HEADER TRANSFERASE 10-JUN-19 6P9V TITLE CRYSTAL STRUCTURE OF HMAT MUTANT K289L 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS ADENOSYL TRANSFERASE, ADOMET SYNTHASE, NATURAL PRODUCT ENZYME, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.D.MILLER,W.XU,T.D.HUBER,J.A.CLINGER,Y.LIU,J.S.THORSON,G.N.PHILLIPS AUTHOR 2 JR. REVDAT 3 11-OCT-23 6P9V 1 REMARK REVDAT 2 15-SEP-21 6P9V 1 AUTHOR LINK REVDAT 1 22-APR-20 6P9V 0 JRNL AUTH T.D.HUBER,J.A.CLINGER,Y.LIU,W.XU,M.D.MILLER, JRNL AUTH 2 G.N.PHILLIPS JR.,J.S.THORSON JRNL TITL METHIONINE ADENOSYLTRANSFERASE ENGINEERING TO ENABLE JRNL TITL 2 BIOORTHOGONAL PLATFORMS FOR ADOMET-UTILIZING ENZYMES. JRNL REF ACS CHEM.BIOL. V. 15 695 2020 JRNL REFN ESSN 1554-8937 JRNL PMID 32091873 JRNL DOI 10.1021/ACSCHEMBIO.9B00943 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 72.0 REMARK 3 NUMBER OF REFLECTIONS : 16835 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 825 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 39.7400 - 3.7261 1.00 3836 215 0.1544 0.1745 REMARK 3 2 3.7261 - 2.9578 1.00 3719 192 0.1619 0.1978 REMARK 3 3 2.9578 - 2.5840 0.85 3124 167 0.1902 0.2420 REMARK 3 4 2.5840 - 2.3478 0.63 2319 102 0.2098 0.2412 REMARK 3 5 2.3478 - 2.1795 0.49 1799 91 0.2225 0.2508 REMARK 3 6 2.1795 - 2.0510 0.33 1213 58 0.2497 0.3250 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.360 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 45.82 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.93 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.002 3155 REMARK 3 ANGLE : 0.642 4308 REMARK 3 CHIRALITY : 0.048 477 REMARK 3 PLANARITY : 0.004 564 REMARK 3 DIHEDRAL : 11.291 1929 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 16 THROUGH 395) REMARK 3 ORIGIN FOR THE GROUP (A): 8.3014 7.9366 32.2543 REMARK 3 T TENSOR REMARK 3 T11: 0.1783 T22: 0.1289 REMARK 3 T33: 0.1513 T12: -0.0340 REMARK 3 T13: 0.0077 T23: 0.0133 REMARK 3 L TENSOR REMARK 3 L11: 0.7535 L22: 1.0158 REMARK 3 L33: 1.2797 L12: -0.1176 REMARK 3 L13: -0.0769 L23: 0.0115 REMARK 3 S TENSOR REMARK 3 S11: -0.0315 S12: 0.0422 S13: 0.0332 REMARK 3 S21: -0.0762 S22: 0.0241 S23: -0.1209 REMARK 3 S31: -0.0415 S32: 0.0845 S33: 0.0065 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 1. DATA WAS ANIOSTROPICALLY TRUNCATED WITH STARANISO. REMARK 3 2. REFERENCE MODEL RESTRAINTS DERRIVED FROM A HIGHER RESOLUTION REMARK 3 NATIVE STRUCTURE, REMARK 3 PDB-ID 2P02, WERE APPLIED THROUGHOUT. REMARK 3 3. WHILE THE CRYSTALLIZATION DROP WAS SETUP WITH PROTEIN IN A REMARK 3 BUFFER CONTAINING 0.002M ADP, REMARK 3 THE DENSITY IN THE ATP BINDING SITE HAD A BREAK INDICATING THAT IT REMARK 3 WAS LIKELY ADENOSINE AND REMARK 3 NOT ADP BOUND. THE DENSITY IN THE REGION OF THE PHOSPHATE BINDING REMARK 3 SITE WAS DISORDERED. IN THE END, REMARK 3 IT WAS MODELED AS A DISORDERED PYROPHOSPHATE WITH A MAGNESIUM ION REMARK 3 FROM THE PROTEIN BUFFER AND A REMARK 3 POTASSIUM ION FROM THE CRYSTALLIZATION CONDITION. REMARK 4 REMARK 4 6P9V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUN-19. REMARK 100 THE DEPOSITION ID IS D_1000242071. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-DEC-17 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 : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9787 REMARK 200 MONOCHROMATOR : DIAMOND REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS VERSION JUN 1, 2017 REMARK 200 BUILT=20170923 REMARK 200 DATA SCALING SOFTWARE : XDS VERSION JUN 1, 2017 REMARK 200 BUILT=20170923 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16840 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.051 REMARK 200 RESOLUTION RANGE LOW (A) : 39.742 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 72.0 REMARK 200 DATA REDUNDANCY : 8.680 REMARK 200 R MERGE (I) : 0.19400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.2900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 6.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 39.74 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 7.46 REMARK 200 R MERGE FOR SHELL (I) : 0.04700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 30.74 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 2P02 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M KCL, 0.05M HEPES, 35% (V/V) REMARK 280 PENTAEYTHRITOL PROPOXYLATE (5/4 PO/OH), PROTEIN BUFFER ADDITIVES: REMARK 280 0.002M ADP, 0.005M MAGNESIUM CHLORIDE, 0.010M METOL -- [(S)-(-)- REMARK 280 METHIONINOL], PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 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 33.17400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.31200 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 58.28650 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 33.17400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.31200 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 58.28650 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 33.17400 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 47.31200 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 58.28650 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 33.17400 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 47.31200 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 58.28650 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: 8450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 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 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 548 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 -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 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 147 CD OE1 OE2 REMARK 470 GLU A 212 CD OE1 OE2 REMARK 470 GLU A 238 CD OE1 OE2 REMARK 470 ARG A 343 NE CZ NH1 NH2 REMARK 470 GLU A 347 CD OE1 OE2 REMARK 470 LYS A 394 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 HZ3 LYS A 265 O2 POP A 404 1.59 REMARK 500 HD22 ASN A 126 O HOH A 507 1.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OD2 ASP A 291 O1 POP A 404 2555 1.91 REMARK 500 OD2 ASP A 291 O5 POP A 404 2555 1.95 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 VAL A 226 -67.94 -108.53 REMARK 500 THR A 270 -103.24 -121.32 REMARK 500 ARG A 292 -62.08 -92.64 REMARK 500 TYR A 335 18.50 59.98 REMARK 500 ASP A 383 10.26 55.14 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 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 31 OD2 REMARK 620 2 POP A 404 O3 82.6 REMARK 620 3 POP A 404 O5 92.5 10.0 REMARK 620 4 POP A 404 O2 172.2 97.5 87.5 REMARK 620 5 POP A 404 O4 171.4 99.1 89.0 1.6 REMARK 620 6 POP A 404 O2 88.8 78.6 80.5 98.8 99.8 REMARK 620 7 POP A 404 O4 86.8 106.9 109.3 100.5 100.7 28.9 REMARK 620 8 HOH A 501 O 92.7 108.8 110.2 94.6 94.7 30.2 6.0 REMARK 620 9 HOH A 502 O 105.3 24.5 14.9 73.8 75.2 88.5 116.8 116.2 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 402 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 57 OE2 REMARK 620 2 ASP A 258 OD1 43.7 REMARK 620 3 ASP A 258 OD2 38.6 6.3 REMARK 620 4 ALA A 259 O 38.8 6.1 6.9 REMARK 620 5 POP A 404 O2 47.5 11.7 11.2 16.7 REMARK 620 6 POP A 404 O4 47.3 11.4 11.0 16.4 0.2 REMARK 620 7 HOH A 508 O 37.8 8.9 3.0 9.8 10.3 10.1 REMARK 620 8 HOH A 545 O 42.6 8.5 6.0 12.2 5.4 5.2 5.0 REMARK 620 9 HOH A 561 O 51.1 8.4 14.6 12.2 16.1 16.0 17.1 15.4 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ADN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K 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 POP A 404 DBREF 6P9V A 1 395 UNP P31153 METK2_HUMAN 1 395 SEQADV 6P9V MET A -19 UNP P31153 INITIATING METHIONINE SEQADV 6P9V GLY A -18 UNP P31153 EXPRESSION TAG SEQADV 6P9V SER A -17 UNP P31153 EXPRESSION TAG SEQADV 6P9V SER A -16 UNP P31153 EXPRESSION TAG SEQADV 6P9V HIS A -15 UNP P31153 EXPRESSION TAG SEQADV 6P9V HIS A -14 UNP P31153 EXPRESSION TAG SEQADV 6P9V HIS A -13 UNP P31153 EXPRESSION TAG SEQADV 6P9V HIS A -12 UNP P31153 EXPRESSION TAG SEQADV 6P9V HIS A -11 UNP P31153 EXPRESSION TAG SEQADV 6P9V HIS A -10 UNP P31153 EXPRESSION TAG SEQADV 6P9V SER A -9 UNP P31153 EXPRESSION TAG SEQADV 6P9V SER A -8 UNP P31153 EXPRESSION TAG SEQADV 6P9V GLY A -7 UNP P31153 EXPRESSION TAG SEQADV 6P9V LEU A -6 UNP P31153 EXPRESSION TAG SEQADV 6P9V VAL A -5 UNP P31153 EXPRESSION TAG SEQADV 6P9V PRO A -4 UNP P31153 EXPRESSION TAG SEQADV 6P9V ARG A -3 UNP P31153 EXPRESSION TAG SEQADV 6P9V GLY A -2 UNP P31153 EXPRESSION TAG SEQADV 6P9V SER A -1 UNP P31153 EXPRESSION TAG SEQADV 6P9V HIS A 0 UNP P31153 EXPRESSION TAG SEQADV 6P9V LEU A 289 UNP P31153 LYS 289 ENGINEERED MUTATION SEQRES 1 A 415 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 415 LEU VAL PRO ARG GLY SER HIS MET ASN GLY GLN LEU ASN SEQRES 3 A 415 GLY PHE HIS GLU ALA PHE ILE GLU GLU GLY THR PHE LEU SEQRES 4 A 415 PHE THR SER GLU SER VAL GLY GLU GLY HIS PRO ASP LYS SEQRES 5 A 415 ILE CYS ASP GLN ILE SER ASP ALA VAL LEU ASP ALA HIS SEQRES 6 A 415 LEU GLN GLN ASP PRO ASP ALA LYS VAL ALA CYS GLU THR SEQRES 7 A 415 VAL ALA LYS THR GLY MET ILE LEU LEU ALA GLY GLU ILE SEQRES 8 A 415 THR SER ARG ALA ALA VAL ASP TYR GLN LYS VAL VAL ARG SEQRES 9 A 415 GLU ALA VAL LYS HIS ILE GLY TYR ASP ASP SER SER LYS SEQRES 10 A 415 GLY PHE ASP TYR LYS THR CYS ASN VAL LEU VAL ALA LEU SEQRES 11 A 415 GLU GLN GLN SER PRO ASP ILE ALA GLN GLY VAL HIS LEU SEQRES 12 A 415 ASP ARG ASN GLU GLU ASP ILE GLY ALA GLY ASP GLN GLY SEQRES 13 A 415 LEU MET PHE GLY TYR ALA THR ASP GLU THR GLU GLU CYS SEQRES 14 A 415 MET PRO LEU THR ILE VAL LEU ALA HIS LYS LEU ASN ALA SEQRES 15 A 415 LYS LEU ALA GLU LEU ARG ARG ASN GLY THR LEU PRO TRP SEQRES 16 A 415 LEU ARG PRO ASP SER LYS THR GLN VAL THR VAL GLN TYR SEQRES 17 A 415 MET GLN ASP ARG GLY ALA VAL LEU PRO ILE ARG VAL HIS SEQRES 18 A 415 THR ILE VAL ILE SER VAL GLN HIS ASP GLU GLU VAL CYS SEQRES 19 A 415 LEU ASP GLU MET ARG ASP ALA LEU LYS GLU LYS VAL ILE SEQRES 20 A 415 LYS ALA VAL VAL PRO ALA LYS TYR LEU ASP GLU ASP THR SEQRES 21 A 415 ILE TYR HIS LEU GLN PRO SER GLY ARG PHE VAL ILE GLY SEQRES 22 A 415 GLY PRO GLN GLY ASP ALA GLY LEU THR GLY ARG LYS ILE SEQRES 23 A 415 ILE VAL ASP THR TYR GLY GLY TRP GLY ALA HIS GLY GLY SEQRES 24 A 415 GLY ALA PHE SER GLY LYS ASP TYR THR LEU VAL ASP ARG SEQRES 25 A 415 SER ALA ALA TYR ALA ALA ARG TRP VAL ALA LYS SER LEU SEQRES 26 A 415 VAL LYS GLY GLY LEU CYS ARG ARG VAL LEU VAL GLN VAL SEQRES 27 A 415 SER TYR ALA ILE GLY VAL SER HIS PRO LEU SER ILE SER SEQRES 28 A 415 ILE PHE HIS TYR GLY THR SER GLN LYS SER GLU ARG GLU SEQRES 29 A 415 LEU LEU GLU ILE VAL LYS LYS ASN PHE ASP LEU ARG PRO SEQRES 30 A 415 GLY VAL ILE VAL ARG ASP LEU ASP LEU LYS LYS PRO ILE SEQRES 31 A 415 TYR GLN ARG THR ALA ALA TYR GLY HIS PHE GLY ARG ASP SEQRES 32 A 415 SER PHE PRO TRP GLU VAL PRO LYS LYS LEU LYS TYR HET ADN A 401 31 HET K A 402 1 HET MG A 403 1 HET POP A 404 36 HETNAM ADN ADENOSINE HETNAM K POTASSIUM ION HETNAM MG MAGNESIUM ION HETNAM POP PYROPHOSPHATE 2- FORMUL 2 ADN C10 H13 N5 O4 FORMUL 3 K K 1+ FORMUL 4 MG MG 2+ FORMUL 5 POP H2 O7 P2 2- FORMUL 6 HOH *158(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 LEU A 289 GLY A 308 1 20 HELIX 12 AB3 SER A 341 PHE A 353 1 13 HELIX 13 AB4 ARG A 356 ASP A 365 1 10 HELIX 14 AB5 ILE A 370 ALA A 375 5 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 VAL A 184 N SER A 22 SHEET 3 AA1 4 ALA A 194 HIS A 209 -1 O GLN A 208 N ASP A 179 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 MG A 403 1555 1555 2.16 LINK OE2 GLU A 57 K K A 402 1555 2555 2.78 LINK OD1 ASP A 258 K K A 402 1555 1555 2.76 LINK OD2 ASP A 258 K K A 402 1555 1555 3.39 LINK O ALA A 259 K K A 402 1555 1555 3.06 LINK K K A 402 O2 BPOP A 404 1555 1555 2.75 LINK K K A 402 O4 DPOP A 404 1555 1555 2.69 LINK K K A 402 O HOH A 508 1555 1555 3.04 LINK K K A 402 O HOH A 545 1555 1555 3.10 LINK K K A 402 O HOH A 561 1555 2555 2.73 LINK K K A 402 O AHOH A 625 1555 1555 2.88 LINK K K A 402 O CHOH A 634 1555 1555 3.00 LINK MG MG A 403 O3 APOP A 404 1555 1555 2.11 LINK MG MG A 403 O5 BPOP A 404 1555 1555 1.79 LINK MG MG A 403 O2 BPOP A 404 1555 1555 2.25 LINK MG MG A 403 O4 DPOP A 404 1555 1555 2.21 LINK MG MG A 403 O2 DPOP A 404 1555 1555 2.17 LINK MG MG A 403 O4 CPOP A 404 1555 1555 1.86 LINK MG MG A 403 O BHOH A 501 1555 1555 2.14 LINK MG MG A 403 O CHOH A 502 1555 1555 2.09 LINK MG MG A 403 O HOH A 508 1555 1555 2.07 LINK MG MG A 403 O HOH A 545 1555 1555 1.99 LINK MG MG A 403 O AHOH A 625 1555 1555 2.27 SITE 1 AC1 14 HIS A 29 PRO A 30 ASP A 116 ILE A 117 SITE 2 AC1 14 ASP A 134 ASP A 179 LYS A 181 SER A 247 SITE 3 AC1 14 ARG A 249 PHE A 250 ASP A 258 POP A 404 SITE 4 AC1 14 HOH A 509 HOH A 598 SITE 1 AC2 9 GLU A 57 ASP A 258 ALA A 259 MG A 403 SITE 2 AC2 9 POP A 404 HOH A 508 HOH A 561 HOH A 625 SITE 3 AC2 9 HOH A 634 SITE 1 AC3 9 ASP A 31 LYS A 265 K A 402 POP A 404 SITE 2 AC3 9 HOH A 501 HOH A 502 HOH A 508 HOH A 545 SITE 3 AC3 9 HOH A 625 SITE 1 AC4 27 HIS A 29 ASP A 31 ASP A 134 LYS A 181 SITE 2 AC4 27 ASP A 258 ARG A 264 LYS A 265 GLY A 279 SITE 3 AC4 27 GLY A 280 ALA A 281 LYS A 285 ASP A 291 SITE 4 AC4 27 ADN A 401 K A 402 MG A 403 HOH A 501 SITE 5 AC4 27 HOH A 502 HOH A 503 HOH A 504 HOH A 508 SITE 6 AC4 27 HOH A 516 HOH A 545 HOH A 549 HOH A 574 SITE 7 AC4 27 HOH A 607 HOH A 625 HOH A 634 CRYST1 66.348 94.624 116.573 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 0.015072 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010568 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008578 0.00000