG B 343 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 351 CG CD CE NZ REMARK 470 ARG B 373 CD NE CZ NH1 NH2 REMARK 470 LYS B 394 CG CD CE NZ 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 ALA A 376 NH2 ARG A 382 2.19 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 CYS A 214 CA - CB - SG ANGL. DEV. = 7.0 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 62 104.51 -29.00 REMARK 500 CYS A 149 40.26 70.55 REMARK 500 ILE A 198 -62.90 -101.34 REMARK 500 VAL A 226 -71.98 -107.29 REMARK 500 THR A 270 -87.73 -117.22 REMARK 500 THR B 62 110.92 -34.67 REMARK 500 GLN B 135 -168.06 -126.31 REMARK 500 ASP B 191 94.81 -166.59 REMARK 500 PHE B 250 62.01 -157.28 REMARK 500 ASP B 258 118.04 -161.80 REMARK 500 THR B 270 -100.81 -117.39 REMARK 500 PRO B 369 66.24 -68.18 REMARK 500 ASP B 383 49.71 -87.04 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 K B 405 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 57 OE2 REMARK 620 2 HOH A 503 O 89.5 REMARK 620 3 ASP B 258 OD1 160.4 70.9 REMARK 620 4 ALA B 259 O 98.7 98.3 85.2 REMARK 620 5 PPK B 402 O1B 93.6 146.9 102.5 113.8 REMARK 620 6 HOH B 507 O 115.0 147.6 83.6 59.0 56.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 404 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 31 OD1 REMARK 620 2 ASP B 31 OD2 49.3 REMARK 620 3 PPK B 402 O2G 115.9 78.7 REMARK 620 4 PPK B 402 O1B 169.1 128.7 71.2 REMARK 620 5 PPK B 402 O1A 110.0 63.9 61.0 65.2 REMARK 620 6 HOH B 507 O 81.8 89.1 139.0 87.5 78.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PPK B 402 O3G REMARK 620 2 PPK B 402 O4A 72.9 REMARK 620 3 HOH B 501 O 71.8 64.9 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 PEG A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SAM B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PPK B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K B 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 408 DBREF 6FBN A 1 395 UNP P31153 METK2_HUMAN 1 395 DBREF 6FBN B 1 395 UNP P31153 METK2_HUMAN 1 395 SEQADV 6FBN ALA A 113 UNP P31153 GLN 113 ENGINEERED MUTATION SEQADV 6FBN ALA B 113 UNP P31153 GLN 113 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 ALA 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 SEQRES 1 B 395 MET ASN GLY GLN LEU ASN GLY PHE HIS GLU ALA PHE ILE SEQRES 2 B 395 GLU GLU GLY THR PHE LEU PHE THR SER GLU SER VAL GLY SEQRES 3 B 395 GLU GLY HIS PRO ASP LYS ILE CYS ASP GLN ILE SER ASP SEQRES 4 B 395 ALA VAL LEU ASP ALA HIS LEU GLN GLN ASP PRO ASP ALA SEQRES 5 B 395 LYS VAL ALA CYS GLU THR VAL ALA LYS THR GLY MET ILE SEQRES 6 B 395 LEU LEU ALA GLY GLU ILE THR SER ARG ALA ALA VAL ASP SEQRES 7 B 395 TYR GLN LYS VAL VAL ARG GLU ALA VAL LYS HIS ILE GLY SEQRES 8 B 395 TYR ASP ASP SER SER LYS GLY PHE ASP TYR LYS THR CYS SEQRES 9 B 395 ASN VAL LEU VAL ALA LEU GLU GLN ALA SER PRO ASP ILE SEQRES 10 B 395 ALA GLN GLY VAL HIS LEU ASP ARG ASN GLU GLU ASP ILE SEQRES 11 B 395 GLY ALA GLY ASP GLN GLY LEU MET PHE GLY TYR ALA THR SEQRES 12 B 395 ASP GLU THR GLU GLU CYS MET PRO LEU THR ILE VAL LEU SEQRES 13 B 395 ALA HIS LYS LEU ASN ALA LYS LEU ALA GLU LEU ARG ARG SEQRES 14 B 395 ASN GLY THR LEU PRO TRP LEU ARG PRO ASP SER LYS THR SEQRES 15 B 395 GLN VAL THR VAL GLN TYR MET GLN ASP ARG GLY ALA VAL SEQRES 16 B 395 LEU PRO ILE ARG VAL HIS THR ILE VAL ILE SER VAL GLN SEQRES 17 B 395 HIS ASP GLU GLU VAL CYS LEU ASP GLU MET ARG ASP ALA SEQRES 18 B 395 LEU LYS GLU LYS VAL ILE LYS ALA VAL VAL PRO ALA LYS SEQRES 19 B 395 TYR LEU ASP GLU ASP THR ILE TYR HIS LEU GLN PRO SER SEQRES 20 B 395 GLY ARG PHE VAL ILE GLY GLY PRO GLN GLY ASP ALA GLY SEQRES 21 B 395 LEU THR GLY ARG LYS ILE ILE VAL ASP THR TYR GLY GLY SEQRES 22 B 395 TRP GLY ALA HIS GLY GLY GLY ALA PHE SER GLY LYS ASP SEQRES 23 B 395 TYR THR LYS VAL ASP ARG SER ALA ALA TYR ALA ALA ARG SEQRES 24 B 395 TRP VAL ALA LYS SER LEU VAL LYS GLY GLY LEU CYS ARG SEQRES 25 B 395 ARG VAL LEU VAL GLN VAL SER TYR ALA ILE GLY VAL SER SEQRES 26 B 395 HIS PRO LEU SER ILE SER ILE PHE HIS TYR GLY THR SER SEQRES 27 B 395 GLN LYS SER GLU ARG GLU LEU LEU GLU ILE VAL LYS LYS SEQRES 28 B 395 ASN PHE ASP LEU ARG PRO GLY VAL ILE VAL ARG ASP LEU SEQRES 29 B 395 ASP LEU LYS LYS PRO ILE TYR GLN ARG THR ALA ALA TYR SEQRES 30 B 395 GLY HIS PHE GLY ARG ASP SER PHE PRO TRP GLU VAL PRO SEQRES 31 B 395 LYS LYS LEU LYS TYR HET PEG A 401 7 HET PEG A 402 7 HET EDO A 403 4 HET EDO A 404 4 HET SAM B 401 27 HET PPK B 402 13 HET MG B 403 1 HET MG B 404 1 HET K B 405 1 HET EDO B 406 4 HET EDO B 407 4 HET EDO B 408 4 HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM EDO 1,2-ETHANEDIOL HETNAM SAM S-ADENOSYLMETHIONINE HETNAM PPK (DIPHOSPHONO)AMINOPHOSPHONIC ACID HETNAM MG MAGNESIUM ION HETNAM K POTASSIUM ION HETSYN EDO ETHYLENE GLYCOL FORMUL 3 PEG 2(C4 H10 O3) FORMUL 5 EDO 5(C2 H6 O2) FORMUL 7 SAM C15 H22 N6 O5 S FORMUL 8 PPK H6 N O9 P3 FORMUL 9 MG 2(MG 2+) FORMUL 11 K K 1+ FORMUL 15 HOH *85(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 PRO A 151 GLY A 171 1 21 HELIX 6 AA6 CYS A 214 VAL A 226 1 13 HELIX 7 AA7 PRO A 232 LEU A 236 5 5 HELIX 8 AA8 LYS A 289 GLY A 308 1 20 HELIX 9 AA9 SER A 341 PHE A 353 1 13 HELIX 10 AB1 ARG A 356 ASP A 365 1 10 HELIX 11 AB2 ILE A 370 ALA A 376 5 7 HELIX 12 AB3 PHE A 385 VAL A 389 5 5 HELIX 13 AB4 HIS B 29 ASP B 49 1 21 HELIX 14 AB5 ASP B 78 GLY B 91 1 14 HELIX 15 AB6 SER B 95 GLY B 98 5 4 HELIX 16 AB7 PRO B 151 GLY B 171 1 21 HELIX 17 AB8 CYS B 214 VAL B 226 1 13 HELIX 18 AB9 PRO B 232 LEU B 236 5 5 HELIX 19 AC1 GLY B 253 ASP B 258 1 6 HELIX 20 AC2 LYS B 265 THR B 270 1 6 HELIX 21 AC3 LYS B 289 GLY B 308 1 20 HELIX 22 AC4 SER B 341 PHE B 353 1 13 HELIX 23 AC5 ARG B 356 LEU B 364 1 9 HELIX 24 AC6 TYR B 371 ALA B 376 5 6 HELIX 25 AC7 PHE B 385 VAL B 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 THR A 182 N SER A 24 SHEET 3 AA1 4 ALA A 194 HIS A 209 -1 O GLN A 208 N ARG A 177 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 61 O MET A 64 SHEET 4 AA2 4 ALA A 259 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 318 N MET A 138 SHEET 3 AA4 3 SER A 329 PHE A 333 -1 O PHE A 333 N LEU A 315 SHEET 1 AA5 4 THR B 17 VAL B 25 0 SHEET 2 AA5 4 LEU B 176 ASP B 191 -1 O TYR B 188 N PHE B 18 SHEET 3 AA5 4 ALA B 194 HIS B 209 -1 O THR B 202 N THR B 185 SHEET 4 AA5 4 ILE B 241 LEU B 244 1 O ILE B 241 N HIS B 201 SHEET 1 AA6 3 ASN B 105 VAL B 108 0 SHEET 2 AA6 3 MET B 64 THR B 72 1 N ILE B 65 O ASN B 105 SHEET 3 AA6 3 GLU B 111 ALA B 113 1 O ALA B 113 N ILE B 71 SHEET 1 AA7 4 ASN B 105 VAL B 108 0 SHEET 2 AA7 4 MET B 64 THR B 72 1 N ILE B 65 O ASN B 105 SHEET 3 AA7 4 LYS B 53 LYS B 61 -1 N LYS B 53 O THR B 72 SHEET 4 AA7 4 GLY B 260 LEU B 261 -1 O GLY B 260 N ALA B 60 SHEET 1 AA8 2 ASP B 93 ASP B 94 0 SHEET 2 AA8 2 PHE B 99 ASP B 100 -1 O PHE B 99 N ASP B 94 SHEET 1 AA9 3 GLY B 136 THR B 143 0 SHEET 2 AA9 3 ARG B 313 TYR B 320 -1 O VAL B 316 N GLY B 140 SHEET 3 AA9 3 SER B 329 PHE B 333 -1 O PHE B 333 N LEU B 315 LINK OE2 GLU A 57 K K B 405 1555 1555 2.99 LINK O HOH A 503 K K B 405 1555 1555 3.08 LINK OD1 ASP B 31 MG MG B 404 1555 1555 2.86 LINK OD2 ASP B 31 MG MG B 404 1555 1555 2.20 LINK OD1 ASP B 258 K K B 405 1555 1555 2.89 LINK O ALA B 259 K K B 405 1555 1555 2.94 LINK O3G PPK B 402 MG MG B 403 1555 1555 2.44 LINK O4A PPK B 402 MG MG B 403 1555 1555 2.21 LINK O2G PPK B 402 MG MG B 404 1555 1555 2.55 LINK O1B PPK B 402 MG MG B 404 1555 1555 1.91 LINK O1A PPK B 402 MG MG B 404 1555 1555 2.62 LINK O1B PPK B 402 K K B 405 1555 1555 2.89 LINK MG MG B 403 O HOH B 501 1555 1555 2.52 LINK MG MG B 404 O HOH B 507 1555 1555 1.99 LINK K K B 405 O HOH B 507 1555 1555 2.77 SITE 1 AC1 6 ASP A 78 TYR A 79 GLN A 80 VAL A 108 SITE 2 AC1 6 ALA A 109 LEU A 110 SITE 1 AC2 6 HIS A 209 GLU A 211 VAL A 213 ARG A 249 SITE 2 AC2 6 LYS B 307 ASP B 383 SITE 1 AC3 1 ARG B 313 SITE 1 AC4 3 GLN A 256 HOH A 504 GLU B 111 SITE 1 AC5 14 GLU A 70 ILE A 117 ASP A 134 LYS A 289 SITE 2 AC5 14 HIS B 29 PRO B 30 ASP B 179 LYS B 181 SITE 3 AC5 14 SER B 247 ARG B 249 PHE B 250 ASP B 258 SITE 4 AC5 14 PPK B 402 HOH B 519 SITE 1 AC6 17 ASP A 134 GLY A 279 GLY A 280 ALA A 281 SITE 2 AC6 17 LYS A 285 ASP A 291 HIS B 29 ASP B 31 SITE 3 AC6 17 LYS B 181 ARG B 264 LYS B 265 SAM B 401 SITE 4 AC6 17 MG B 403 MG B 404 K B 405 HOH B 501 SITE 5 AC6 17 HOH B 507 SITE 1 AC7 4 GLU B 23 LYS B 265 PPK B 402 HOH B 501 SITE 1 AC8 5 ASP B 31 ARG B 264 PPK B 402 K B 405 SITE 2 AC8 5 HOH B 507 SITE 1 AC9 7 GLU A 57 HOH A 503 ASP B 258 ALA B 259 SITE 2 AC9 7 PPK B 402 MG B 404 HOH B 507 SITE 1 AD1 4 ASP A 100 THR A 103 CYS A 104 THR B 103 SITE 1 AD2 6 MET B 138 PHE B 139 THR B 270 HIS B 277 SITE 2 AD2 6 GLY B 278 ALA B 295 SITE 1 AD3 1 PRO B 232 CRYST1 63.634 103.934 109.787 90.00 90.00 90.00 P 2 21 21 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 0.015715 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009621 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009109 0.00000