HEADER TRANSFERASE 04-MAY-13 4BLW TITLE CRYSTAL STRUCTURE OF ESCHERICHIA COLI 23S RRNA (A2030-N6)- TITLE 2 METHYLTRANSFERASE RLMJ IN COMPLEX WITH S-ADENOSYLHOMOCYSTEINE TITLE 3 (ADOHCY) AND ADENOSINE MONOPHOSPHATE (AMP) 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 BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 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 6 20-DEC-23 4BLW 1 REMARK LINK REVDAT 5 07-MAR-18 4BLW 1 SOURCE REMARK REVDAT 4 17-DEC-14 4BLW 1 REMARK REVDAT 3 13-NOV-13 4BLW 1 JRNL REVDAT 2 28-AUG-13 4BLW 1 JRNL REVDAT 1 21-AUG-13 4BLW 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. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 41772 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2088 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 45.9638 - 4.8074 0.98 2747 145 0.1622 0.2069 REMARK 3 2 4.8074 - 3.8164 0.97 2666 140 0.1380 0.1473 REMARK 3 3 3.8164 - 3.3341 0.99 2703 143 0.1483 0.1500 REMARK 3 4 3.3341 - 3.0294 0.96 2619 138 0.1692 0.2207 REMARK 3 5 3.0294 - 2.8123 0.98 2659 139 0.1650 0.1960 REMARK 3 6 2.8123 - 2.6465 0.98 2686 142 0.1684 0.1973 REMARK 3 7 2.6465 - 2.5139 0.95 2582 136 0.1687 0.2174 REMARK 3 8 2.5139 - 2.4045 0.97 2657 140 0.1747 0.2021 REMARK 3 9 2.4045 - 2.3120 0.98 2628 138 0.1738 0.2459 REMARK 3 10 2.3120 - 2.2322 0.98 2659 140 0.1875 0.2292 REMARK 3 11 2.2322 - 2.1624 0.95 2601 137 0.1924 0.2536 REMARK 3 12 2.1624 - 2.1006 0.97 2623 137 0.1910 0.2498 REMARK 3 13 2.1006 - 2.0453 0.97 2610 137 0.1977 0.2302 REMARK 3 14 2.0453 - 1.9954 0.97 2662 140 0.2072 0.2455 REMARK 3 15 1.9954 - 1.9500 0.96 2582 136 0.2295 0.2515 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.850 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.07 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.22 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 4842 REMARK 3 ANGLE : 1.315 6563 REMARK 3 CHIRALITY : 0.074 711 REMARK 3 PLANARITY : 0.008 826 REMARK 3 DIHEDRAL : 14.488 1856 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 1:279)) REMARK 3 SELECTION : (CHAIN B AND (RESSEQ 1:279)) REMARK 3 ATOM PAIRS NUMBER : 279 REMARK 3 RMSD : 0.184 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RESIDUE 280 IN CHAIN B IS DISORDERED REMARK 3 AND WAS NOT MODELED. REMARK 4 REMARK 4 4BLW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-MAY-13. REMARK 100 THE DEPOSITION ID IS D_1290056758. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-NOV-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 : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P13 (MX1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.3776 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41777 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 46.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.40000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.300 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: PDB ENTRY 4BLU REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM SULFATE DECAHYDRATE, 0.1 REMARK 280 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 38.53000 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 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 GLU B 280 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: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ILE B 68 N ILE B 68 CA 0.201 REMARK 500 REMARK 500 REMARK: NULL 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 ILE B 68 C - N - CA ANGL. DEV. = -15.4 DEGREES REMARK 500 ILE B 68 N - CA - CB ANGL. DEV. = -18.4 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 LEU A 2 53.40 39.64 REMARK 500 ASN A 89 55.82 -142.54 REMARK 500 PHE A 187 78.70 -155.75 REMARK 500 LYS A 218 62.76 60.38 REMARK 500 ASN B 89 55.93 -140.94 REMARK 500 PHE B 187 79.56 -154.67 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ILE B 68 TRP B 69 -143.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ILE B 68 17.59 REMARK 500 ILE B 68 14.34 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 NA A1294 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 4 OH REMARK 620 2 HOH A2019 O 98.6 REMARK 620 3 HOH A2126 O 131.6 66.8 REMARK 620 4 HOH A2128 O 104.4 125.6 121.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B1287 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR B 4 OH REMARK 620 2 HOH B2013 O 104.8 REMARK 620 3 HOH B2077 O 137.9 73.3 REMARK 620 4 HOH B2078 O 98.3 117.0 120.5 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AMP A 1281 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAH A 1282 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1283 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1284 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1285 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1286 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1287 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1288 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1289 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1290 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1291 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1292 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1293 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1294 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AMP B 1280 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAH B 1281 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1282 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 1283 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 1284 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 1286 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 1285 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 1288 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 1287 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1295 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4BLU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ESCHERICHIA COLI 23S RRNA (A2030- N6)- REMARK 900 METHYLTRANSFERASE RLMJ REMARK 900 RELATED ID: 4BLV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ESCHERICHIA COLI 23S RRNA (A2030- N6)- REMARK 900 METHYLTRANSFERASE RLMJ IN COMPLEX WITH S- ADENOSYLMETHIONINE REMARK 900 (ADOMET) DBREF 4BLW A 1 280 UNP P37634 RLMJ_ECOLI 1 280 DBREF 4BLW B 1 280 UNP P37634 RLMJ_ECOLI 1 280 SEQADV 4BLW SER A 281 UNP P37634 EXPRESSION TAG SEQADV 4BLW LYS A 282 UNP P37634 EXPRESSION TAG SEQADV 4BLW GLY A 283 UNP P37634 EXPRESSION TAG SEQADV 4BLW HIS A 284 UNP P37634 EXPRESSION TAG SEQADV 4BLW HIS A 285 UNP P37634 EXPRESSION TAG SEQADV 4BLW HIS A 286 UNP P37634 EXPRESSION TAG SEQADV 4BLW HIS A 287 UNP P37634 EXPRESSION TAG SEQADV 4BLW HIS A 288 UNP P37634 EXPRESSION TAG SEQADV 4BLW HIS A 289 UNP P37634 EXPRESSION TAG SEQADV 4BLW SER B 281 UNP P37634 EXPRESSION TAG SEQADV 4BLW LYS B 282 UNP P37634 EXPRESSION TAG SEQADV 4BLW GLY B 283 UNP P37634 EXPRESSION TAG SEQADV 4BLW HIS B 284 UNP P37634 EXPRESSION TAG SEQADV 4BLW HIS B 285 UNP P37634 EXPRESSION TAG SEQADV 4BLW HIS B 286 UNP P37634 EXPRESSION TAG SEQADV 4BLW HIS B 287 UNP P37634 EXPRESSION TAG SEQADV 4BLW HIS B 288 UNP P37634 EXPRESSION TAG SEQADV 4BLW 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 AMP A1281 23 HET SAH A1282 26 HET GOL A1283 6 HET GOL A1284 6 HET EDO A1285 4 HET EDO A1286 4 HET EDO A1287 4 HET EDO A1288 4 HET EDO A1289 4 HET EDO A1290 4 HET EDO A1291 4 HET EDO A1292 4 HET EDO A1293 4 HET NA A1294 1 HET SO4 A1295 5 HET AMP B1280 23 HET SAH B1281 26 HET GOL B1282 6 HET EDO B1283 4 HET EDO B1284 4 HET EDO B1285 4 HET EDO B1286 4 HET NA B1287 1 HET EDO B1288 4 HETNAM AMP ADENOSINE MONOPHOSPHATE HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM GOL GLYCEROL HETNAM EDO 1,2-ETHANEDIOL HETNAM NA SODIUM ION HETNAM SO4 SULFATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 AMP 2(C10 H14 N5 O7 P) FORMUL 4 SAH 2(C14 H20 N6 O5 S) FORMUL 5 GOL 3(C3 H8 O3) FORMUL 7 EDO 14(C2 H6 O2) FORMUL 16 NA 2(NA 1+) FORMUL 17 SO4 O4 S 2- FORMUL 27 HOH *335(H2 O) HELIX 1 1 HIS A 6 PHE A 8 5 3 HELIX 2 2 ASN A 12 LYS A 30 1 19 HELIX 3 3 SER A 52 THR A 58 1 7 HELIX 4 4 GLU A 60 GLU A 63 5 4 HELIX 5 5 ILE A 65 ARG A 67 5 3 HELIX 6 6 PRO A 75 GLU A 77 5 3 HELIX 7 7 LEU A 78 PHE A 88 1 11 HELIX 8 8 GLY A 99 LEU A 108 1 10 HELIX 9 9 SER A 122 GLN A 132 1 11 HELIX 10 10 GLN A 146 LYS A 151 1 6 HELIX 11 11 THR A 171 PHE A 187 1 17 HELIX 12 12 LEU A 200 ALA A 213 1 14 HELIX 13 13 LYS A 248 VAL A 265 1 18 HELIX 14 14 HIS B 6 PHE B 8 5 3 HELIX 15 15 ASN B 12 LYS B 30 1 19 HELIX 16 16 SER B 52 THR B 58 1 7 HELIX 17 17 GLU B 60 GLU B 63 5 4 HELIX 18 18 ILE B 65 ARG B 67 5 3 HELIX 19 19 PRO B 75 GLU B 77 5 3 HELIX 20 20 LEU B 78 PHE B 88 1 11 HELIX 21 21 GLY B 99 LEU B 108 1 10 HELIX 22 22 SER B 122 GLN B 132 1 11 HELIX 23 23 ASP B 143 LYS B 151 1 9 HELIX 24 24 THR B 171 PHE B 187 1 17 HELIX 25 25 LEU B 200 ALA B 213 1 14 HELIX 26 26 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 LINK OH TYR A 4 NA NA A1294 1555 1555 2.87 LINK NA NA A1294 O HOH A2019 1555 1555 2.93 LINK NA NA A1294 O HOH A2126 1555 1555 2.49 LINK NA NA A1294 O HOH A2128 1555 1555 2.53 LINK OH TYR B 4 NA NA B1287 1555 1555 2.76 LINK NA NA B1287 O HOH B2013 1555 1555 2.84 LINK NA NA B1287 O HOH B2077 1555 1555 2.35 LINK NA NA B1287 O HOH B2078 1555 1555 2.60 CISPEP 1 LEU A 152 PRO A 153 0 0.54 CISPEP 2 LEU B 152 PRO B 153 0 1.57 SITE 1 AC1 11 TYR A 4 HIS A 9 ASN A 12 GLU A 60 SITE 2 AC1 11 VAL A 199 MET A 235 NA A1294 HOH A2015 SITE 3 AC1 11 HOH A2128 HOH A2201 HOH A2202 SITE 1 AC2 22 LEU A 2 TYR A 4 LYS A 18 HIS A 19 SITE 2 AC2 22 THR A 41 HIS A 42 ALA A 43 GLY A 44 SITE 3 AC2 22 GLY A 99 SER A 100 GLU A 118 LEU A 119 SITE 4 AC2 22 HIS A 120 ALA A 142 ASP A 143 GLY A 144 SITE 5 AC2 22 ASP A 164 HOH A2003 HOH A2006 HOH A2009 SITE 6 AC2 22 HOH A2041 HOH A2042 SITE 1 AC3 13 ALA A 66 ARG A 67 LYS A 185 ARG A 186 SITE 2 AC3 13 PHE A 187 ALA A 188 EDO A1285 HOH A2060 SITE 3 AC3 13 HOH A2061 HOH A2146 HOH A2149 HOH A2150 SITE 4 AC3 13 HOH A2204 SITE 1 AC4 6 VAL A 155 SER A 156 ARG A 157 HOH A2205 SITE 2 AC4 6 GLU B 110 GLN B 111 SITE 1 AC5 5 ARG A 67 PRO A 266 GOL A1283 HOH A2147 SITE 2 AC5 5 HOH A2192 SITE 1 AC6 6 HIS A 13 GLU A 60 GLU A 63 HOH A2016 SITE 2 AC6 6 HOH A2055 HOH A2056 SITE 1 AC7 2 LEU A 106 ARG B 90 SITE 1 AC8 10 SER A 7 PHE A 8 HIS A 9 ALA A 10 SITE 2 AC8 10 LEU A 50 ALA A 55 THR A 58 GLY A 59 SITE 3 AC8 10 GLU A 60 TYR A 61 SITE 1 AC9 3 PRO A 228 THR A 269 GLY A 270 SITE 1 BC1 2 PRO A 266 ALA A 267 SITE 1 BC2 6 LYS A 30 LEU A 106 LEU A 107 LEU A 108 SITE 2 BC2 6 HOH A2206 HOH A2207 SITE 1 BC3 9 LEU A 39 GLN A 115 LEU A 116 THR A 117 SITE 2 BC3 9 ARG A 138 GLU A 140 GLN A 147 LYS A 151 SITE 3 BC3 9 HOH A2039 SITE 1 BC4 4 ARG A 47 GLU A 130 SO4 A1295 HOH A2107 SITE 1 BC5 8 TYR A 4 PRO A 165 PRO A 166 TRP A 195 SITE 2 BC5 8 AMP A1281 HOH A2019 HOH A2126 HOH A2128 SITE 1 BC6 13 TYR B 4 HIS B 9 ASN B 12 GLU B 60 SITE 2 BC6 13 VAL B 199 MET B 235 EDO B1283 NA B1287 SITE 3 BC6 13 HOH B2009 HOH B2013 HOH B2078 HOH B2080 SITE 4 BC6 13 HOH B2115 SITE 1 BC7 22 TYR B 4 HIS B 6 LYS B 18 HIS B 19 SITE 2 BC7 22 THR B 41 HIS B 42 ALA B 43 GLY B 99 SITE 3 BC7 22 SER B 100 GLU B 118 LEU B 119 HIS B 120 SITE 4 BC7 22 ALA B 142 ASP B 143 GLY B 144 ASP B 164 SITE 5 BC7 22 EDO B1284 HOH B2001 HOH B2005 HOH B2007 SITE 6 BC7 22 HOH B2028 HOH B2029 SITE 1 BC8 4 LEU B 29 LYS B 32 ARG B 158 HOH B2076 SITE 1 BC9 5 TYR B 4 ARG B 5 PHE B 8 HIS B 9 SITE 2 BC9 5 AMP B1280 SITE 1 CC1 8 PRO B 166 TYR B 167 GLU B 168 MET B 169 SITE 2 CC1 8 ASP B 172 SAH B1281 HOH B2028 HOH B2083 SITE 1 CC2 6 ALA B 66 ARG B 67 HOH B2042 HOH B2044 SITE 2 CC2 6 HOH B2094 HOH B2096 SITE 1 CC3 9 ARG A 105 LYS A 133 HOH A2109 HIS B 87 SITE 2 CC3 9 PHE B 88 ASN B 89 ARG B 90 SER B 91 SITE 3 CC3 9 HOH B2055 SITE 1 CC4 6 GLU A 110 HOH A2096 TRP B 69 LYS B 86 SITE 2 CC4 6 ASN B 89 ARG B 90 SITE 1 CC5 8 TYR B 4 PRO B 165 PRO B 166 TRP B 195 SITE 2 CC5 8 AMP B1280 HOH B2013 HOH B2077 HOH B2078 SITE 1 CC6 6 HIS A 87 EDO A1293 HOH A2047 HOH A2094 SITE 2 CC6 6 HOH A2208 HIS B 87 CRYST1 46.590 77.060 84.370 90.00 99.50 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 0.021464 0.000000 0.003592 0.00000 SCALE2 0.000000 0.012977 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012017 0.00000 MTRIX1 1 -1.000000 -0.003500 0.006200 50.27450 1 MTRIX2 1 0.000700 0.818000 0.575200 -17.66540 1 MTRIX3 1 -0.007100 0.575200 -0.818000 55.90490 1