HEADER TRANSFERASE 01-JUL-08 3DMH TITLE T. THERMOPHILUS 16S RRNA N2 G1207 METHYLTRANSFERASE (RSMC) IN COMPLEX TITLE 2 WITH ADOMET AND GUANOSINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE RIBOSOMAL RNA SMALL SUBUNIT METHYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.1.1.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 300852; SOURCE 4 STRAIN: HB8; SOURCE 5 GENE: TTHA0533; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 DE3 (STAR); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET26B KEYWDS MONOMETHYLTRANSERASE, 16S RRNA METHYLTRANSFERASE, N2 G1207 KEYWDS 2 METHYLTRANSFERASE, S-ADENOSYL-L-HOMOCYSTEINE, TRANSLATION, KEYWDS 3 METHYLTRANSFERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.DEMIRCI,S.T.GREGORY,A.E.DAHLBERG,G.JOGL REVDAT 6 21-FEB-24 3DMH 1 REMARK SEQADV REVDAT 5 13-JUL-11 3DMH 1 VERSN REVDAT 4 24-FEB-09 3DMH 1 VERSN REVDAT 3 07-OCT-08 3DMH 1 JRNL REVDAT 2 09-SEP-08 3DMH 1 JRNL REVDAT 1 29-JUL-08 3DMH 0 JRNL AUTH H.DEMIRCI,S.T.GREGORY,A.E.DAHLBERG,G.JOGL JRNL TITL CRYSTAL STRUCTURE OF THE THERMUS THERMOPHILUS 16 S RRNA JRNL TITL 2 METHYLTRANSFERASE RSMC IN COMPLEX WITH COFACTOR AND JRNL TITL 3 SUBSTRATE GUANOSINE. JRNL REF J.BIOL.CHEM. V. 283 26548 2008 JRNL REFN ISSN 0021-9258 JRNL PMID 18667428 JRNL DOI 10.1074/JBC.M804005200 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 57244 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) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3060 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3603 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.3030 REMARK 3 BIN FREE R VALUE SET COUNT : 200 REMARK 3 BIN FREE R VALUE : 0.3230 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2833 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 55 REMARK 3 SOLVENT ATOMS : 420 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.13000 REMARK 3 B22 (A**2) : 0.86000 REMARK 3 B33 (A**2) : -0.73000 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): 0.086 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.087 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.053 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.679 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2963 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4027 ; 1.361 ; 2.011 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 372 ; 6.019 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 125 ;33.099 ;22.240 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 466 ;12.167 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 29 ;14.175 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 444 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2260 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1443 ; 0.193 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2022 ; 0.304 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 298 ; 0.111 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 34 ; 0.136 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 15 ; 0.150 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1885 ; 0.707 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2931 ; 1.078 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1216 ; 1.892 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1096 ; 2.976 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 3 A 178 REMARK 3 ORIGIN FOR THE GROUP (A): 33.9392 50.0008 -1.8573 REMARK 3 T TENSOR REMARK 3 T11: -0.0403 T22: -0.0425 REMARK 3 T33: -0.0535 T12: -0.0098 REMARK 3 T13: 0.0053 T23: -0.0131 REMARK 3 L TENSOR REMARK 3 L11: 0.8496 L22: 1.1963 REMARK 3 L33: 2.0769 L12: -0.0706 REMARK 3 L13: -0.6183 L23: 0.5419 REMARK 3 S TENSOR REMARK 3 S11: -0.0666 S12: 0.1336 S13: -0.0974 REMARK 3 S21: 0.0587 S22: -0.0029 S23: 0.0297 REMARK 3 S31: 0.3558 S32: -0.0012 S33: 0.0695 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 187 A 372 REMARK 3 ORIGIN FOR THE GROUP (A): 25.3191 61.1243 25.2918 REMARK 3 T TENSOR REMARK 3 T11: -0.0225 T22: -0.0834 REMARK 3 T33: -0.0630 T12: 0.0107 REMARK 3 T13: 0.0447 T23: 0.0082 REMARK 3 L TENSOR REMARK 3 L11: 1.9553 L22: 0.9861 REMARK 3 L33: 2.9803 L12: 0.4829 REMARK 3 L13: -0.0165 L23: -0.1021 REMARK 3 S TENSOR REMARK 3 S11: 0.0439 S12: -0.1721 S13: 0.0421 REMARK 3 S21: 0.2696 S22: -0.0383 S23: 0.1007 REMARK 3 S31: -0.0464 S32: -0.2093 S33: -0.0056 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. FOR STRUCTURE DETERMINATION, AUTHORS STATE THAT THE REMARK 3 INITIAL MODEL IS SOLVED BY USING ANOMALOUS DATA ON A CRYSTAL REMARK 3 DIFFERENT FROM WHAT WAS DESCRIBED IN REMARK 200. THE FINAL REMARK 3 STRUCTURE WAS REFINED BY USING THE INITIAL MODEL AND THE DATA REMARK 3 DESCRIBED IN REMARK 3 AND REMARK 200. REMARK 4 REMARK 4 3DMH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000048222. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 2008 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 : NSLS REMARK 200 BEAMLINE : X4C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9797 REMARK 200 MONOCHROMATOR : MONOCHROMATOR SYSTEM CONSISTING REMARK 200 OF A HORIZONTALLY DEFLECTING AND REMARK 200 FOCUSING CRYSTAL PRECEDED BY A REMARK 200 VERTICALLY FOCUSING MIRROR. REMARK 200 DISTANCE FROM MONOCHROMATOR TO REMARK 200 SAMPLE IS VARIABLE BETWEEN 2.5 REMARK 200 AND 4.5 M. DISTANCE FROM THE REMARK 200 MONOCHROMATOR TO SOURCE IS ~10.5 REMARK 200 M. REMARK 200 OPTICS : SLITS: VARIABLE VERTICAL AND REMARK 200 HORIZONTAL SLITS. MONOCHROMATOR: REMARK 200 MONOCHROMATOR SYSTEM CONSISTING REMARK 200 OF A HORIZONTALLY DEFLECTING AND REMARK 200 FOCUSING CRYSTAL PRECEDED BY A REMARK 200 VERTICALLY FOCUSING MIRROR. REMARK 200 DISTANCE FROM MONOCHROMATOR TO REMARK 200 SAMPLE IS VARIABLE BETWEEN 2.5 REMARK 200 AND 4.5 M. DISTANCE FROM THE REMARK 200 MONOCHROMATOR TO SOURCE IS ~10.5 REMARK 200 M. REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57244 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.41800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.085 M TRIS HCL (PH 8.5), 25.5% W/V REMARK 280 PEG4000 15% GLYCEROL, MICROBATCH TECHNIQUE UNDER OIL, REMARK 280 TEMPERATURE 277K 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 25.43150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.54550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.11700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.54550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.43150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.11700 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 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 MET A 1 REMARK 465 SER A 2 REMARK 465 GLY A 374 REMARK 465 ARG A 375 REMARK 465 HIS A 376 REMARK 465 HIS A 377 REMARK 465 HIS A 378 REMARK 465 HIS A 379 REMARK 465 HIS A 380 REMARK 465 HIS A 381 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 PHE A 79 CD2 CE1 CE2 CZ REMARK 470 VAL A 310 CB CG1 CG2 REMARK 470 ARG A 373 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 561 O HOH A 639 2665 2.11 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 ASN A 53 63.27 -156.44 REMARK 500 VAL A 289 -123.03 51.87 REMARK 500 VAL A 310 -75.99 -22.59 REMARK 500 ALA A 363 -106.58 -145.70 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 GMP A 385 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 382 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 383 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAM A 384 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GMP A 385 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3DMF RELATED DB: PDB REMARK 900 T. THERMOPHILUS 16S RRNA N2 G1207 METHYLTRANSFERASE (RSMC) IN REMARK 900 COMPLEX WITH ADOMET REMARK 900 RELATED ID: 3DMG RELATED DB: PDB REMARK 900 T. THERMOPHILUS 16S RRNA N2 G1207 METHYLTRANSFERASE (RSMC) IN REMARK 900 COMPLEX WITH ADOHCY DBREF 3DMH A 1 375 UNP Q5SKW0 Q5SKW0_THET8 1 375 SEQADV 3DMH HIS A 376 UNP Q5SKW0 EXPRESSION TAG SEQADV 3DMH HIS A 377 UNP Q5SKW0 EXPRESSION TAG SEQADV 3DMH HIS A 378 UNP Q5SKW0 EXPRESSION TAG SEQADV 3DMH HIS A 379 UNP Q5SKW0 EXPRESSION TAG SEQADV 3DMH HIS A 380 UNP Q5SKW0 EXPRESSION TAG SEQADV 3DMH HIS A 381 UNP Q5SKW0 EXPRESSION TAG SEQRES 1 A 381 MET SER LEU THR ARG GLU ALA TYR HIS ARG LEU THR PRO SEQRES 2 A 381 LEU PRO HIS PRO GLY GLY ARG LEU PHE ILE LYS PRO GLY SEQRES 3 A 381 ALA ARG GLY TYR ARG ASP PRO VAL HIS ASP LEU LEU GLN SEQRES 4 A 381 LYS THR VAL GLU PRO PHE GLY GLU ARG ALA LEU ASP LEU SEQRES 5 A 381 ASN PRO GLY VAL GLY TRP GLY SER LEU PRO LEU GLU GLY SEQRES 6 A 381 ARG MET ALA VAL GLU ARG LEU GLU THR SER ARG ALA ALA SEQRES 7 A 381 PHE ARG CYS LEU THR ALA SER GLY LEU GLN ALA ARG LEU SEQRES 8 A 381 ALA LEU PRO TRP GLU ALA ALA ALA GLY ALA TYR ASP LEU SEQRES 9 A 381 VAL VAL LEU ALA LEU PRO ALA GLY ARG GLY THR ALA TYR SEQRES 10 A 381 VAL GLN ALA SER LEU VAL ALA ALA ALA ARG ALA LEU ARG SEQRES 11 A 381 MET GLY GLY ARG LEU TYR LEU ALA GLY ASP LYS ASN LYS SEQRES 12 A 381 GLY PHE GLU ARG TYR PHE LYS GLU ALA ARG ALA LEU LEU SEQRES 13 A 381 GLY TYR GLY VAL VAL VAL ARG ARG GLU GLY PRO TYR ARG SEQRES 14 A 381 VAL ALA LEU LEU GLU LYS GLU LYS GLU ALA PRO PRO LEU SEQRES 15 A 381 PRO SER LEU TRP ARG ALA PHE SER ALA ARG ILE LEU GLY SEQRES 16 A 381 ALA GLU TYR THR PHE HIS HIS LEU PRO GLY VAL PHE SER SEQRES 17 A 381 ALA GLY LYS VAL ASP PRO ALA SER LEU LEU LEU LEU GLU SEQRES 18 A 381 ALA LEU GLN GLU ARG LEU GLY PRO GLU GLY VAL ARG GLY SEQRES 19 A 381 ARG GLN VAL LEU ASP LEU GLY ALA GLY TYR GLY ALA LEU SEQRES 20 A 381 THR LEU PRO LEU ALA ARG MET GLY ALA GLU VAL VAL GLY SEQRES 21 A 381 VAL GLU ASP ASP LEU ALA SER VAL LEU SER LEU GLN LYS SEQRES 22 A 381 GLY LEU GLU ALA ASN ALA LEU LYS ALA GLN ALA LEU HIS SEQRES 23 A 381 SER ASP VAL ASP GLU ALA LEU THR GLU GLU ALA ARG PHE SEQRES 24 A 381 ASP ILE ILE VAL THR ASN PRO PRO PHE HIS VAL GLY GLY SEQRES 25 A 381 ALA VAL ILE LEU ASP VAL ALA GLN ALA PHE VAL ASN VAL SEQRES 26 A 381 ALA ALA ALA ARG LEU ARG PRO GLY GLY VAL PHE PHE LEU SEQRES 27 A 381 VAL SER ASN PRO PHE LEU LYS TYR GLU PRO LEU LEU GLU SEQRES 28 A 381 GLU LYS PHE GLY ALA PHE GLN THR LEU LYS VAL ALA GLU SEQRES 29 A 381 TYR LYS VAL LEU PHE ALA GLU LYS ARG GLY ARG HIS HIS SEQRES 30 A 381 HIS HIS HIS HIS HET SO4 A 382 5 HET SO4 A 383 5 HET SAM A 384 27 HET GMP A 385 18 HETNAM SO4 SULFATE ION HETNAM SAM S-ADENOSYLMETHIONINE HETNAM GMP GUANOSINE FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 SAM C15 H22 N6 O5 S FORMUL 5 GMP C10 H13 N5 O5 FORMUL 6 HOH *420(H2 O) HELIX 1 1 THR A 4 ARG A 10 1 7 HELIX 2 2 ASP A 32 VAL A 42 1 11 HELIX 3 3 SER A 60 GLU A 64 5 5 HELIX 4 4 SER A 75 SER A 85 1 11 HELIX 5 5 LEU A 93 ALA A 97 5 5 HELIX 6 6 PRO A 110 ARG A 113 5 4 HELIX 7 7 GLY A 114 ALA A 128 1 15 HELIX 8 8 GLY A 144 GLY A 157 1 14 HELIX 9 9 ASP A 213 GLY A 228 1 16 HELIX 10 10 LEU A 247 MET A 254 1 8 HELIX 11 11 ASP A 264 ASN A 278 1 15 HELIX 12 12 LEU A 316 ARG A 329 1 14 HELIX 13 13 LYS A 345 GLY A 355 1 11 SHEET 1 A 2 THR A 12 HIS A 16 0 SHEET 2 A 2 GLY A 19 ILE A 23 -1 O LEU A 21 N LEU A 14 SHEET 1 B 7 ARG A 90 LEU A 91 0 SHEET 2 B 7 ALA A 68 GLU A 73 1 N ARG A 71 O ARG A 90 SHEET 3 B 7 ARG A 48 ASP A 51 1 N ALA A 49 O ALA A 68 SHEET 4 B 7 TYR A 102 ALA A 108 1 O VAL A 106 N LEU A 50 SHEET 5 B 7 LEU A 129 ASP A 140 1 O TYR A 136 N VAL A 105 SHEET 6 B 7 TYR A 168 GLU A 174 -1 O ALA A 171 N LEU A 137 SHEET 7 B 7 GLY A 159 GLU A 165 -1 N VAL A 160 O LEU A 172 SHEET 1 C 2 ARG A 187 ILE A 193 0 SHEET 2 C 2 ALA A 196 HIS A 202 -1 O ALA A 196 N ILE A 193 SHEET 1 D 7 GLN A 283 HIS A 286 0 SHEET 2 D 7 GLU A 257 GLU A 262 1 N GLY A 260 O GLN A 283 SHEET 3 D 7 GLN A 236 LEU A 240 1 N ASP A 239 O VAL A 259 SHEET 4 D 7 PHE A 299 THR A 304 1 O VAL A 303 N LEU A 240 SHEET 5 D 7 LEU A 330 SER A 340 1 O ARG A 331 N PHE A 299 SHEET 6 D 7 LYS A 366 GLU A 371 -1 O LEU A 368 N LEU A 338 SHEET 7 D 7 GLN A 358 VAL A 362 -1 N GLN A 358 O PHE A 369 SITE 1 AC1 5 THR A 4 ARG A 5 LYS A 353 HOH A 443 SITE 2 AC1 5 HOH A 528 SITE 1 AC2 9 ARG A 28 ASN A 53 PRO A 110 ALA A 111 SITE 2 AC2 9 GLY A 112 ARG A 113 HOH A 491 HOH A 515 SITE 3 AC2 9 HOH A 551 SITE 1 AC3 22 TYR A 8 PHE A 207 SER A 216 GLY A 241 SITE 2 AC3 22 ALA A 242 GLY A 243 ALA A 246 GLU A 262 SITE 3 AC3 22 ASP A 263 SER A 287 ASP A 288 ASN A 305 SITE 4 AC3 22 PRO A 306 HOH A 392 HOH A 393 HOH A 396 SITE 5 AC3 22 HOH A 398 HOH A 400 HOH A 402 HOH A 525 SITE 6 AC3 22 HOH A 644 HOH A 781 SITE 1 AC4 11 ASP A 213 ALA A 215 ASN A 305 PHE A 308 SITE 2 AC4 11 ASN A 341 LEU A 344 TYR A 365 HOH A 403 SITE 3 AC4 11 HOH A 454 HOH A 549 HOH A 616 CRYST1 50.863 86.234 95.091 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 0.019661 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011596 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010516 0.00000