PDB Short entry for 3FTC HEADER TRANSFERASE 12-JAN-09 3FTC TITLE CRYSTAL STRUCTURE OF A. AEOLICUS KSGA AT 1.72-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: PDONR201; 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 3FTC 1 REMARK REVDAT 3 30-AUG-23 3FTC 1 AUTHOR JRNL SEQADV REVDAT 2 13-JUL-11 3FTC 1 VERSN REVDAT 1 24-MAR-09 3FTC 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. 1.68 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.68 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.51 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 23831 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1255 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1893 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 180 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 1. THE EFFECTIVE RESOLUTION FOR THIS REMARK 3 STRUCTURE IS 1.72 ANGSTROM, AT WHICH THE COMPLETENESS OF X-RAY REMARK 3 DATA > 93% AND THE OBSERVABLE DATA > 70% FOR HIGHEST RESOLUTION REMARK 3 SHELL. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 4 REMARK 4 3FTC 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_1000051017. 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 : 25134 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.680 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 (%) : 92.3 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 54.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.50000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.700 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 1QYR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3000, 0.1 M MES, PH 6.5, VAPOR REMARK 280 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 21.43750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.51100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.78850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.51100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.43750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.78850 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 SER A 7 REMARK 465 PHE A 8 REMARK 465 GLY A 9 REMARK 465 GLN A 10 REMARK 465 HIS A 11 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 44.40 -77.98 REMARK 500 PHE A 166 41.61 -98.52 REMARK 500 ASN A 182 84.89 -165.33 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: 3FTD RELATED DB: PDB REMARK 900 LIGAND-FREE A. AEOLICUS KSGA (KSGA1) 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 3FTC A 1 248 UNP O67680 KSGA_AQUAE 1 248 SEQADV 3FTC 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 *180(H2 O) HELIX 1 1 SER A 15 LEU A 26 1 12 HELIX 2 2 GLY A 42 LEU A 49 1 8 HELIX 3 3 ASP A 62 SER A 71 1 10 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 GLN A 137 1 8 HELIX 8 8 GLY A 143 PHE A 152 1 10 HELIX 9 9 ASP A 189 GLN A 202 1 14 HELIX 10 10 VAL A 207 LYS A 211 5 5 HELIX 11 11 PRO A 213 ALA A 220 1 8 HELIX 12 12 ARG A 227 LEU A 231 5 5 HELIX 13 13 SER A 232 GLU A 244 1 13 SHEET 1 A 7 LEU A 77 ILE A 80 0 SHEET 2 A 7 LYS A 55 ILE A 59 1 N VAL A 58 O ILE A 80 SHEET 3 A 7 THR A 33 VAL A 37 1 N GLU A 36 O TYR A 57 SHEET 4 A 7 LYS A 97 ASN A 101 1 O LYS A 97 N VAL A 35 SHEET 5 A 7 LEU A 123 GLN A 129 1 O MET A 127 N GLY A 100 SHEET 6 A 7 SER A 174 LYS A 181 -1 O LEU A 179 N ALA A 124 SHEET 7 A 7 TYR A 153 VAL A 161 -1 N ASN A 156 O LYS A 178 SSBOND 1 CYS A 90 CYS A 120 1555 1555 2.04 CISPEP 1 GLY A 40 THR A 41 0 -5.65 CISPEP 2 PRO A 169 PRO A 170 0 4.60 CRYST1 42.875 53.577 101.022 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 0.023324 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018665 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009899 0.00000