HEADER TRANSFERASE 01-JUL-24 9CHK TITLE STRUCTURE OF THE ALPHA-N-METHYLTRANSFERASE (SONM) AND RIPP PRECURSOR TITLE 2 (SONA-Y62A) 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 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: EXTRADIOL RING-CLEAVAGE DIOXYGENASE LIGAB LIGA SUBUNIT COMPND 8 DOMAIN-CONTAINING PROTEIN; COMPND 9 CHAIN: B, D; COMPND 10 ENGINEERED: YES; COMPND 11 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 9CHK 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. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.5 REMARK 3 NUMBER OF REFLECTIONS : 90783 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) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4778 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6791 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.26 REMARK 3 BIN R VALUE (WORKING SET) : 0.2090 REMARK 3 BIN FREE R VALUE SET COUNT : 357 REMARK 3 BIN FREE R VALUE : 0.2580 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4865 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 66 REMARK 3 SOLVENT ATOMS : 346 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.58000 REMARK 3 B22 (A**2) : 1.83000 REMARK 3 B33 (A**2) : -0.15000 REMARK 3 B12 (A**2) : -0.44000 REMARK 3 B13 (A**2) : -0.18000 REMARK 3 B23 (A**2) : 0.42000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.091 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.077 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.056 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.429 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5146 ; 0.002 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 4866 ; 0.000 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7019 ; 0.921 ; 1.811 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11225 ; 0.341 ; 1.741 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 653 ; 5.791 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 22 ; 3.801 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 852 ;13.287 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 791 ; 0.049 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6074 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1156 ; 0.001 ; 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): 2543 ; 5.109 ; 1.768 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2543 ; 5.093 ; 1.768 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3180 ; 7.267 ; 3.180 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3181 ; 7.266 ; 3.181 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2603 ; 6.821 ; 2.137 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2604 ; 6.819 ; 2.137 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3827 ; 9.870 ; 3.758 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5794 ;14.329 ;21.380 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5743 ;13.800 ;21.130 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 10012 ; 3.953 ; 3.000 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 : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 260 REMARK 3 RESIDUE RANGE : A 301 A 302 REMARK 3 ORIGIN FOR THE GROUP (A): -1.605 9.610 2.873 REMARK 3 T TENSOR REMARK 3 T11: 0.0204 T22: 0.0008 REMARK 3 T33: 0.0113 T12: 0.0024 REMARK 3 T13: 0.0005 T23: -0.0020 REMARK 3 L TENSOR REMARK 3 L11: 0.0625 L22: 0.0134 REMARK 3 L33: 0.0572 L12: 0.0026 REMARK 3 L13: 0.0097 L23: -0.0099 REMARK 3 S TENSOR REMARK 3 S11: 0.0013 S12: 0.0001 S13: 0.0028 REMARK 3 S21: 0.0026 S22: -0.0007 S23: 0.0012 REMARK 3 S31: -0.0048 S32: 0.0016 S33: -0.0005 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 9 B 53 REMARK 3 ORIGIN FOR THE GROUP (A): 15.335 15.006 -17.501 REMARK 3 T TENSOR REMARK 3 T11: 0.0146 T22: 0.0013 REMARK 3 T33: 0.0046 T12: 0.0040 REMARK 3 T13: 0.0010 T23: -0.0000 REMARK 3 L TENSOR REMARK 3 L11: 0.5000 L22: 0.7077 REMARK 3 L33: 0.2754 L12: 0.1722 REMARK 3 L13: -0.0492 L23: 0.0116 REMARK 3 S TENSOR REMARK 3 S11: 0.0098 S12: 0.0001 S13: 0.0208 REMARK 3 S21: 0.0040 S22: -0.0070 S23: 0.0136 REMARK 3 S31: -0.0177 S32: -0.0013 S33: -0.0028 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 2 C 263 REMARK 3 RESIDUE RANGE : C 301 C 302 REMARK 3 ORIGIN FOR THE GROUP (A): 1.456 -10.007 2.789 REMARK 3 T TENSOR REMARK 3 T11: 0.0202 T22: 0.0005 REMARK 3 T33: 0.0154 T12: 0.0019 REMARK 3 T13: 0.0002 T23: 0.0002 REMARK 3 L TENSOR REMARK 3 L11: 0.0429 L22: 0.0113 REMARK 3 L33: 0.0593 L12: -0.0046 REMARK 3 L13: -0.0118 L23: 0.0122 REMARK 3 S TENSOR REMARK 3 S11: 0.0016 S12: -0.0002 S13: -0.0145 REMARK 3 S21: 0.0032 S22: -0.0014 S23: -0.0016 REMARK 3 S31: 0.0060 S32: -0.0020 S33: -0.0002 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 9 D 53 REMARK 3 ORIGIN FOR THE GROUP (A): -15.119 -15.563 -17.885 REMARK 3 T TENSOR REMARK 3 T11: 0.0152 T22: 0.0012 REMARK 3 T33: 0.0069 T12: 0.0026 REMARK 3 T13: -0.0016 T23: -0.0021 REMARK 3 L TENSOR REMARK 3 L11: 0.7238 L22: 0.6022 REMARK 3 L33: 0.3682 L12: 0.1319 REMARK 3 L13: 0.0331 L23: -0.0589 REMARK 3 S TENSOR REMARK 3 S11: 0.0026 S12: 0.0058 S13: -0.0425 REMARK 3 S21: -0.0008 S22: 0.0039 S23: -0.0058 REMARK 3 S31: 0.0263 S32: -0.0025 S33: -0.0065 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 9CHK 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_1000285511. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-FEB-23 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) : 1.0332 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 95561 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 45.990 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.3 REMARK 200 DATA REDUNDANCY : 2.740 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.4900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.60 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.54000 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 (%): 48.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 240 MM SODIUM MALONATE PH 5.5, 12% PEG REMARK 280 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: 9420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.0 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 ASP A 261 REMARK 465 LEU A 262 REMARK 465 GLY A 263 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 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 ALA B 62 REMARK 465 LEU B 63 REMARK 465 VAL B 64 REMARK 465 ILE 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 54 REMARK 465 GLY D 55 REMARK 465 ASP D 56 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 ALA D 62 REMARK 465 LEU D 63 REMARK 465 VAL D 64 REMARK 465 ILE 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 OE1 GLN A 143 OE1 GLN C 143 1.92 REMARK 500 OE2 GLU C 126 O HOH C 401 2.12 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 NE2 HIS A 180 NE2 GLN C 178 1565 1.01 REMARK 500 CE1 HIS A 180 NE2 GLN C 178 1565 1.58 REMARK 500 CD2 HIS A 180 NE2 GLN C 178 1565 2.07 REMARK 500 OE1 GLN A 60 OE2 GLU D 48 1565 2.19 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 -43.64 76.90 REMARK 500 THR A 181 -164.03 -105.74 REMARK 500 ASN B 24 81.84 -152.54 REMARK 500 ALA C 14 -43.61 76.83 REMARK 500 ASN D 24 77.43 -151.31 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9CHI RELATED DB: PDB REMARK 900 STRUCTURE OF THE ALPHA-N-METHYLTRANSFERASE (SONM) AND RIPP REMARK 900 PRECURSOR (SONA-Y62A) HETEROMERIC COMPLEX (BOUND TO SAH - STRUCTURE REMARK 900 2) REMARK 900 RELATED ID: 9CH7 RELATED DB: PDB REMARK 900 STRUCTURE OF THE ALPHA-N-METHYLTRANSFERASE (SONM) AND RIPP REMARK 900 PRECURSOR (SONA-Y62A) HETEROMERIC COMPLEX (BOUND TO SAH - STRUCTURE REMARK 900 1) REMARK 900 RELATED ID: 9CH5 RELATED DB: PDB REMARK 900 STRUCTURE OF THE ALPHA-N-METHYLTRANSFERASE (SONM) AND RIPP REMARK 900 PRECURSOR (SONA-L63D) HETEROMERIC COMPLEX (BOUND TO SAM) REMARK 900 RELATED ID: 9CH3 RELATED DB: PDB REMARK 900 STRUCTURE OF THE ALPHA-N-METHYLTRANSFERASE (SONM) AND RIPP REMARK 900 PRECURSOR (SONA-L63D) HETEROMERIC COMPLEX (BOUND TO SAH) REMARK 900 RELATED ID: 9CH2 RELATED DB: PDB REMARK 900 STRUCTURE OF THE ALPHA-N-METHYLTRANSFERASE (SONM) AND RIPP REMARK 900 PRECURSOR (SONA-L63D) HETEROMERIC COMPLEX REMARK 900 RELATED ID: 9CH1 RELATED DB: PDB REMARK 900 STRUCTURE OF THE ALPHA-N-METHYLTRANSFERASE (SONM) AND RIPP REMARK 900 PRECURSOR (SONA-I65W) HETEROMERIC COMPLEX (BOUND TO SAM) 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 9CHK A 1 263 UNP Q8EGW3 Q8EGW3_SHEON 1 263 DBREF 9CHK B 1 71 UNP Q8EGW2 Q8EGW2_SHEON 1 71 DBREF 9CHK C 1 263 UNP Q8EGW3 Q8EGW3_SHEON 1 263 DBREF 9CHK D 1 71 UNP Q8EGW2 Q8EGW2_SHEON 1 71 SEQADV 9CHK MET B -6 UNP Q8EGW2 INITIATING METHIONINE SEQADV 9CHK HIS B -5 UNP Q8EGW2 EXPRESSION TAG SEQADV 9CHK HIS B -4 UNP Q8EGW2 EXPRESSION TAG SEQADV 9CHK HIS B -3 UNP Q8EGW2 EXPRESSION TAG SEQADV 9CHK HIS B -2 UNP Q8EGW2 EXPRESSION TAG SEQADV 9CHK HIS B -1 UNP Q8EGW2 EXPRESSION TAG SEQADV 9CHK HIS B 0 UNP Q8EGW2 EXPRESSION TAG SEQADV 9CHK ALA B 62 UNP Q8EGW2 TYR 62 ENGINEERED MUTATION SEQADV 9CHK MET D -6 UNP Q8EGW2 INITIATING METHIONINE SEQADV 9CHK HIS D -5 UNP Q8EGW2 EXPRESSION TAG SEQADV 9CHK HIS D -4 UNP Q8EGW2 EXPRESSION TAG SEQADV 9CHK HIS D -3 UNP Q8EGW2 EXPRESSION TAG SEQADV 9CHK HIS D -2 UNP Q8EGW2 EXPRESSION TAG SEQADV 9CHK HIS D -1 UNP Q8EGW2 EXPRESSION TAG SEQADV 9CHK HIS D 0 UNP Q8EGW2 EXPRESSION TAG SEQADV 9CHK ALA D 62 UNP Q8EGW2 TYR 62 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 ALA LEU VAL ILE 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 ALA LEU VAL ILE SER HIS GLY ASN GLY ASP HET SAM A 301 27 HET GOL A 302 6 HET SAM C 301 27 HET GOL C 302 6 HETNAM SAM S-ADENOSYLMETHIONINE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 SAM 2(C15 H22 N6 O5 S) FORMUL 6 GOL 2(C3 H8 O3) FORMUL 9 HOH *346(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 GLY A 134 1 11 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 B 3 ASP B 14 1 12 HELIX 13 AB4 ASP B 14 ASN B 24 1 11 HELIX 14 AB5 ASN B 24 HIS B 32 1 9 HELIX 15 AB6 THR B 35 THR B 44 1 10 HELIX 16 AB7 ASP B 46 LEU B 53 1 8 HELIX 17 AB8 SER C 18 ALA C 28 1 11 HELIX 18 AB9 ASP C 37 ASN C 48 1 12 HELIX 19 AC1 GLN C 55 TYR C 58 5 4 HELIX 20 AC2 ASN C 66 GLY C 85 1 20 HELIX 21 AC3 CYS C 101 GLU C 113 1 13 HELIX 22 AC4 SER C 124 GLY C 134 1 11 HELIX 23 AC5 ALA C 147 PHE C 153 1 7 HELIX 24 AC6 GLN C 167 ALA C 171 5 5 HELIX 25 AC7 SER C 182 ASN C 194 1 13 HELIX 26 AC8 ALA C 224 ALA C 229 5 6 HELIX 27 AC9 ASN C 248 GLY C 256 1 9 HELIX 28 AD1 GLY C 258 LEU C 262 5 5 HELIX 29 AD2 GLY D 3 ASP D 14 1 12 HELIX 30 AD3 ASP D 14 ASN D 24 1 11 HELIX 31 AD4 ASN D 24 HIS D 32 1 9 HELIX 32 AD5 THR D 35 GLY D 45 1 11 HELIX 33 AD6 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 SER C 144 N HIS A 142 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 LYS C 118 N CYS C 6 CRYST1 52.250 58.960 59.230 95.77 112.61 93.88 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 0.019139 0.001297 0.008227 0.00000 SCALE2 0.000000 0.017000 0.002358 0.00000 SCALE3 0.000000 0.000000 0.018464 0.00000