HEADER TRANSFERASE 01-JUL-24 9CH2 TITLE STRUCTURE OF THE ALPHA-N-METHYLTRANSFERASE (SONM) AND RIPP PRECURSOR TITLE 2 (SONA-L63D) HETEROMERIC COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: TP-METHYLASE FAMILY PROTEIN; COMPND 3 CHAIN: A; 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; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: TP-METHYLASE FAMILY PROTEIN; COMPND 13 CHAIN: C; COMPND 14 ENGINEERED: 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; SOURCE 13 MOL_ID: 3; SOURCE 14 ORGANISM_SCIENTIFIC: SHEWANELLA ONEIDENSIS; SOURCE 15 ORGANISM_TAXID: 70863; SOURCE 16 GENE: SO_1478; SOURCE 17 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 18 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 9CH2 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. 2.35 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) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.83 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 31799 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) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1674 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) : 2.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.41 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2308 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2570 REMARK 3 BIN FREE R VALUE SET COUNT : 121 REMARK 3 BIN FREE R VALUE : 0.2860 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4785 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 27 REMARK 3 SOLVENT ATOMS : 127 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 81.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.12000 REMARK 3 B22 (A**2) : 0.12000 REMARK 3 B33 (A**2) : -0.37000 REMARK 3 B12 (A**2) : 0.06000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.297 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.229 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.178 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.568 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4985 ; 0.001 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 4706 ; 0.000 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6788 ; 0.565 ; 1.810 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10848 ; 0.188 ; 1.741 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 623 ; 4.902 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 20 ; 8.096 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 824 ;13.094 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 763 ; 0.025 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5861 ; 0.001 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1116 ; 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): 2480 ; 5.989 ; 6.829 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2480 ; 5.978 ; 6.830 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3098 ; 7.368 ;12.253 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3099 ; 7.370 ;12.254 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2505 ; 8.383 ; 7.580 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2506 ; 8.381 ; 7.582 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3688 ;11.461 ;13.586 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5660 ;13.026 ;68.130 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5648 ;13.035 ;68.140 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 301 REMARK 3 ORIGIN FOR THE GROUP (A): 55.2243 -20.1760 -11.8755 REMARK 3 T TENSOR REMARK 3 T11: 0.0270 T22: 0.0345 REMARK 3 T33: 0.0436 T12: 0.0057 REMARK 3 T13: 0.0024 T23: -0.0118 REMARK 3 L TENSOR REMARK 3 L11: 0.8098 L22: 0.9433 REMARK 3 L33: 0.7169 L12: -0.0459 REMARK 3 L13: -0.1950 L23: -0.0797 REMARK 3 S TENSOR REMARK 3 S11: 0.0133 S12: 0.0094 S13: -0.0319 REMARK 3 S21: -0.0658 S22: 0.0031 S23: -0.1759 REMARK 3 S31: 0.0363 S32: 0.1450 S33: -0.0164 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 61 REMARK 3 ORIGIN FOR THE GROUP (A): 69.6517 -5.6928 7.2525 REMARK 3 T TENSOR REMARK 3 T11: 0.0696 T22: 0.0725 REMARK 3 T33: 0.2573 T12: -0.0408 REMARK 3 T13: -0.0831 T23: 0.0183 REMARK 3 L TENSOR REMARK 3 L11: 6.4956 L22: 4.9410 REMARK 3 L33: 5.4597 L12: -1.2912 REMARK 3 L13: -2.3638 L23: 1.2392 REMARK 3 S TENSOR REMARK 3 S11: 0.1276 S12: -0.0968 S13: 0.3743 REMARK 3 S21: 0.0792 S22: 0.0630 S23: -0.9220 REMARK 3 S31: -0.2098 S32: 0.5810 S33: -0.1906 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 262 REMARK 3 ORIGIN FOR THE GROUP (A): 38.9439 -10.2151 -9.8270 REMARK 3 T TENSOR REMARK 3 T11: 0.0348 T22: 0.0182 REMARK 3 T33: 0.0230 T12: -0.0095 REMARK 3 T13: -0.0112 T23: 0.0100 REMARK 3 L TENSOR REMARK 3 L11: 0.5975 L22: 0.7511 REMARK 3 L33: 1.2316 L12: 0.1380 REMARK 3 L13: 0.4034 L23: 0.3623 REMARK 3 S TENSOR REMARK 3 S11: -0.0419 S12: -0.0422 S13: 0.0307 REMARK 3 S21: -0.0100 S22: 0.0168 S23: 0.1145 REMARK 3 S31: -0.0562 S32: -0.0962 S33: 0.0251 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 61 REMARK 3 ORIGIN FOR THE GROUP (A): 29.9946 -21.8256 13.6119 REMARK 3 T TENSOR REMARK 3 T11: 0.1164 T22: 0.0760 REMARK 3 T33: 0.0411 T12: -0.0265 REMARK 3 T13: 0.0047 T23: -0.0082 REMARK 3 L TENSOR REMARK 3 L11: 4.8863 L22: 2.9375 REMARK 3 L33: 4.8519 L12: 0.6303 REMARK 3 L13: -0.5000 L23: 0.9037 REMARK 3 S TENSOR REMARK 3 S11: 0.0718 S12: -0.2463 S13: 0.2720 REMARK 3 S21: 0.0011 S22: -0.0763 S23: 0.2868 REMARK 3 S31: -0.2554 S32: -0.4006 S33: 0.0045 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 9CH2 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_1000285502. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-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-B 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 : 33473 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 19.830 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 12.05 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 36.3200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.45 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 (%): 53.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 240 MM SODIUM MALONATE PH 5.5 WITH 8% REMARK 280 PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 108.23333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 54.11667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 54.11667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 108.23333 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: 9180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -96.0 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 ALA A 59 REMARK 465 GLN A 60 REMARK 465 ASN A 61 REMARK 465 GLY A 62 REMARK 465 GLU A 63 REMARK 465 VAL A 64 REMARK 465 LYS A 65 REMARK 465 GLY A 262 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 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 ASP 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 ASN C 61 REMARK 465 GLY C 62 REMARK 465 GLU C 63 REMARK 465 VAL C 64 REMARK 465 GLY C 263 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 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 TYR D 62 REMARK 465 ASP 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: 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 TYR A 93 N - CA - CB ANGL. DEV. = -12.8 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 ALA A 14 -40.90 78.52 REMARK 500 LEU A 34 77.93 -156.84 REMARK 500 ASN A 50 71.29 -100.40 REMARK 500 GLN A 55 2.70 -55.56 REMARK 500 ALA C 14 -39.33 78.95 REMARK 500 ALA C 59 107.11 -59.77 REMARK 500 PRO C 96 5.21 -67.71 REMARK 500 PRO C 259 -35.36 -38.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 67 0.13 SIDE CHAIN REMARK 500 ARG A 68 0.12 SIDE CHAIN 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 ZN C 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 126 OE2 REMARK 620 2 GLU C 126 OE2 97.2 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES 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 9CH2 A 1 261 UNP Q8EGW3 Q8EGW3_SHEON 1 261 DBREF 9CH2 B 1 71 UNP Q8EGW2 Q8EGW2_SHEON 1 71 DBREF 9CH2 C 1 263 UNP Q8EGW3 Q8EGW3_SHEON 1 263 DBREF 9CH2 D 1 71 UNP Q8EGW2 Q8EGW2_SHEON 1 71 SEQADV 9CH2 GLY A 262 UNP Q8EGW3 EXPRESSION TAG SEQADV 9CH2 MET B -6 UNP Q8EGW2 INITIATING METHIONINE SEQADV 9CH2 HIS B -5 UNP Q8EGW2 EXPRESSION TAG SEQADV 9CH2 HIS B -4 UNP Q8EGW2 EXPRESSION TAG SEQADV 9CH2 HIS B -3 UNP Q8EGW2 EXPRESSION TAG SEQADV 9CH2 HIS B -2 UNP Q8EGW2 EXPRESSION TAG SEQADV 9CH2 HIS B -1 UNP Q8EGW2 EXPRESSION TAG SEQADV 9CH2 HIS B 0 UNP Q8EGW2 EXPRESSION TAG SEQADV 9CH2 ASP B 63 UNP Q8EGW2 LEU 63 ENGINEERED MUTATION SEQADV 9CH2 MET D -6 UNP Q8EGW2 INITIATING METHIONINE SEQADV 9CH2 HIS D -5 UNP Q8EGW2 EXPRESSION TAG SEQADV 9CH2 HIS D -4 UNP Q8EGW2 EXPRESSION TAG SEQADV 9CH2 HIS D -3 UNP Q8EGW2 EXPRESSION TAG SEQADV 9CH2 HIS D -2 UNP Q8EGW2 EXPRESSION TAG SEQADV 9CH2 HIS D -1 UNP Q8EGW2 EXPRESSION TAG SEQADV 9CH2 HIS D 0 UNP Q8EGW2 EXPRESSION TAG SEQADV 9CH2 ASP D 63 UNP Q8EGW2 LEU 63 ENGINEERED MUTATION SEQRES 1 A 262 MET GLY SER LEU VAL CYS VAL GLY THR GLY LEU GLN LEU SEQRES 2 A 262 ALA GLY GLN ILE SER VAL LEU SER ARG SER TYR ILE GLU SEQRES 3 A 262 HIS ALA ASP ILE VAL PHE SER LEU LEU PRO ASP GLY PHE SEQRES 4 A 262 SER GLN ARG TRP LEU THR LYS LEU ASN PRO ASN VAL ILE SEQRES 5 A 262 ASN LEU GLN GLN PHE TYR ALA GLN ASN GLY GLU VAL LYS SEQRES 6 A 262 ASN ARG ARG ASP THR TYR GLU GLN MET VAL ASN ALA ILE SEQRES 7 A 262 LEU ASP ALA VAL ARG ALA GLY LYS LYS THR VAL CYS ALA SEQRES 8 A 262 LEU TYR GLY HIS PRO GLY VAL PHE ALA CYS VAL SER HIS SEQRES 9 A 262 MET ALA ILE THR ARG ALA LYS ALA GLU GLY PHE SER ALA SEQRES 10 A 262 LYS MET GLU PRO GLY ILE SER ALA GLU ALA CYS LEU TRP SEQRES 11 A 262 ALA ASP LEU GLY ILE ASP PRO GLY ASN SER GLY HIS GLN SEQRES 12 A 262 SER PHE GLU ALA SER GLN PHE MET PHE PHE ASN HIS VAL SEQRES 13 A 262 PRO ASP PRO THR THR HIS LEU LEU LEU TRP GLN ILE ALA SEQRES 14 A 262 ILE ALA GLY GLU HIS THR LEU THR GLN PHE HIS THR SER SEQRES 15 A 262 SER ASP ARG LEU GLN ILE LEU VAL GLU GLN LEU ASN GLN SEQRES 16 A 262 TRP TYR PRO LEU ASP HIS GLU VAL VAL ILE TYR GLU ALA SEQRES 17 A 262 ALA ASN LEU PRO ILE GLN ALA PRO ARG ILE GLU ARG LEU SEQRES 18 A 262 PRO LEU ALA ASN LEU PRO GLN ALA HIS LEU MET PRO ILE SEQRES 19 A 262 SER THR LEU LEU ILE PRO PRO ALA LYS LYS LEU GLU TYR SEQRES 20 A 262 ASN TYR ALA ILE LEU ALA LYS LEU GLY ILE GLY PRO GLU SEQRES 21 A 262 ASP 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 ASP 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 TYR ASP VAL ILE SER HIS GLY ASN GLY ASP HET SAH A 301 26 HET ZN C 301 1 HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM ZN ZINC ION FORMUL 5 SAH C14 H20 N6 O5 S FORMUL 6 ZN ZN 2+ FORMUL 7 HOH *127(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 PHE A 57 5 3 HELIX 4 AA4 ARG A 67 ALA A 84 1 18 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 ASP A 136 GLY A 141 1 6 HELIX 8 AA8 ALA A 147 PHE A 153 1 7 HELIX 9 AA9 GLN A 167 ALA A 171 5 5 HELIX 10 AB1 THR A 181 ASN A 194 1 14 HELIX 11 AB2 ALA A 224 ALA A 229 5 6 HELIX 12 AB3 ASN A 248 GLY A 256 1 9 HELIX 13 AB4 LEU B 4 GLY B 12 1 9 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 THR B 44 1 10 HELIX 17 AB8 ASP B 46 SER B 54 1 9 HELIX 18 AB9 SER C 18 HIS C 27 1 10 HELIX 19 AC1 ASP C 37 LYS C 46 1 10 HELIX 20 AC2 GLN C 55 PHE C 57 5 3 HELIX 21 AC3 ASN C 66 ALA C 84 1 19 HELIX 22 AC4 ALA C 100 GLU C 113 1 14 HELIX 23 AC5 SER C 124 GLY C 134 1 11 HELIX 24 AC6 ALA C 147 PHE C 153 1 7 HELIX 25 AC7 ILE C 168 ALA C 171 5 4 HELIX 26 AC8 THR C 181 ASN C 194 1 14 HELIX 27 AC9 ALA C 224 ALA C 229 5 6 HELIX 28 AD1 ASN C 248 LEU C 255 1 8 HELIX 29 AD2 SER D 5 ASP D 14 1 10 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 LEU A 92 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 ILE A 205 O GLU A 219 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 PHE A 145 O TRP A 166 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 SER C 33 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 C 301 1555 1555 2.24 LINK OE2 GLU C 126 ZN ZN C 301 1555 1555 2.11 CRYST1 92.270 92.270 162.350 90.00 90.00 120.00 P 32 2 1 12 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 0.010838 0.006257 0.000000 0.00000 SCALE2 0.000000 0.012514 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006160 0.00000