HEADER TRANSFERASE 01-JUL-24 9CH1 TITLE STRUCTURE OF THE ALPHA-N-METHYLTRANSFERASE (SONM) AND RIPP PRECURSOR TITLE 2 (SONA-I65W) HETEROMERIC COMPLEX (BOUND TO SAM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: TP-METHYLASE FAMILY PROTEIN; COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: EXTRADIOL RING-CLEAVAGE DIOXYGENASE LIGAB LIGA SUBUNIT COMPND 7 DOMAIN-CONTAINING PROTEIN; COMPND 8 CHAIN: B, D; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SHEWANELLA ONEIDENSIS; SOURCE 3 ORGANISM_TAXID: 70863; SOURCE 4 GENE: SO_1478; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: SHEWANELLA ONEIDENSIS; SOURCE 9 ORGANISM_TAXID: 70863; SOURCE 10 GENE: SO_1479; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ALPHA-N-METHYLTRANSFERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR K.K.CRONE,J.W.LABONTE,M.ELIAS,M.F.FREEMAN REVDAT 1 29-JAN-25 9CH1 0 JRNL AUTH K.K.CRONE,J.W.LABONTE,M.H.ELIAS,M.F.FREEMAN JRNL TITL ALPHA-N-METHYLTRANSFERASE REGIOSPECIFICITY IS MEDIATED BY JRNL TITL 2 PROXIMAL, REDUNDANT ENZYME-SUBSTRATE INTERACTIONS. JRNL REF PROTEIN SCI. V. 34 70021 2025 JRNL REFN ESSN 1469-896X JRNL PMID 39840790 JRNL DOI 10.1002/PRO.70021 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0419 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.22 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 88.7 REMARK 3 NUMBER OF REFLECTIONS : 31868 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) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1678 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2433 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.2400 REMARK 3 BIN FREE R VALUE SET COUNT : 128 REMARK 3 BIN FREE R VALUE : 0.3030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4888 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 66 REMARK 3 SOLVENT ATOMS : 343 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.64 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.03000 REMARK 3 B22 (A**2) : -0.25000 REMARK 3 B33 (A**2) : 1.55000 REMARK 3 B12 (A**2) : -0.92000 REMARK 3 B13 (A**2) : 0.08000 REMARK 3 B23 (A**2) : 0.49000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.328 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.226 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.174 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.277 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.937 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.902 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5066 ; 0.001 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 4786 ; 0.000 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6887 ; 0.655 ; 1.810 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11022 ; 0.216 ; 1.740 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 624 ; 5.599 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 20 ; 2.806 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 830 ;11.286 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 776 ; 0.032 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5924 ; 0.002 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1122 ; 0.000 ; 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): 2514 ; 2.008 ; 2.427 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2514 ; 1.999 ; 2.427 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3132 ; 2.932 ; 4.348 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3133 ; 2.933 ; 4.350 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2552 ; 2.596 ; 2.753 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2551 ; 2.595 ; 2.751 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3756 ; 4.077 ; 4.911 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5829 ; 5.983 ;26.330 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5785 ; 5.954 ;25.820 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 302 REMARK 3 ORIGIN FOR THE GROUP (A): 1.4658 -9.7048 2.8193 REMARK 3 T TENSOR REMARK 3 T11: 0.1080 T22: 0.0698 REMARK 3 T33: 0.0353 T12: -0.0102 REMARK 3 T13: 0.0070 T23: 0.0097 REMARK 3 L TENSOR REMARK 3 L11: 0.2330 L22: 0.2074 REMARK 3 L33: 0.3288 L12: -0.0471 REMARK 3 L13: -0.0637 L23: 0.0069 REMARK 3 S TENSOR REMARK 3 S11: 0.0073 S12: -0.0177 S13: -0.0837 REMARK 3 S21: 0.0465 S22: -0.0095 S23: 0.0015 REMARK 3 S31: 0.0277 S32: -0.0153 S33: 0.0022 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 10 B 60 REMARK 3 ORIGIN FOR THE GROUP (A): -15.2959 -15.1101 -17.7800 REMARK 3 T TENSOR REMARK 3 T11: 0.0759 T22: 0.0770 REMARK 3 T33: 0.0365 T12: 0.0044 REMARK 3 T13: -0.0107 T23: -0.0040 REMARK 3 L TENSOR REMARK 3 L11: 2.9929 L22: 1.0479 REMARK 3 L33: 2.5633 L12: 0.8418 REMARK 3 L13: 0.5280 L23: -0.2125 REMARK 3 S TENSOR REMARK 3 S11: 0.1163 S12: -0.0187 S13: -0.2243 REMARK 3 S21: -0.0253 S22: 0.0446 S23: 0.0353 REMARK 3 S31: 0.2537 S32: -0.0058 S33: -0.1609 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 2 C 302 REMARK 3 ORIGIN FOR THE GROUP (A): -1.4114 9.7223 2.9696 REMARK 3 T TENSOR REMARK 3 T11: 0.0975 T22: 0.0648 REMARK 3 T33: 0.0140 T12: -0.0017 REMARK 3 T13: 0.0130 T23: 0.0019 REMARK 3 L TENSOR REMARK 3 L11: 0.2179 L22: 0.2326 REMARK 3 L33: 0.3910 L12: 0.0476 REMARK 3 L13: 0.1340 L23: 0.0376 REMARK 3 S TENSOR REMARK 3 S11: 0.0049 S12: -0.0128 S13: 0.0410 REMARK 3 S21: 0.0407 S22: 0.0020 S23: -0.0040 REMARK 3 S31: -0.0229 S32: 0.0063 S33: -0.0069 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 11 D 63 REMARK 3 ORIGIN FOR THE GROUP (A): 15.0950 15.6335 -17.4454 REMARK 3 T TENSOR REMARK 3 T11: 0.0903 T22: 0.0916 REMARK 3 T33: 0.0116 T12: 0.0125 REMARK 3 T13: 0.0226 T23: -0.0042 REMARK 3 L TENSOR REMARK 3 L11: 1.8102 L22: 1.9556 REMARK 3 L33: 1.5498 L12: 0.4745 REMARK 3 L13: -0.4778 L23: -0.8664 REMARK 3 S TENSOR REMARK 3 S11: 0.0256 S12: -0.0259 S13: 0.0818 REMARK 3 S21: 0.0230 S22: 0.0220 S23: -0.0408 REMARK 3 S31: -0.1815 S32: -0.0350 S33: -0.0477 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 9CH1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUL-24. REMARK 100 THE DEPOSITION ID IS D_1000285501. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-NOV-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.033167 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33547 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 29.220 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.5 REMARK 200 DATA REDUNDANCY : 2.290 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.6400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 240 MM SODIUM MALONATE PH 5.5 WITH 14% REMARK 280 PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z 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 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: 9960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -99.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 MET B -6 REMARK 465 HIS B -5 REMARK 465 HIS B -4 REMARK 465 HIS B -3 REMARK 465 HIS B -2 REMARK 465 HIS B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 SER B 54 REMARK 465 GLY B 55 REMARK 465 ASP B 56 REMARK 465 SER B 57 REMARK 465 SER B 58 REMARK 465 TYR B 59 REMARK 465 GLN B 60 REMARK 465 SER B 61 REMARK 465 TYR B 62 REMARK 465 LEU B 63 REMARK 465 VAL B 64 REMARK 465 TRP B 65 REMARK 465 SER B 66 REMARK 465 HIS B 67 REMARK 465 GLY B 68 REMARK 465 ASN B 69 REMARK 465 GLY B 70 REMARK 465 ASP B 71 REMARK 465 MET C 1 REMARK 465 MET D -6 REMARK 465 HIS D -5 REMARK 465 HIS D -4 REMARK 465 HIS D -3 REMARK 465 HIS D -2 REMARK 465 HIS D -1 REMARK 465 HIS D 0 REMARK 465 MET D 1 REMARK 465 SER D 2 REMARK 465 GLY D 3 REMARK 465 SER D 57 REMARK 465 SER D 58 REMARK 465 TYR D 59 REMARK 465 GLN D 60 REMARK 465 SER D 61 REMARK 465 TYR D 62 REMARK 465 LEU D 63 REMARK 465 VAL D 64 REMARK 465 TRP D 65 REMARK 465 SER D 66 REMARK 465 HIS D 67 REMARK 465 GLY D 68 REMARK 465 ASN D 69 REMARK 465 GLY D 70 REMARK 465 ASP D 71 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 HOH C 476 O HOH C 531 1.96 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 ALA A 14 -38.02 78.12 REMARK 500 ASN A 61 72.18 -108.26 REMARK 500 THR A 181 -165.58 -100.35 REMARK 500 ALA C 14 -40.73 78.43 REMARK 500 ASN C 61 48.30 81.46 REMARK 500 ASN C 248 76.25 -100.22 REMARK 500 SER D 54 -17.62 -142.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 541 DISTANCE = 7.08 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 303 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 126 OE2 REMARK 620 2 GLU C 126 OE2 77.3 REMARK 620 3 HIS C 142 NE2 137.3 105.9 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9CH0 RELATED DB: PDB REMARK 900 STRUCTURE OF THE ALPHA-N-METHYLTRANSFERASE (SONM) AND RIPP REMARK 900 PRECURSOR (SONA-I65W) HETEROMERIC COMPLEX (BOUND TO SAH) REMARK 900 RELATED ID: 9CGW RELATED DB: PDB REMARK 900 STRUCTURE OF THE ALPHA-N-METHYLTRANSFERASE (SONM) AND RIPP REMARK 900 PRECURSOR (SONA-I65W) HETEROMERIC COMPLEX (NO COFACTOR) REMARK 900 RELATED ID: 7LTE RELATED DB: PDB REMARK 900 STRUCTURE OF THE ALPHA-N-METHYLTRANSFERASE (SONM) AND RIPP REMARK 900 PRECURSOR (SONA) HETEROMERIC COMPLEX (WITH SAH) REMARK 900 RELATED ID: 7LTF RELATED DB: PDB REMARK 900 STRUCTURE OF THE ALPHA-N-METHYLTRANSFERASE (SONM MUTANT Y58F) AND REMARK 900 RIPP PRECURSOR (SONA) HETEROMERIC COMPLEX (NO COFACTOR) REMARK 900 RELATED ID: 7LTH RELATED DB: PDB REMARK 900 STRUCTURE OF THE ALPHA-N-METHYLTRANSFERASE (SONM MUTANT Y93F) AND REMARK 900 RIPP PRECURSOR (SONA) HETEROMERIC COMPLEX (NO COFACTOR) REMARK 900 RELATED ID: 7LTR RELATED DB: PDB REMARK 900 STRUCTURE OF THE HETEROMERIC COMPLEX BETWEEN THE ALPHA-N- REMARK 900 METHYLTRANSFERASE (SONM) AND A TRUNCATED CONSTRUCT OF THE RIPP REMARK 900 PRECURSOR (SONA) (WITH SAM) REMARK 900 RELATED ID: 7LTS RELATED DB: PDB REMARK 900 STRUCTURE OF THE ALPHA-N-METHYLTRANSFERASE (SONM MUTANT R67A) AND REMARK 900 RIPP PRECURSOR (SONA) HETEROMERIC COMPLEX (WITH SAH) REMARK 900 RELATED ID: 8T1T RELATED DB: PDB REMARK 900 STRUCTURE OF THE ALPHA-N-METHYLTRANSFERASE (SONM) AND RIPP REMARK 900 PRECURSOR (SONA WITH QSY DELETION) HETEROMERIC COMPLEX (BOUND TO REMARK 900 SAM) REMARK 900 RELATED ID: 8T1S RELATED DB: PDB REMARK 900 STRUCTURE OF THE ALPHA-N-METHYLTRANSFERASE (SONM) AND RIPP REMARK 900 PRECURSOR (SONA WITH QSY DELETION) HETEROMERIC COMPLEX (BOUND TO REMARK 900 SAH) DBREF 9CH1 A 1 263 UNP Q8EGW3 Q8EGW3_SHEON 1 263 DBREF 9CH1 B 1 71 UNP Q8EGW2 Q8EGW2_SHEON 1 71 DBREF 9CH1 C 1 263 UNP Q8EGW3 Q8EGW3_SHEON 1 263 DBREF 9CH1 D 1 71 UNP Q8EGW2 Q8EGW2_SHEON 1 71 SEQADV 9CH1 MET B -6 UNP Q8EGW2 INITIATING METHIONINE SEQADV 9CH1 HIS B -5 UNP Q8EGW2 EXPRESSION TAG SEQADV 9CH1 HIS B -4 UNP Q8EGW2 EXPRESSION TAG SEQADV 9CH1 HIS B -3 UNP Q8EGW2 EXPRESSION TAG SEQADV 9CH1 HIS B -2 UNP Q8EGW2 EXPRESSION TAG SEQADV 9CH1 HIS B -1 UNP Q8EGW2 EXPRESSION TAG SEQADV 9CH1 HIS B 0 UNP Q8EGW2 EXPRESSION TAG SEQADV 9CH1 TRP B 65 UNP Q8EGW2 ILE 65 ENGINEERED MUTATION SEQADV 9CH1 MET D -6 UNP Q8EGW2 INITIATING METHIONINE SEQADV 9CH1 HIS D -5 UNP Q8EGW2 EXPRESSION TAG SEQADV 9CH1 HIS D -4 UNP Q8EGW2 EXPRESSION TAG SEQADV 9CH1 HIS D -3 UNP Q8EGW2 EXPRESSION TAG SEQADV 9CH1 HIS D -2 UNP Q8EGW2 EXPRESSION TAG SEQADV 9CH1 HIS D -1 UNP Q8EGW2 EXPRESSION TAG SEQADV 9CH1 HIS D 0 UNP Q8EGW2 EXPRESSION TAG SEQADV 9CH1 TRP D 65 UNP Q8EGW2 ILE 65 ENGINEERED MUTATION SEQRES 1 A 263 MET GLY SER LEU VAL CYS VAL GLY THR GLY LEU GLN LEU SEQRES 2 A 263 ALA GLY GLN ILE SER VAL LEU SER ARG SER TYR ILE GLU SEQRES 3 A 263 HIS ALA ASP ILE VAL PHE SER LEU LEU PRO ASP GLY PHE SEQRES 4 A 263 SER GLN ARG TRP LEU THR LYS LEU ASN PRO ASN VAL ILE SEQRES 5 A 263 ASN LEU GLN GLN PHE TYR ALA GLN ASN GLY GLU VAL LYS SEQRES 6 A 263 ASN ARG ARG ASP THR TYR GLU GLN MET VAL ASN ALA ILE SEQRES 7 A 263 LEU ASP ALA VAL ARG ALA GLY LYS LYS THR VAL CYS ALA SEQRES 8 A 263 LEU TYR GLY HIS PRO GLY VAL PHE ALA CYS VAL SER HIS SEQRES 9 A 263 MET ALA ILE THR ARG ALA LYS ALA GLU GLY PHE SER ALA SEQRES 10 A 263 LYS MET GLU PRO GLY ILE SER ALA GLU ALA CYS LEU TRP SEQRES 11 A 263 ALA ASP LEU GLY ILE ASP PRO GLY ASN SER GLY HIS GLN SEQRES 12 A 263 SER PHE GLU ALA SER GLN PHE MET PHE PHE ASN HIS VAL SEQRES 13 A 263 PRO ASP PRO THR THR HIS LEU LEU LEU TRP GLN ILE ALA SEQRES 14 A 263 ILE ALA GLY GLU HIS THR LEU THR GLN PHE HIS THR SER SEQRES 15 A 263 SER ASP ARG LEU GLN ILE LEU VAL GLU GLN LEU ASN GLN SEQRES 16 A 263 TRP TYR PRO LEU ASP HIS GLU VAL VAL ILE TYR GLU ALA SEQRES 17 A 263 ALA ASN LEU PRO ILE GLN ALA PRO ARG ILE GLU ARG LEU SEQRES 18 A 263 PRO LEU ALA ASN LEU PRO GLN ALA HIS LEU MET PRO ILE SEQRES 19 A 263 SER THR LEU LEU ILE PRO PRO ALA LYS LYS LEU GLU TYR SEQRES 20 A 263 ASN TYR ALA ILE LEU ALA LYS LEU GLY ILE GLY PRO GLU SEQRES 21 A 263 ASP LEU GLY SEQRES 1 B 78 MET HIS HIS HIS HIS HIS HIS MET SER GLY LEU SER ASP SEQRES 2 B 78 PHE PHE THR GLN LEU GLY GLN ASP ALA GLN LEU MET GLU SEQRES 3 B 78 ASP TYR LYS GLN ASN PRO GLU ALA VAL MET ARG ALA HIS SEQRES 4 B 78 GLY LEU THR ASP GLU GLN ILE ASN ALA VAL MET THR GLY SEQRES 5 B 78 ASP MET GLU LYS LEU LYS THR LEU SER GLY ASP SER SER SEQRES 6 B 78 TYR GLN SER TYR LEU VAL TRP SER HIS GLY ASN GLY ASP SEQRES 1 C 263 MET GLY SER LEU VAL CYS VAL GLY THR GLY LEU GLN LEU SEQRES 2 C 263 ALA GLY GLN ILE SER VAL LEU SER ARG SER TYR ILE GLU SEQRES 3 C 263 HIS ALA ASP ILE VAL PHE SER LEU LEU PRO ASP GLY PHE SEQRES 4 C 263 SER GLN ARG TRP LEU THR LYS LEU ASN PRO ASN VAL ILE SEQRES 5 C 263 ASN LEU GLN GLN PHE TYR ALA GLN ASN GLY GLU VAL LYS SEQRES 6 C 263 ASN ARG ARG ASP THR TYR GLU GLN MET VAL ASN ALA ILE SEQRES 7 C 263 LEU ASP ALA VAL ARG ALA GLY LYS LYS THR VAL CYS ALA SEQRES 8 C 263 LEU TYR GLY HIS PRO GLY VAL PHE ALA CYS VAL SER HIS SEQRES 9 C 263 MET ALA ILE THR ARG ALA LYS ALA GLU GLY PHE SER ALA SEQRES 10 C 263 LYS MET GLU PRO GLY ILE SER ALA GLU ALA CYS LEU TRP SEQRES 11 C 263 ALA ASP LEU GLY ILE ASP PRO GLY ASN SER GLY HIS GLN SEQRES 12 C 263 SER PHE GLU ALA SER GLN PHE MET PHE PHE ASN HIS VAL SEQRES 13 C 263 PRO ASP PRO THR THR HIS LEU LEU LEU TRP GLN ILE ALA SEQRES 14 C 263 ILE ALA GLY GLU HIS THR LEU THR GLN PHE HIS THR SER SEQRES 15 C 263 SER ASP ARG LEU GLN ILE LEU VAL GLU GLN LEU ASN GLN SEQRES 16 C 263 TRP TYR PRO LEU ASP HIS GLU VAL VAL ILE TYR GLU ALA SEQRES 17 C 263 ALA ASN LEU PRO ILE GLN ALA PRO ARG ILE GLU ARG LEU SEQRES 18 C 263 PRO LEU ALA ASN LEU PRO GLN ALA HIS LEU MET PRO ILE SEQRES 19 C 263 SER THR LEU LEU ILE PRO PRO ALA LYS LYS LEU GLU TYR SEQRES 20 C 263 ASN TYR ALA ILE LEU ALA LYS LEU GLY ILE GLY PRO GLU SEQRES 21 C 263 ASP LEU GLY SEQRES 1 D 78 MET HIS HIS HIS HIS HIS HIS MET SER GLY LEU SER ASP SEQRES 2 D 78 PHE PHE THR GLN LEU GLY GLN ASP ALA GLN LEU MET GLU SEQRES 3 D 78 ASP TYR LYS GLN ASN PRO GLU ALA VAL MET ARG ALA HIS SEQRES 4 D 78 GLY LEU THR ASP GLU GLN ILE ASN ALA VAL MET THR GLY SEQRES 5 D 78 ASP MET GLU LYS LEU LYS THR LEU SER GLY ASP SER SER SEQRES 6 D 78 TYR GLN SER TYR LEU VAL TRP SER HIS GLY ASN GLY ASP HET SAH A 301 26 HET GOL A 302 6 HET ZN A 303 1 HET SAM C 301 27 HET GOL C 302 6 HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM GOL GLYCEROL HETNAM ZN ZINC ION HETNAM SAM S-ADENOSYLMETHIONINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 SAH C14 H20 N6 O5 S FORMUL 6 GOL 2(C3 H8 O3) FORMUL 7 ZN ZN 2+ FORMUL 8 SAM C15 H22 N6 O5 S FORMUL 10 HOH *343(H2 O) HELIX 1 AA1 SER A 18 ALA A 28 1 11 HELIX 2 AA2 ASP A 37 ASN A 48 1 12 HELIX 3 AA3 GLN A 55 TYR A 58 5 4 HELIX 4 AA4 ASN A 66 GLY A 85 1 20 HELIX 5 AA5 ALA A 100 GLU A 113 1 14 HELIX 6 AA6 SER A 124 LEU A 133 1 10 HELIX 7 AA7 ALA A 147 PHE A 153 1 7 HELIX 8 AA8 GLN A 167 ALA A 171 5 5 HELIX 9 AA9 SER A 182 ASN A 194 1 13 HELIX 10 AB1 ALA A 224 ALA A 229 5 6 HELIX 11 AB2 ASN A 248 GLY A 256 1 9 HELIX 12 AB3 GLY A 258 LEU A 262 5 5 HELIX 13 AB4 LEU B 4 ASP B 14 1 11 HELIX 14 AB5 ASP B 14 ASN B 24 1 11 HELIX 15 AB6 ASN B 24 HIS B 32 1 9 HELIX 16 AB7 THR B 35 GLY B 45 1 11 HELIX 17 AB8 ASP B 46 LYS B 51 1 6 HELIX 18 AB9 SER C 18 ALA C 28 1 11 HELIX 19 AC1 ASP C 37 ASN C 48 1 12 HELIX 20 AC2 GLN C 55 TYR C 58 5 4 HELIX 21 AC3 ASN C 66 GLY C 85 1 20 HELIX 22 AC4 ALA C 100 GLU C 113 1 14 HELIX 23 AC5 SER C 124 LEU C 133 1 10 HELIX 24 AC6 ALA C 147 PHE C 153 1 7 HELIX 25 AC7 GLN C 167 ALA C 171 5 5 HELIX 26 AC8 SER C 182 ASN C 194 1 13 HELIX 27 AC9 ALA C 224 ALA C 229 5 6 HELIX 28 AD1 ASN C 248 GLY C 256 1 9 HELIX 29 AD2 GLY C 258 LEU C 262 5 5 HELIX 30 AD3 SER D 5 ASP D 14 1 10 HELIX 31 AD4 ASP D 14 ASN D 24 1 11 HELIX 32 AD5 ASN D 24 HIS D 32 1 9 HELIX 33 AD6 THR D 35 GLY D 45 1 11 HELIX 34 AD7 ASP D 46 LEU D 53 1 8 SHEET 1 AA1 5 VAL A 51 ASN A 53 0 SHEET 2 AA1 5 ILE A 30 LEU A 34 1 N VAL A 31 O ILE A 52 SHEET 3 AA1 5 LYS A 87 LEU A 92 1 O ALA A 91 N PHE A 32 SHEET 4 AA1 5 SER A 3 GLY A 8 1 N VAL A 7 O CYS A 90 SHEET 5 AA1 5 SER A 116 MET A 119 1 O LYS A 118 N CYS A 6 SHEET 1 AA210 ARG A 217 PRO A 222 0 SHEET 2 AA210 GLU A 202 GLU A 207 -1 N VAL A 203 O LEU A 221 SHEET 3 AA210 THR A 236 ILE A 239 -1 O LEU A 238 N VAL A 204 SHEET 4 AA210 HIS A 162 TRP A 166 -1 N LEU A 163 O ILE A 239 SHEET 5 AA210 HIS A 142 GLU A 146 1 N GLN A 143 O LEU A 164 SHEET 6 AA210 HIS C 142 GLU C 146 -1 O HIS C 142 N SER A 144 SHEET 7 AA210 HIS C 162 TRP C 166 1 O LEU C 164 N GLN C 143 SHEET 8 AA210 THR C 236 ILE C 239 -1 O ILE C 239 N LEU C 163 SHEET 9 AA210 GLU C 202 GLU C 207 -1 N VAL C 204 O LEU C 238 SHEET 10 AA210 ARG C 217 PRO C 222 -1 O LEU C 221 N VAL C 203 SHEET 1 AA3 5 VAL C 51 ASN C 53 0 SHEET 2 AA3 5 ILE C 30 LEU C 34 1 N VAL C 31 O ILE C 52 SHEET 3 AA3 5 LYS C 87 LEU C 92 1 O ALA C 91 N PHE C 32 SHEET 4 AA3 5 SER C 3 GLY C 8 1 N VAL C 7 O CYS C 90 SHEET 5 AA3 5 SER C 116 MET C 119 1 O SER C 116 N LEU C 4 LINK OE2 GLU A 126 ZN ZN A 303 1555 1555 2.08 LINK ZN ZN A 303 OE2 GLU C 126 1555 1555 1.96 LINK ZN ZN A 303 NE2 HIS C 142 1555 1555 2.16 CRYST1 52.200 59.100 59.300 96.00 112.40 93.40 P 1 2 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 0.019157 0.001138 0.008130 0.00000 SCALE2 0.000000 0.016950 0.002357 0.00000 SCALE3 0.000000 0.000000 0.018415 0.00000