HEADER TRANSFERASE 08-JAN-09 3FRH TITLE STRUCTURE OF THE 16S RRNA METHYLASE RMTB, P21 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 16S RRNA METHYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RMTB, 16S RIBOSOMAL RNA METHYLASE, RMTB PROTEIN; COMPND 5 EC: 2.1.1.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: RMTB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21-ROSETTA; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS METHYLTRANSFERASE DOMAIN, HELICAL N-TERMINAL DOMAIN, KEYWDS 2 METHYLTRANSFERASE, PLASMID, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR E.SCHMITT,M.GALIMAND,M.PANVERT,M.DUPECHEZ,P.COURVALIN,Y.MECHULAM REVDAT 3 01-NOV-23 3FRH 1 REMARK SEQADV REVDAT 2 02-MAR-10 3FRH 1 TITLE REVDAT 1 11-AUG-09 3FRH 0 JRNL AUTH E.SCHMITT,M.GALIMAND,M.PANVERT,P.COURVALIN,Y.MECHULAM JRNL TITL STRUCTURAL BASES FOR 16 S RRNA METHYLATION CATALYZED BY ARMA JRNL TITL 2 AND RMTB METHYLTRANSFERASES JRNL REF J.MOL.BIOL. V. 388 570 2009 JRNL REFN ISSN 0022-2836 JRNL PMID 19303884 JRNL DOI 10.1016/J.JMB.2009.03.034 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 71813 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.139 REMARK 3 R VALUE (WORKING SET) : 0.139 REMARK 3 FREE R VALUE : 0.159 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.090 REMARK 3 FREE R VALUE TEST SET COUNT : 4376 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 1.2139 - 1.2003 0.89 0 138 0.1340 0.1675 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.64 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.57800 REMARK 3 B22 (A**2) : 0.04800 REMARK 3 B33 (A**2) : -0.62600 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.28700 REMARK 3 B23 (A**2) : 0.00000 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 : 0.005 NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : 9.991 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 3FRH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-JAN-09. REMARK 100 THE DEPOSITION ID IS D_1000050951. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-DEC-07 REMARK 200 TEMPERATURE (KELVIN) : 150 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 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 : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 71817 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 46.078 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 2.200 REMARK 200 R MERGE (I) : 0.03900 REMARK 200 R SYM (I) : 0.03900 REMARK 200 FOR THE DATA SET : 14.5600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.14 REMARK 200 R MERGE FOR SHELL (I) : 0.13000 REMARK 200 R SYM FOR SHELL (I) : 0.13000 REMARK 200 FOR SHELL : 7.730 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 3B89 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 50MM BIS-TRIS PH6.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 24.15200 REMARK 290 SMTRY3 2 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 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 SER A 207 REMARK 465 LEU A 208 REMARK 465 GLY A 209 REMARK 465 GLY A 210 REMARK 465 ARG A 211 REMARK 465 GLY A 212 REMARK 465 LYS A 213 REMARK 465 GLY A 214 REMARK 465 MET A 215 REMARK 465 GLU A 216 REMARK 465 ALA A 217 REMARK 465 GLY A 251 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 ARG A 206 CG CD NE CZ NH1 NH2 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 ARG A 206 N - CA - C ANGL. DEV. = -22.0 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 111 60.53 60.90 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 THR A 205 ARG A 206 143.50 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 SAH A 260 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3FRI RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN I 2 2 2 REMARK 900 RELATED ID: 3FZG RELATED DB: PDB REMARK 900 A HOMOLOGOUS PROTEIN IN C 2 2 21 DBREF 3FRH A 1 251 UNP Q763K9 Q763K9_ECOLX 1 251 SEQADV 3FRH TYR A -1 UNP Q763K9 EXPRESSION TAG SEQADV 3FRH PRO A 0 UNP Q763K9 EXPRESSION TAG SEQRES 1 A 253 TYR PRO MET ASN ILE ASN ASP ALA LEU THR SER ILE LEU SEQRES 2 A 253 ALA SER LYS LYS TYR ARG ALA LEU CYS PRO ASP THR VAL SEQRES 3 A 253 ARG ARG ILE LEU THR GLU GLU TRP GLY ARG HIS LYS SER SEQRES 4 A 253 PRO LYS GLN THR VAL GLU ALA ALA ARG THR ARG LEU HIS SEQRES 5 A 253 GLY ILE CYS GLY ALA TYR VAL THR PRO GLU SER LEU LYS SEQRES 6 A 253 ALA ALA ALA ALA ALA LEU SER ALA GLY ASP VAL LYS LYS SEQRES 7 A 253 ALA LEU SER LEU HIS ALA SER THR LYS GLU ARG LEU ALA SEQRES 8 A 253 GLU LEU ASP THR LEU TYR ASP PHE ILE PHE SER ALA GLU SEQRES 9 A 253 THR PRO ARG ARG VAL LEU ASP ILE ALA CYS GLY LEU ASN SEQRES 10 A 253 PRO LEU ALA LEU TYR GLU ARG GLY ILE ALA SER VAL TRP SEQRES 11 A 253 GLY CYS ASP ILE HIS GLN GLY LEU GLY ASP VAL ILE THR SEQRES 12 A 253 PRO PHE ALA ARG GLU LYS ASP TRP ASP PHE THR PHE ALA SEQRES 13 A 253 LEU GLN ASP VAL LEU CYS ALA PRO PRO ALA GLU ALA GLY SEQRES 14 A 253 ASP LEU ALA LEU ILE PHE LYS LEU LEU PRO LEU LEU GLU SEQRES 15 A 253 ARG GLU GLN ALA GLY SER ALA MET ALA LEU LEU GLN SER SEQRES 16 A 253 LEU ASN THR PRO ARG MET ALA VAL SER PHE PRO THR ARG SEQRES 17 A 253 SER LEU GLY GLY ARG GLY LYS GLY MET GLU ALA ASN TYR SEQRES 18 A 253 ALA ALA TRP PHE GLU GLY GLY LEU PRO ALA GLU PHE GLU SEQRES 19 A 253 ILE GLU ASP LYS LYS THR ILE GLY THR GLU LEU ILE TYR SEQRES 20 A 253 LEU ILE LYS LYS ASN GLY HET SAH A 260 26 HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE FORMUL 2 SAH C14 H20 N6 O5 S FORMUL 3 HOH *549(H2 O) HELIX 1 1 ASN A 2 SER A 13 1 12 HELIX 2 2 CYS A 20 GLY A 33 1 14 HELIX 3 3 SER A 37 GLY A 54 1 18 HELIX 4 4 THR A 58 ALA A 71 1 14 HELIX 5 5 ASP A 73 SER A 79 1 7 HELIX 6 6 HIS A 81 LEU A 88 1 8 HELIX 7 7 GLU A 90 PHE A 99 1 10 HELIX 8 8 ASN A 115 ARG A 122 1 8 HELIX 9 9 HIS A 133 LYS A 147 1 15 HELIX 10 10 LEU A 175 GLN A 183 1 9 HELIX 11 11 GLY A 185 LEU A 194 1 10 HELIX 12 12 ASN A 218 LEU A 227 1 10 SHEET 1 A 7 ASP A 150 LEU A 155 0 SHEET 2 A 7 SER A 126 ASP A 131 1 N GLY A 129 O THR A 152 SHEET 3 A 7 ARG A 106 ILE A 110 1 N ASP A 109 O TRP A 128 SHEET 4 A 7 LEU A 169 PHE A 173 1 O LEU A 171 N LEU A 108 SHEET 5 A 7 ARG A 198 PRO A 204 1 O ALA A 200 N ILE A 172 SHEET 6 A 7 GLU A 242 LYS A 249 -1 O LEU A 243 N PHE A 203 SHEET 7 A 7 PHE A 231 ILE A 239 -1 N LYS A 237 O ILE A 244 SITE 1 AC1 18 TYR A 56 SER A 83 ARG A 87 ALA A 111 SITE 2 AC1 18 CYS A 112 ASP A 131 ILE A 132 GLN A 156 SITE 3 AC1 18 ASP A 157 VAL A 158 PHE A 173 LEU A 178 SITE 4 AC1 18 HOH A 411 HOH A 424 HOH A 435 HOH A 486 SITE 5 AC1 18 HOH A 493 HOH A 503 CRYST1 50.856 48.304 54.558 90.00 115.05 90.00 P 1 21 1 2 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 0.019663 0.000000 0.009192 0.00000 SCALE2 0.000000 0.020702 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020233 0.00000