PDB Short entry for 4BLU HEADER TRANSFERASE 04-MAY-13 4BLU TITLE CRYSTAL STRUCTURE OF ESCHERICHIA COLI 23S RRNA (A2030-N6)- TITLE 2 METHYLTRANSFERASE RLMJ COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE J; COMPND 3 CHAIN: A, B; COMPND 4 EC: 2.1.1.266; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: SPECIFICALLY MONOMETHYLATES THE ADENINE IN POSITION COMPND 7 2030 OF 23S RRNA SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K-12; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PEXP5-CT/TOPO KEYWDS TRANSFERASE, N6-METHYLADENINE, ROSSMANN-LIKE FOLD, SUBDOMAIN KEYWDS 2 INSERTION EXPDTA X-RAY DIFFRACTION AUTHOR A.S.PUNEKAR,J.LILJERUHM,T.R.SHEPHERD,A.C.FORSTER,M.SELMER REVDAT 3 13-NOV-13 4BLU 1 JRNL REVDAT 2 28-AUG-13 4BLU 1 JRNL REVDAT 1 21-AUG-13 4BLU 0 JRNL AUTH A.S.PUNEKAR,J.LILJERUHM,T.R.SHEPHERD,A.C.FORSTER,M.SELMER JRNL TITL STRUCTURAL AND FUNCTIONAL INSIGHTS INTO THE MOLECULAR JRNL TITL 2 MECHANISM OF RRNA M6A METHYLTRANSFERASE RLMJ. JRNL REF NUCLEIC ACIDS RES. V. 41 9537 2013 JRNL REFN ISSN 0305-1048 JRNL PMID 23945937 JRNL DOI 10.1093/NAR/GKT719 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.025 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.99 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.61 REMARK 3 NUMBER OF REFLECTIONS : 48903 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.1683 REMARK 3 R VALUE (WORKING SET) : 0.1663 REMARK 3 FREE R VALUE : 0.2064 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0 REMARK 3 FREE R VALUE TEST SET COUNT : 2446 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 40.0340 - 4.7545 0.99 2788 147 0.1601 0.1881 REMARK 3 2 4.7545 - 3.7747 1.00 2776 146 0.1334 0.1369 REMARK 3 3 3.7747 - 3.2978 1.00 2755 145 0.1446 0.1676 REMARK 3 4 3.2978 - 2.9964 1.00 2750 145 0.1573 0.2009 REMARK 3 5 2.9964 - 2.7817 1.00 2734 144 0.1683 0.2350 REMARK 3 6 2.7817 - 2.6177 1.00 2732 144 0.1638 0.2098 REMARK 3 7 2.6177 - 2.4866 1.00 2744 144 0.1629 0.2134 REMARK 3 8 2.4866 - 2.3784 1.00 2744 145 0.1651 0.2265 REMARK 3 9 2.3784 - 2.2868 1.00 2720 143 0.1563 0.1995 REMARK 3 10 2.2868 - 2.2079 1.00 2737 144 0.1749 0.2597 REMARK 3 11 2.2079 - 2.1389 1.00 2721 143 0.1727 0.2269 REMARK 3 12 2.1389 - 2.0778 1.00 2759 145 0.1754 0.2278 REMARK 3 13 2.0778 - 2.0231 1.00 2695 142 0.1757 0.2472 REMARK 3 14 2.0231 - 1.9737 1.00 2736 144 0.1738 0.2102 REMARK 3 15 1.9737 - 1.9288 1.00 2725 143 0.2115 0.2513 REMARK 3 16 1.9288 - 1.8878 1.00 2722 144 0.2488 0.2731 REMARK 3 17 1.8878 - 1.8500 0.96 2619 138 0.2798 0.3099 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) : 0.21 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.89 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.64 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 : 0.010 4797 REMARK 3 ANGLE : 1.220 6499 REMARK 3 CHIRALITY : 0.080 703 REMARK 3 PLANARITY : 0.006 829 REMARK 3 DIHEDRAL : 14.465 1849 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 : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: (CHAIN A AND (RESSEQ 3:52 OR RESSEQ 56: REMARK 3 280)) REMARK 3 SELECTION : (CHAIN B AND (RESSEQ 3:52 OR RESSEQ 56: REMARK 3 280)) REMARK 3 ATOM PAIRS NUMBER : 275 REMARK 3 RMSD : 0.26 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RESIDUES 53-55 IN CHAIN B ARE REMARK 3 DISORDERED AND WERE NOT MODELED. REMARK 4 REMARK 4 4BLU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-MAY-13. REMARK 100 THE PDBE ID CODE IS EBI-56746. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-OCT-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8726 REMARK 200 MONOCHROMATOR : SI (111) MONOCHROMATOR REMARK 200 OPTICS : PT COATED MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48904 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.85 REMARK 200 RESOLUTION RANGE LOW (A) : 40.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.8 REMARK 200 R MERGE (I) : 0.12 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.10 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.7 REMARK 200 R MERGE FOR SHELL (I) : 0.60 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.40 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.2 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM SULFATE REMARK 280 DECAHYDRATE, 0.1 M TRIS-HCL PH 8.5 AND 30% W/V PEG 4000 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 38.87500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 281 REMARK 465 LYS A 282 REMARK 465 GLY A 283 REMARK 465 HIS A 284 REMARK 465 HIS A 285 REMARK 465 HIS A 286 REMARK 465 HIS A 287 REMARK 465 HIS A 288 REMARK 465 HIS A 289 REMARK 465 MET B 1 REMARK 465 GLU B 53 REMARK 465 HIS B 54 REMARK 465 ALA B 55 REMARK 465 SER B 281 REMARK 465 LYS B 282 REMARK 465 GLY B 283 REMARK 465 HIS B 284 REMARK 465 HIS B 285 REMARK 465 HIS B 286 REMARK 465 HIS B 287 REMARK 465 HIS B 288 REMARK 465 HIS B 289 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 A 2101 O HOH A 2102 2.20 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 SER A 52 163.20 84.08 REMARK 500 ASN A 89 54.90 -143.62 REMARK 500 PHE A 187 77.70 -150.27 REMARK 500 LYS A 218 62.13 61.67 REMARK 500 ASP B 33 44.34 -78.59 REMARK 500 ASN B 89 54.98 -145.13 REMARK 500 PHE B 187 76.95 -151.12 REMARK 500 VAL B 199 -61.06 -105.32 REMARK 500 LYS B 218 63.92 60.36 REMARK 500 ARG B 232 20.68 -146.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS A1281 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1282 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1283 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1284 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1285 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1286 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1287 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1288 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS B1281 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B1282 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG B1283 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG B1284 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG B1285 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B1286 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B1287 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B1288 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B1289 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B1290 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B1291 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B1292 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B1293 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B1294 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B1295 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4BLV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ESCHERICHIA COLI 23S RRNA (A2030- REMARK 900 N6)-METHYLTRANSFERASE RLMJ IN COMPLEX WITH S- REMARK 900 ADENOSYLMETHIONINE (ADOMET) REMARK 900 RELATED ID: 4BLW RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ESCHERICHIA COLI 23S RRNA (A2030- REMARK 900 N6)-METHYLTRANSFERASE RLMJ IN COMPLEX WITH S- REMARK 900 ADENOSYLHOMOCYSTEINE (ADOHCY) AND ADENOSINE MONOPHOSPHATE ( REMARK 900 AMP) DBREF 4BLU A 1 280 UNP P37634 RLMJ_ECOLI 1 280 DBREF 4BLU B 1 280 UNP P37634 RLMJ_ECOLI 1 280 SEQADV 4BLU SER A 281 UNP P37634 EXPRESSION TAG SEQADV 4BLU LYS A 282 UNP P37634 EXPRESSION TAG SEQADV 4BLU GLY A 283 UNP P37634 EXPRESSION TAG SEQADV 4BLU HIS A 284 UNP P37634 EXPRESSION TAG SEQADV 4BLU HIS A 285 UNP P37634 EXPRESSION TAG SEQADV 4BLU HIS A 286 UNP P37634 EXPRESSION TAG SEQADV 4BLU HIS A 287 UNP P37634 EXPRESSION TAG SEQADV 4BLU HIS A 288 UNP P37634 EXPRESSION TAG SEQADV 4BLU HIS A 289 UNP P37634 EXPRESSION TAG SEQADV 4BLU SER B 281 UNP P37634 EXPRESSION TAG SEQADV 4BLU LYS B 282 UNP P37634 EXPRESSION TAG SEQADV 4BLU GLY B 283 UNP P37634 EXPRESSION TAG SEQADV 4BLU HIS B 284 UNP P37634 EXPRESSION TAG SEQADV 4BLU HIS B 285 UNP P37634 EXPRESSION TAG SEQADV 4BLU HIS B 286 UNP P37634 EXPRESSION TAG SEQADV 4BLU HIS B 287 UNP P37634 EXPRESSION TAG SEQADV 4BLU HIS B 288 UNP P37634 EXPRESSION TAG SEQADV 4BLU HIS B 289 UNP P37634 EXPRESSION TAG SEQRES 1 A 289 MET LEU SER TYR ARG HIS SER PHE HIS ALA GLY ASN HIS SEQRES 2 A 289 ALA ASP VAL LEU LYS HIS THR VAL GLN SER LEU ILE ILE SEQRES 3 A 289 GLU SER LEU LYS GLU LYS ASP LYS PRO PHE LEU TYR LEU SEQRES 4 A 289 ASP THR HIS ALA GLY ALA GLY ARG TYR GLN LEU GLY SER SEQRES 5 A 289 GLU HIS ALA GLU ARG THR GLY GLU TYR LEU GLU GLY ILE SEQRES 6 A 289 ALA ARG ILE TRP GLN GLN ASP ASP LEU PRO ALA GLU LEU SEQRES 7 A 289 GLU ALA TYR ILE ASN VAL VAL LYS HIS PHE ASN ARG SER SEQRES 8 A 289 GLY GLN LEU ARG TYR TYR PRO GLY SER PRO LEU ILE ALA SEQRES 9 A 289 ARG LEU LEU LEU ARG GLU GLN ASP SER LEU GLN LEU THR SEQRES 10 A 289 GLU LEU HIS PRO SER ASP TYR PRO LEU LEU ARG SER GLU SEQRES 11 A 289 PHE GLN LYS ASP SER ARG ALA ARG VAL GLU LYS ALA ASP SEQRES 12 A 289 GLY PHE GLN GLN LEU LYS ALA LYS LEU PRO PRO VAL SER SEQRES 13 A 289 ARG ARG GLY LEU ILE LEU ILE ASP PRO PRO TYR GLU MET SEQRES 14 A 289 LYS THR ASP TYR GLN ALA VAL VAL SER GLY ILE ALA GLU SEQRES 15 A 289 GLY TYR LYS ARG PHE ALA THR GLY ILE TYR ALA LEU TRP SEQRES 16 A 289 TYR PRO VAL VAL LEU ARG GLN GLN ILE LYS ARG MET ILE SEQRES 17 A 289 HIS ASP LEU GLU ALA THR GLY ILE ARG LYS ILE LEU GLN SEQRES 18 A 289 ILE GLU LEU ALA VAL LEU PRO ASP SER ASP ARG ARG GLY SEQRES 19 A 289 MET THR ALA SER GLY MET ILE VAL ILE ASN PRO PRO TRP SEQRES 20 A 289 LYS LEU GLU GLN GLN MET ASN ASN VAL LEU PRO TRP LEU SEQRES 21 A 289 HIS SER LYS LEU VAL PRO ALA GLY THR GLY HIS ALA THR SEQRES 22 A 289 VAL SER TRP ILE VAL PRO GLU SER LYS GLY HIS HIS HIS SEQRES 23 A 289 HIS HIS HIS SEQRES 1 B 289 MET LEU SER TYR ARG HIS SER PHE HIS ALA GLY ASN HIS SEQRES 2 B 289 ALA ASP VAL LEU LYS HIS THR VAL GLN SER LEU ILE ILE SEQRES 3 B 289 GLU SER LEU LYS GLU LYS ASP LYS PRO PHE LEU TYR LEU SEQRES 4 B 289 ASP THR HIS ALA GLY ALA GLY ARG TYR GLN LEU GLY SER SEQRES 5 B 289 GLU HIS ALA GLU ARG THR GLY GLU TYR LEU GLU GLY ILE SEQRES 6 B 289 ALA ARG ILE TRP GLN GLN ASP ASP LEU PRO ALA GLU LEU SEQRES 7 B 289 GLU ALA TYR ILE ASN VAL VAL LYS HIS PHE ASN ARG SER SEQRES 8 B 289 GLY GLN LEU ARG TYR TYR PRO GLY SER PRO LEU ILE ALA SEQRES 9 B 289 ARG LEU LEU LEU ARG GLU GLN ASP SER LEU GLN LEU THR SEQRES 10 B 289 GLU LEU HIS PRO SER ASP TYR PRO LEU LEU ARG SER GLU SEQRES 11 B 289 PHE GLN LYS ASP SER ARG ALA ARG VAL GLU LYS ALA ASP SEQRES 12 B 289 GLY PHE GLN GLN LEU LYS ALA LYS LEU PRO PRO VAL SER SEQRES 13 B 289 ARG ARG GLY LEU ILE LEU ILE ASP PRO PRO TYR GLU MET SEQRES 14 B 289 LYS THR ASP TYR GLN ALA VAL VAL SER GLY ILE ALA GLU SEQRES 15 B 289 GLY TYR LYS ARG PHE ALA THR GLY ILE TYR ALA LEU TRP SEQRES 16 B 289 TYR PRO VAL VAL LEU ARG GLN GLN ILE LYS ARG MET ILE SEQRES 17 B 289 HIS ASP LEU GLU ALA THR GLY ILE ARG LYS ILE LEU GLN SEQRES 18 B 289 ILE GLU LEU ALA VAL LEU PRO ASP SER ASP ARG ARG GLY SEQRES 19 B 289 MET THR ALA SER GLY MET ILE VAL ILE ASN PRO PRO TRP SEQRES 20 B 289 LYS LEU GLU GLN GLN MET ASN ASN VAL LEU PRO TRP LEU SEQRES 21 B 289 HIS SER LYS LEU VAL PRO ALA GLY THR GLY HIS ALA THR SEQRES 22 B 289 VAL SER TRP ILE VAL PRO GLU SER LYS GLY HIS HIS HIS SEQRES 23 B 289 HIS HIS HIS HET TRS A1281 8 HET GOL A1282 6 HET EDO A1283 4 HET EDO A1284 4 HET EDO A1285 4 HET EDO A1286 4 HET EDO A1287 4 HET SO4 A1288 5 HET TRS B1281 8 HET GOL B1282 6 HET PEG B1283 7 HET PEG B1284 7 HET PEG B1285 7 HET EDO B1286 4 HET EDO B1287 4 HET EDO B1288 4 HET EDO B1289 4 HET EDO B1290 4 HET EDO B1291 4 HET EDO B1292 4 HET EDO B1293 4 HET EDO B1294 4 HET SO4 B1295 10 HETNAM EDO 1,2-ETHANEDIOL HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN TRS TRIS BUFFER FORMUL 3 EDO 14(C2 H6 O2) FORMUL 4 SO4 2(O4 S 2-) FORMUL 5 GOL 2(C3 H8 O3) FORMUL 6 TRS 2(C4 H12 N O3 1+) FORMUL 7 PEG 3(C4 H10 O3) FORMUL 8 HOH *557(H2 O) HELIX 1 1 ASN A 12 LYS A 30 1 19 HELIX 2 2 GLU A 60 GLU A 63 5 4 HELIX 3 3 ILE A 65 ARG A 67 5 3 HELIX 4 4 PRO A 75 GLU A 77 5 3 HELIX 5 5 LEU A 78 PHE A 88 1 11 HELIX 6 6 GLY A 99 LEU A 108 1 10 HELIX 7 7 SER A 122 PHE A 131 1 10 HELIX 8 8 GLN A 146 LYS A 151 1 6 HELIX 9 9 MET A 169 PHE A 187 1 19 HELIX 10 10 LEU A 200 THR A 214 1 15 HELIX 11 11 LYS A 248 VAL A 265 1 18 HELIX 12 12 ASN B 12 LYS B 30 1 19 HELIX 13 13 GLU B 60 GLU B 63 5 4 HELIX 14 14 ILE B 65 ARG B 67 5 3 HELIX 15 15 PRO B 75 GLU B 77 5 3 HELIX 16 16 LEU B 78 PHE B 88 1 11 HELIX 17 17 GLY B 99 LEU B 108 1 10 HELIX 18 18 SER B 122 PHE B 131 1 10 HELIX 19 19 ASP B 143 LYS B 151 1 9 HELIX 20 20 MET B 169 PHE B 187 1 19 HELIX 21 21 LEU B 200 THR B 214 1 15 HELIX 22 22 LYS B 248 VAL B 265 1 18 SHEET 1 AA 8 ALA A 137 GLU A 140 0 SHEET 2 AA 8 SER A 113 THR A 117 1 O LEU A 114 N ARG A 138 SHEET 3 AA 8 LEU A 37 ASP A 40 1 O TYR A 38 N GLN A 115 SHEET 4 AA 8 GLY A 159 ILE A 163 1 O LEU A 160 N LEU A 39 SHEET 5 AA 8 ILE A 191 VAL A 198 1 O ILE A 191 N ILE A 161 SHEET 6 AA 8 ALA A 237 ILE A 243 -1 O ALA A 237 N VAL A 198 SHEET 7 AA 8 ILE A 219 ALA A 225 -1 O LEU A 220 N VAL A 242 SHEET 8 AA 8 HIS A 271 VAL A 278 -1 O HIS A 271 N ALA A 225 SHEET 1 AB 2 ARG A 47 GLN A 49 0 SHEET 2 AB 2 TYR A 96 PRO A 98 -1 O TYR A 97 N TYR A 48 SHEET 1 BA 8 ALA B 137 GLU B 140 0 SHEET 2 BA 8 SER B 113 THR B 117 1 O LEU B 114 N ARG B 138 SHEET 3 BA 8 LEU B 37 ASP B 40 1 O TYR B 38 N GLN B 115 SHEET 4 BA 8 GLY B 159 ILE B 163 1 O LEU B 160 N LEU B 39 SHEET 5 BA 8 ILE B 191 VAL B 198 1 O ILE B 191 N ILE B 161 SHEET 6 BA 8 ALA B 237 ILE B 243 -1 O ALA B 237 N VAL B 198 SHEET 7 BA 8 ILE B 219 ALA B 225 -1 O LEU B 220 N VAL B 242 SHEET 8 BA 8 HIS B 271 VAL B 278 -1 O HIS B 271 N ALA B 225 SHEET 1 BB 2 ARG B 47 GLN B 49 0 SHEET 2 BB 2 TYR B 96 PRO B 98 -1 O TYR B 97 N TYR B 48 CISPEP 1 LEU A 152 PRO A 153 0 -1.36 CISPEP 2 LEU B 152 PRO B 153 0 -1.44 SITE 1 AC1 9 ASN A 12 ASP A 15 LYS A 18 ASP A 164 SITE 2 AC1 9 TRP A 195 EDO A1283 EDO A1284 EDO A1287 SITE 3 AC1 9 HOH A2290 SITE 1 AC2 7 ARG A 157 THR A 189 HOH A2039 HOH A2110 SITE 2 AC2 7 HOH A2111 HOH A2118 HOH A2227 SITE 1 AC3 9 SER A 7 ALA A 10 ASP A 15 TYR A 48 SITE 2 AC3 9 TYR A 97 PRO A 98 TRS A1281 EDO A1287 SITE 3 AC3 9 HOH A2032 SITE 1 AC4 7 LYS A 18 HIS A 42 ASP A 164 TRS A1281 SITE 2 AC4 7 HOH A2030 HOH A2074 HOH A2199 SITE 1 AC5 5 PRO A 228 ARG A 233 THR A 269 HOH A2282 SITE 2 AC5 5 HOH A2291 SITE 1 AC6 7 ASN A 83 LYS A 86 HIS A 87 ARG A 90 SITE 2 AC6 7 HOH A2292 EDO B1293 EDO B1294 SITE 1 AC7 6 SER A 7 HIS A 9 ALA A 10 TRS A1281 SITE 2 AC7 6 EDO A1283 HOH A2015 SITE 1 AC8 9 LEU A 29 LYS A 32 ARG A 158 HOH A2043 SITE 2 AC8 9 HOH A2197 HOH A2228 HOH A2287 HOH A2288 SITE 3 AC8 9 HOH A2289 SITE 1 AC9 11 ASN B 12 ASP B 15 LYS B 18 ASP B 164 SITE 2 AC9 11 TRP B 195 GOL B1282 PEG B1285 EDO B1286 SITE 3 AC9 11 HOH B2254 HOH B2255 HOH B2256 SITE 1 BC1 9 LYS B 18 TYR B 48 ASP B 164 TRS B1281 SITE 2 BC1 9 EDO B1286 HOH B2051 HOH B2054 HOH B2257 SITE 3 BC1 9 HOH B2258 SITE 1 BC2 7 ARG B 67 TYR B 184 LYS B 185 GLY B 215 SITE 2 BC2 7 HOH B2175 HOH B2178 HOH B2181 SITE 1 BC3 4 SER B 262 LYS B 263 PRO B 266 HOH B2243 SITE 1 BC4 6 SER B 7 PHE B 8 HIS B 9 TRS B1281 SITE 2 BC4 6 HOH B2254 HOH B2256 SITE 1 BC5 9 SER B 7 ALA B 10 ASP B 15 TYR B 48 SITE 2 BC5 9 TYR B 97 TRS B1281 GOL B1282 HOH B2018 SITE 3 BC5 9 HOH B2254 SITE 1 BC6 4 PRO B 246 TRP B 247 HOH B2035 HOH B2036 SITE 1 BC7 3 LYS B 32 ARG B 158 HOH B2260 SITE 1 BC8 4 ARG B 109 GLN B 111 HOH B2119 HOH B2261 SITE 1 BC9 3 PRO B 166 GLU B 168 ASP B 172 SITE 1 CC1 6 THR B 58 GLU B 182 LYS B 185 ARG B 186 SITE 2 CC1 6 HOH B2063 HOH B2176 SITE 1 CC2 6 ARG A 206 GLU B 250 SER B 275 TRP B 276 SITE 2 CC2 6 HOH B2252 HOH B2262 SITE 1 CC3 5 ARG A 90 EDO A1286 LEU B 106 EDO B1294 SITE 2 CC3 5 HOH B2037 SITE 1 CC4 7 ARG A 90 EDO A1286 HOH A2046 ARG B 90 SITE 2 CC4 7 EDO B1293 HOH B2264 HOH B2265 SITE 1 CC5 6 HIS A 87 HOH A2151 ARG B 47 HIS B 87 SITE 2 CC5 6 PHE B 88 HOH B2115 CRYST1 46.870 77.750 82.500 90.00 104.00 90.00 P 1 21 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 0.021336 0.000000 0.005320 0.00000 SCALE2 0.000000 0.012862 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012492 0.00000 MTRIX1 1 -1.000000 -0.007800 0.002800 50.45650 1 MTRIX2 1 -0.004600 0.808800 0.588100 -17.73830 1 MTRIX3 1 -0.006800 0.588000 -0.808800 55.14890 1 MTRIX1 2 -1.000000 -0.007800 0.002800 50.45650 1 MTRIX2 2 -0.004600 0.808800 0.588100 -17.73830 1 MTRIX3 2 -0.006800 0.588000 -0.808800 55.14890 1