HEADER TRANSFERASE 01-JUL-21 7F8A TITLE CRYSTAL STRUCTURE OF RRNA METHYLTRANSFERASE ERM38 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ERM(38); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOLICIBACTERIUM SMEGMATIS; SOURCE 3 ORGANISM_COMMON: MYCOBACTERIUM SMEGMATIS; SOURCE 4 ORGANISM_TAXID: 1772; SOURCE 5 GENE: ERM(38); SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS ERYTHROMYCIN RESISTANCE METHYLTRANSFERASE, METHYLTRANSFERASE, SAM, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR B.C.GOH,J.LESCAR REVDAT 3 29-NOV-23 7F8A 1 REMARK REVDAT 2 27-JUL-22 7F8A 1 JRNL REVDAT 1 12-JAN-22 7F8A 0 JRNL AUTH B.C.GOH,X.XIANG,J.LESCAR,P.C.DEDON JRNL TITL CRYSTAL STRUCTURE AND FUNCTIONAL ANALYSIS OF MYCOBACTERIAL JRNL TITL 2 ERYTHROMYCIN RESISTANCE METHYLTRANSFERASE ERM38 REVEALS ITS JRNL TITL 3 RNA-BINDING SITE. JRNL REF J.BIOL.CHEM. V. 298 01571 2022 JRNL REFN ESSN 1083-351X JRNL PMID 35007529 JRNL DOI 10.1016/J.JBC.2022.101571 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 (19-MAR-2020) REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.26 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 25049 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) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120 REMARK 3 FREE R VALUE TEST SET COUNT : 1283 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 51 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 501 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2432 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 467 REMARK 3 BIN R VALUE (WORKING SET) : 0.2406 REMARK 3 BIN FREE R VALUE : 0.2758 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 6.79 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 34 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1900 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 192 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.83 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.18900 REMARK 3 B22 (A**2) : -0.18900 REMARK 3 B33 (A**2) : 0.37800 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.250 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.150 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.131 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.140 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.126 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.955 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1944 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 2650 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 656 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 325 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1944 ; 10.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 257 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 1771 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 0.85 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.20 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 15.58 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7F8A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1300023077. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-DEC-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.3 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27116 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 48.260 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 25.90 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.9 REMARK 200 DATA REDUNDANCY IN SHELL : 24.80 REMARK 200 R MERGE FOR SHELL (I) : 1.57000 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: BALBES REMARK 200 STARTING MODEL: 3FTF, 3FUV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0 M SUCCINIC ACID PH 7, 5% GLYCEROL, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 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 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 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 Y,X,-Z REMARK 290 8555 -Y,-X,-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 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 0.000000 -1.000000 0.000000 38.83150 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 38.83150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 50.55800 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 38.83150 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 38.83150 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 50.55800 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 38.83150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.83150 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 50.55800 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 38.83150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.83150 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 50.55800 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 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: MONOMERIC 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 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 SER A 2 REMARK 465 THR A 3 REMARK 465 PRO A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 GLY A 7 REMARK 465 ARG A 8 REMARK 465 HIS A 9 REMARK 465 GLU A 10 REMARK 465 LEU A 11 REMARK 465 GLY A 12 REMARK 465 ARG A 84 REMARK 465 PRO A 226 REMARK 465 LEU A 260 REMARK 465 THR A 261 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 HIS A 214 CG ND1 CD2 CE1 NE2 REMARK 470 THR A 225 OG1 CG2 REMARK 470 ARG A 229 CG CD NE CZ NH1 NH2 DBREF 7F8A A 1 261 UNP Q79N53 Q79N53_MYCSM 1 261 SEQRES 1 A 261 MET SER THR PRO HIS HIS GLY ARG HIS GLU LEU GLY GLN SEQRES 2 A 261 ASN PHE LEU SER ASP ARG ARG VAL ILE ALA ASP ILE VAL SEQRES 3 A 261 GLU ILE VAL SER ARG THR ASN GLY PRO ILE ILE GLU ILE SEQRES 4 A 261 GLY ALA GLY ASP GLY ALA LEU THR ILE PRO LEU GLN ARG SEQRES 5 A 261 LEU ALA ARG PRO LEU THR ALA VAL GLU VAL ASP ALA ARG SEQRES 6 A 261 ARG ALA ARG ARG LEU ALA GLN ARG THR ALA ARG SER ALA SEQRES 7 A 261 PRO GLY PRO ALA SER ARG PRO THR GLU VAL VAL ALA ALA SEQRES 8 A 261 ASP PHE LEU ARG TYR PRO LEU PRO ARG SER PRO HIS VAL SEQRES 9 A 261 VAL VAL GLY ASN LEU PRO PHE HIS LEU THR THR ALA ILE SEQRES 10 A 261 LEU ARG ARG LEU LEU HIS GLY PRO GLY TRP THR THR ALA SEQRES 11 A 261 VAL LEU LEU MET GLN TRP GLU VAL ALA ARG ARG ARG ALA SEQRES 12 A 261 ALA VAL GLY GLY ALA THR MET MET THR ALA GLN TRP TRP SEQRES 13 A 261 PRO TRP PHE GLU PHE GLY LEU ALA ARG LYS VAL SER ALA SEQRES 14 A 261 ALA SER PHE THR PRO ARG PRO ALA VAL ASP ALA GLY LEU SEQRES 15 A 261 LEU THR ILE THR ARG ARG SER ARG PRO LEU VAL ASP VAL SEQRES 16 A 261 ALA ASP ARG ALA ARG TYR GLN ALA LEU VAL HIS ARG VAL SEQRES 17 A 261 PHE THR GLY ARG GLY HIS GLY MET ALA GLN ILE LEU GLN SEQRES 18 A 261 ARG LEU PRO THR PRO VAL PRO ARG THR TRP LEU ARG ALA SEQRES 19 A 261 ASN GLY ILE ALA PRO ASN SER LEU PRO ARG GLN LEU SER SEQRES 20 A 261 ALA ALA GLN TRP ALA ALA LEU PHE GLU GLN THR ARG LEU SEQRES 21 A 261 THR FORMUL 2 HOH *192(H2 O) HELIX 1 AA1 ASP A 18 ARG A 31 1 14 HELIX 2 AA2 LEU A 46 ARG A 52 1 7 HELIX 3 AA3 ASP A 63 ALA A 78 1 16 HELIX 4 AA4 ASP A 92 TYR A 96 5 5 HELIX 5 AA5 PRO A 110 HIS A 112 5 3 HELIX 6 AA6 LEU A 113 GLY A 124 1 12 HELIX 7 AA7 TRP A 136 ALA A 143 1 8 HELIX 8 AA8 THR A 149 TRP A 156 1 8 HELIX 9 AA9 SER A 168 ALA A 170 5 3 HELIX 10 AB1 ASP A 194 ALA A 196 5 3 HELIX 11 AB2 ASP A 197 GLY A 211 1 15 HELIX 12 AB3 GLY A 215 ARG A 222 1 8 HELIX 13 AB4 THR A 230 ASN A 235 1 6 HELIX 14 AB5 LEU A 242 LEU A 246 5 5 HELIX 15 AB6 SER A 247 ARG A 259 1 13 SHEET 1 AA1 2 PHE A 15 LEU A 16 0 SHEET 2 AA1 2 PHE A 172 THR A 173 -1 O THR A 173 N PHE A 15 SHEET 1 AA2 7 GLU A 87 ALA A 90 0 SHEET 2 AA2 7 LEU A 57 GLU A 61 1 N ALA A 59 O VAL A 89 SHEET 3 AA2 7 ILE A 36 ILE A 39 1 N GLU A 38 O VAL A 60 SHEET 4 AA2 7 HIS A 103 ASN A 108 1 O VAL A 104 N ILE A 37 SHEET 5 AA2 7 TRP A 127 GLN A 135 1 O LEU A 133 N GLY A 107 SHEET 6 AA2 7 ALA A 180 ARG A 187 -1 O LEU A 183 N LEU A 132 SHEET 7 AA2 7 PHE A 159 VAL A 167 -1 N VAL A 167 O ALA A 180 CISPEP 1 THR A 173 PRO A 174 0 -9.30 CRYST1 77.663 77.663 101.116 90.00 90.00 90.00 P 42 21 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 0.012876 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012876 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009890 0.00000