PDB Short entry for 3FTD HEADER TRANSFERASE 12-JAN-09 3FTD TITLE CRYSTAL STRUCTURE OF A. AEOLICUS KSGA AT 1.44-ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIMETHYLADENOSINE TRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: S-ADENOSYLMETHIONINE-6-N', N'-ADENOSYL(RRNA) COMPND 5 DIMETHYLTRANSFERASE, 16S RRNA DIMETHYLASE, HIGH LEVEL KASUGAMYCIN COMPND 6 RESISTANCE PROTEIN KSGA, KASUGAMYCIN DIMETHYLTRANSFERASE; COMPND 7 EC: 2.1.1.-; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AQUIFEX AEOLICUS; SOURCE 3 ORGANISM_TAXID: 224324; SOURCE 4 STRAIN: VF5; SOURCE 5 GENE: AQ_1816, KSGA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS(DE3)-RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PDONR221; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PBA1939 KEYWDS KSGA, ROSSMANN-LIKE FOLD, RNA METHYLTRANSFERASE, MTASE, ANTIBIOTIC KEYWDS 2 RESISTANCE, METHYLTRANSFERASE, RNA-BINDING, RRNA PROCESSING, S- KEYWDS 3 ADENOSYL-L-METHIONINE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.TU,X.JI REVDAT 4 06-SEP-23 3FTD 1 REMARK REVDAT 3 30-AUG-23 3FTD 1 AUTHOR JRNL SEQADV REVDAT 2 13-JUL-11 3FTD 1 VERSN REVDAT 1 24-MAR-09 3FTD 0 JRNL AUTH C.TU,J.E.TROPEA,B.P.AUSTIN,D.L.COURT,D.S.WAUGH,X.JI JRNL TITL STRUCTURAL BASIS FOR BINDING OF RNA AND COFACTOR BY A KSGA JRNL TITL 2 METHYLTRANSFERASE. JRNL REF STRUCTURE V. 17 374 2009 JRNL REFN ISSN 0969-2126 JRNL PMID 19278652 JRNL DOI 10.1016/J.STR.2009.01.010 REMARK 2 REMARK 2 RESOLUTION. 1.44 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) : 1.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 3 NUMBER OF REFLECTIONS : 37676 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.310 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 28.6972 - 3.4740 1.00 2885 162 0.1619 0.1853 REMARK 3 2 3.4740 - 2.7581 1.00 2751 153 0.1565 0.1600 REMARK 3 3 2.7581 - 2.4097 1.00 2721 153 0.1627 0.2048 REMARK 3 4 2.4097 - 2.1895 1.00 2701 152 0.1469 0.1958 REMARK 3 5 2.1895 - 2.0326 1.00 2698 152 0.1322 0.1814 REMARK 3 6 2.0326 - 1.9128 1.00 2672 149 0.1305 0.1891 REMARK 3 7 1.9128 - 1.8170 1.00 2678 150 0.1319 0.1970 REMARK 3 8 1.8170 - 1.7379 0.99 2645 149 0.1416 0.2523 REMARK 3 9 1.7379 - 1.6710 0.99 2635 147 0.1457 0.1909 REMARK 3 10 1.6710 - 1.6134 0.97 2580 145 0.1530 0.2433 REMARK 3 11 1.6134 - 1.5629 0.94 2530 141 0.1660 0.2438 REMARK 3 12 1.5629 - 1.5182 0.89 2360 133 0.1857 0.2428 REMARK 3 13 1.5182 - 1.4783 0.79 2083 117 0.2195 0.2727 REMARK 3 14 1.4783 - 1.4400 0.66 1737 97 0.2929 0.3355 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 : 0.38 REMARK 3 B_SOL : 50.04 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.76000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : -0.74000 REMARK 3 B13 (A**2) : 1.50000 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 : 14.495 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 3FTD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JAN-09. REMARK 100 THE DEPOSITION ID IS D_1000051018. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-MAR-08 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 : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : SI(111) ROSENBAUM-ROCK DOUBLE REMARK 200 CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38594 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.440 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 24.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.44 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 66.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.44600 REMARK 200 R SYM FOR SHELL (I) : 0.49300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.900 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 3FTC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG MME 5000, 0.1 M BIS-TRIS, PH REMARK 280 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 21.54350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.80900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.69150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.80900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.54350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.69150 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 300 REMARK: THE BIOLOGICAL ASSEMBLY CORRESPONDS TO THE CONTENT OF THE REMARK 300 ASYMMETRIC UNIT. 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 0 REMARK 465 MET A 1 REMARK 465 VAL A 2 REMARK 465 ARG A 3 REMARK 465 LEU A 4 REMARK 465 LYS A 5 REMARK 465 LYS A 6 REMARK 465 GLY A 247 REMARK 465 GLU A 248 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 PRO A 52 31.88 -75.68 REMARK 500 ASN A 182 92.06 -160.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1QYR RELATED DB: PDB REMARK 900 LIGAND-FREE E. COLI KSGA REMARK 900 RELATED ID: 1ZQ9 RELATED DB: PDB REMARK 900 H. SAPIENS DIM1 IN COMPLEX WITH SAM REMARK 900 RELATED ID: 1G38 RELATED DB: PDB REMARK 900 M.TAQI IN COMPLEX WITH DNA AND COFACTOR ANALOG NEA REMARK 900 RELATED ID: 3FTC RELATED DB: PDB REMARK 900 LIGAND-FREE A. AEOLICUS KSGA (KSGA2) REMARK 900 RELATED ID: 3FTE RELATED DB: PDB REMARK 900 A. AEOLICUS KSGA IN COMPLEX WITH RNA (KSGA-RNA) REMARK 900 RELATED ID: 3FTF RELATED DB: PDB REMARK 900 A. AEOLICUS KSGA IN COMPLEX WITH RNA AND SAH (KSGA-RNA-SAH) DBREF 3FTD A 1 248 UNP O67680 KSGA_AQUAE 1 248 SEQADV 3FTD SER A 0 UNP O67680 EXPRESSION TAG SEQRES 1 A 249 SER MET VAL ARG LEU LYS LYS SER PHE GLY GLN HIS LEU SEQRES 2 A 249 LEU VAL SER GLU GLY VAL LEU LYS LYS ILE ALA GLU GLU SEQRES 3 A 249 LEU ASN ILE GLU GLU GLY ASN THR VAL VAL GLU VAL GLY SEQRES 4 A 249 GLY GLY THR GLY ASN LEU THR LYS VAL LEU LEU GLN HIS SEQRES 5 A 249 PRO LEU LYS LYS LEU TYR VAL ILE GLU LEU ASP ARG GLU SEQRES 6 A 249 MET VAL GLU ASN LEU LYS SER ILE GLY ASP GLU ARG LEU SEQRES 7 A 249 GLU VAL ILE ASN GLU ASP ALA SER LYS PHE PRO PHE CYS SEQRES 8 A 249 SER LEU GLY LYS GLU LEU LYS VAL VAL GLY ASN LEU PRO SEQRES 9 A 249 TYR ASN VAL ALA SER LEU ILE ILE GLU ASN THR VAL TYR SEQRES 10 A 249 ASN LYS ASP CYS VAL PRO LEU ALA VAL PHE MET VAL GLN SEQRES 11 A 249 LYS GLU VAL ALA GLU LYS LEU GLN GLY LYS LYS ASP THR SEQRES 12 A 249 GLY TRP LEU SER VAL PHE VAL ARG THR PHE TYR ASP VAL SEQRES 13 A 249 ASN TYR VAL MET THR VAL PRO PRO ARG PHE PHE VAL PRO SEQRES 14 A 249 PRO PRO LYS VAL GLN SER ALA VAL ILE LYS LEU VAL LYS SEQRES 15 A 249 ASN GLU LYS PHE PRO VAL LYS ASP LEU LYS ASN TYR LYS SEQRES 16 A 249 LYS PHE LEU THR LYS ILE PHE GLN ASN ARG ARG LYS VAL SEQRES 17 A 249 LEU ARG LYS LYS ILE PRO GLU GLU LEU LEU LYS GLU ALA SEQRES 18 A 249 GLY ILE ASN PRO ASP ALA ARG VAL GLU GLN LEU SER LEU SEQRES 19 A 249 GLU ASP PHE PHE LYS LEU TYR ARG LEU ILE GLU ASP SER SEQRES 20 A 249 GLY GLU FORMUL 2 HOH *277(H2 O) HELIX 1 1 SER A 15 LEU A 26 1 12 HELIX 2 2 GLY A 40 LEU A 49 1 10 HELIX 3 3 ASP A 62 LYS A 70 1 9 HELIX 4 4 PRO A 88 LEU A 92 5 5 HELIX 5 5 VAL A 106 ASN A 117 1 12 HELIX 6 6 LYS A 118 VAL A 121 5 4 HELIX 7 7 LYS A 130 GLY A 138 1 9 HELIX 8 8 GLY A 143 PHE A 152 1 10 HELIX 9 9 PRO A 162 ARG A 164 5 3 HELIX 10 10 ASP A 189 GLN A 202 1 14 HELIX 11 11 VAL A 207 LYS A 211 5 5 HELIX 12 12 PRO A 213 ALA A 220 1 8 HELIX 13 13 ARG A 227 LEU A 231 5 5 HELIX 14 14 SER A 232 ASP A 245 1 14 SHEET 1 A 2 LEU A 13 VAL A 14 0 SHEET 2 A 2 PHE A 166 VAL A 167 -1 O VAL A 167 N LEU A 13 SHEET 1 B 7 LEU A 77 ILE A 80 0 SHEET 2 B 7 LYS A 55 ILE A 59 1 N VAL A 58 O ILE A 80 SHEET 3 B 7 THR A 33 GLY A 38 1 N GLU A 36 O TYR A 57 SHEET 4 B 7 LEU A 96 ASN A 101 1 O LYS A 97 N VAL A 35 SHEET 5 B 7 LEU A 123 GLN A 129 1 O VAL A 125 N VAL A 98 SHEET 6 B 7 SER A 174 LYS A 181 -1 O LEU A 179 N ALA A 124 SHEET 7 B 7 TYR A 153 VAL A 161 -1 N ASP A 154 O VAL A 180 SSBOND 1 CYS A 90 CYS A 120 1555 1555 2.03 CISPEP 1 VAL A 167 PRO A 168 0 -1.44 CRYST1 43.087 57.383 87.618 90.00 90.00 90.00 P 21 21 21 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 0.023209 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017427 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011413 0.00000