HEADER RNA BINDING PROTEIN 27-JUL-21 7P9O TITLE STRUCTURE OF E.COLI RLMJ IN COMPLEX WITH A SAM ANALOGUE (CA) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE J; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 23S RRNA (ADENINE(2030)-N6)-METHYLTRANSFERASE,23S RRNA COMPND 5 M6A2030 METHYLTRANSFERASE; COMPND 6 EC: 2.1.1.266; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 GENE: RLMJ, YHIR, B3499, JW3466; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS RNA MTASES, METHYLTRANSFERASE, SAM ANALOGUE, M6A, RNA BINDING, SAM KEYWDS 2 CONJUGATE, RLMJ, CONJUGATE ANALOGUE, RNA RECOGNITION, BISUBSTRATE KEYWDS 3 ANALOGUE, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR V.MEYNIER,M.CATALA,S.OERUM,P.BARRAUD,C.TISNE REVDAT 3 31-JAN-24 7P9O 1 REMARK REVDAT 2 15-JUN-22 7P9O 1 JRNL REVDAT 1 25-MAY-22 7P9O 0 JRNL AUTH V.MEYNIER,L.IANNAZZO,M.CATALA,S.OERUM,E.BRAUD,C.ATDJIAN, JRNL AUTH 2 P.BARRAUD,M.FONVIELLE,C.TISNE,M.ETHEVE-QUELQUEJEU JRNL TITL SYNTHESIS OF RNA-COFACTOR CONJUGATES AND STRUCTURAL JRNL TITL 2 EXPLORATION OF RNA RECOGNITION BY AN M6A RNA JRNL TITL 3 METHYLTRANSFERASE. JRNL REF NUCLEIC ACIDS RES. V. 50 5793 2022 JRNL REFN ESSN 1362-4962 JRNL PMID 35580049 JRNL DOI 10.1093/NAR/GKAC354 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.65 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 15959 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.243 REMARK 3 R VALUE (WORKING SET) : 0.240 REMARK 3 FREE R VALUE : 0.306 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 799 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 3.8066 - 3.0217 1.00 2551 135 0.2123 0.2859 REMARK 3 2 3.0217 - 2.6398 1.00 2546 134 0.2914 0.3584 REMARK 3 3 2.6398 - 2.3984 1.00 2519 132 0.2843 0.3563 REMARK 3 4 2.3984 - 2.2265 1.00 2505 132 0.2884 0.3531 REMARK 3 5 2.2265 - 2.0953 0.96 2429 128 0.2935 0.3776 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.410 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.71 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7P9O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1292117294. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9786 REMARK 200 MONOCHROMATOR : M 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 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15974 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.095 REMARK 200 RESOLUTION RANGE LOW (A) : 43.651 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.9000 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) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.44200 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: 6QDX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 6.5 28% (W/V) PEG REMARK 280 MME 2000, VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-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 1.000000 0.000000 0.000000 39.99500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.44500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 39.99500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.44500 REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 GLU A 53 REMARK 465 HIS A 54 REMARK 465 ALA A 55 REMARK 465 GLU A 56 REMARK 465 ARG A 57 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 SER A 7 107.41 -161.68 REMARK 500 ASN A 12 -175.61 -67.25 REMARK 500 PHE A 187 74.48 -153.40 REMARK 500 VAL A 198 76.33 -102.75 REMARK 500 LYS A 218 66.06 61.57 REMARK 500 ARG A 232 52.37 36.92 REMARK 500 VAL A 265 63.35 -117.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6QDX RELATED DB: PDB REMARK 900 RELATED ID: 7P8Q RELATED DB: PDB REMARK 900 RELATED ID: 7P9I RELATED DB: PDB DBREF 7P9O A 1 280 UNP P37634 RLMJ_ECOLI 1 280 SEQADV 7P9O LYS A 60 UNP P37634 GLU 60 CONFLICT SEQADV 7P9O GLN A 106 UNP P37634 LEU 106 CONFLICT SEQADV 7P9O THR A 191 UNP P37634 ILE 191 CONFLICT SEQRES 1 A 280 MET LEU SER TYR ARG HIS SER PHE HIS ALA GLY ASN HIS SEQRES 2 A 280 ALA ASP VAL LEU LYS HIS THR VAL GLN SER LEU ILE ILE SEQRES 3 A 280 GLU SER LEU LYS GLU LYS ASP LYS PRO PHE LEU TYR LEU SEQRES 4 A 280 ASP THR HIS ALA GLY ALA GLY ARG TYR GLN LEU GLY SER SEQRES 5 A 280 GLU HIS ALA GLU ARG THR GLY LYS TYR LEU GLU GLY ILE SEQRES 6 A 280 ALA ARG ILE TRP GLN GLN ASP ASP LEU PRO ALA GLU LEU SEQRES 7 A 280 GLU ALA TYR ILE ASN VAL VAL LYS HIS PHE ASN ARG SER SEQRES 8 A 280 GLY GLN LEU ARG TYR TYR PRO GLY SER PRO LEU ILE ALA SEQRES 9 A 280 ARG GLN LEU LEU ARG GLU GLN ASP SER LEU GLN LEU THR SEQRES 10 A 280 GLU LEU HIS PRO SER ASP TYR PRO LEU LEU ARG SER GLU SEQRES 11 A 280 PHE GLN LYS ASP SER ARG ALA ARG VAL GLU LYS ALA ASP SEQRES 12 A 280 GLY PHE GLN GLN LEU LYS ALA LYS LEU PRO PRO VAL SER SEQRES 13 A 280 ARG ARG GLY LEU ILE LEU ILE ASP PRO PRO TYR GLU MET SEQRES 14 A 280 LYS THR ASP TYR GLN ALA VAL VAL SER GLY ILE ALA GLU SEQRES 15 A 280 GLY TYR LYS ARG PHE ALA THR GLY THR TYR ALA LEU TRP SEQRES 16 A 280 TYR PRO VAL VAL LEU ARG GLN GLN ILE LYS ARG MET ILE SEQRES 17 A 280 HIS ASP LEU GLU ALA THR GLY ILE ARG LYS ILE LEU GLN SEQRES 18 A 280 ILE GLU LEU ALA VAL LEU PRO ASP SER ASP ARG ARG GLY SEQRES 19 A 280 MET THR ALA SER GLY MET ILE VAL ILE ASN PRO PRO TRP SEQRES 20 A 280 LYS LEU GLU GLN GLN MET ASN ASN VAL LEU PRO TRP LEU SEQRES 21 A 280 HIS SER LYS LEU VAL PRO ALA GLY THR GLY HIS ALA THR SEQRES 22 A 280 VAL SER TRP ILE VAL PRO GLU HET 0Y0 A 301 46 HETNAM 0Y0 5'-{[(3S)-3-AMINO-3-CARBOXYPROPYL]AMINO}-5'- HETNAM 2 0Y0 DEOXYADENOSINE FORMUL 2 0Y0 C14 H21 N7 O5 FORMUL 3 HOH *101(H2 O) HELIX 1 AA1 ASN A 12 LYS A 30 1 19 HELIX 2 AA2 GLY A 59 GLU A 63 5 5 HELIX 3 AA3 GLY A 64 TRP A 69 1 6 HELIX 4 AA4 PRO A 75 GLU A 77 5 3 HELIX 5 AA5 LEU A 78 PHE A 88 1 11 HELIX 6 AA6 GLY A 99 LEU A 108 1 10 HELIX 7 AA7 ASP A 123 PHE A 131 1 9 HELIX 8 AA8 ASP A 143 LYS A 151 1 9 HELIX 9 AA9 THR A 171 PHE A 187 1 17 HELIX 10 AB1 LEU A 200 THR A 214 1 15 HELIX 11 AB2 LYS A 248 VAL A 265 1 18 SHEET 1 AA1 8 ALA A 137 GLU A 140 0 SHEET 2 AA1 8 SER A 113 THR A 117 1 N LEU A 116 O ARG A 138 SHEET 3 AA1 8 LEU A 37 ASP A 40 1 N TYR A 38 O SER A 113 SHEET 4 AA1 8 GLY A 159 ILE A 163 1 O LEU A 162 N LEU A 39 SHEET 5 AA1 8 THR A 191 PRO A 197 1 O THR A 191 N ILE A 161 SHEET 6 AA1 8 ALA A 237 ILE A 243 -1 O ILE A 241 N LEU A 194 SHEET 7 AA1 8 ILE A 219 ALA A 225 -1 N LEU A 220 O VAL A 242 SHEET 8 AA1 8 HIS A 271 VAL A 278 -1 O SER A 275 N GLN A 221 SHEET 1 AA2 2 ARG A 47 GLN A 49 0 SHEET 2 AA2 2 TYR A 96 PRO A 98 -1 O TYR A 97 N TYR A 48 CISPEP 1 LEU A 152 PRO A 153 0 -1.87 CRYST1 79.990 38.890 90.650 90.00 105.62 90.00 C 1 2 1 4 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 0.012502 0.000000 0.003495 0.00000 SCALE2 0.000000 0.025714 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011454 0.00000