PDB Short entry for 3CJR HEADER TRANSFERASE/RIBOSOMAL PROTEIN 13-MAR-08 3CJR TITLE RIBOSOMAL PROTEIN L11 METHYLTRANSFERASE (PRMA) IN COMPLEX WITH TITLE 2 RIBOSOMAL PROTEIN L11 (K39A) AND INHIBITOR SINEFUNGIN. COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSOMAL PROTEIN L11 METHYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: L11 MTASE; COMPND 5 EC: 2.1.1.-; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 50S RIBOSOMAL PROTEIN L11; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 STRAIN: HB8; SOURCE 4 GENE: PRMA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) STAR; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET30B; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 11 STRAIN: HB8; SOURCE 12 GENE: RPLK, RPL11; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) PRMA::TC; SOURCE 15 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 16 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS S-ADENOSYL-L-METHIONINE DEPENDENT METHYLTRANSFERASE, POST- KEYWDS 2 TRANSLATIONAL MODIFICATION, MULTI-SPECIFIC TRIMETHYLATION, KEYWDS 3 RIBONUCLEOPROTEIN, RIBOSOMAL PROTEIN, RNA-BINDING, RRNA-BINDING, KEYWDS 4 TRANSFERASE-RIBOSOMAL PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.DEMIRCI,S.T.GREGORY,A.E.DAHLBERG,G.JOGL REVDAT 6 30-AUG-23 3CJR 1 REMARK REVDAT 5 20-OCT-21 3CJR 1 REMARK SEQADV REVDAT 4 13-JUL-11 3CJR 1 VERSN REVDAT 3 24-FEB-09 3CJR 1 VERSN REVDAT 2 22-JUL-08 3CJR 1 JRNL REVDAT 1 20-MAY-08 3CJR 0 JRNL AUTH H.DEMIRCI,S.T.GREGORY,A.E.DAHLBERG,G.JOGL JRNL TITL MULTIPLE-SITE TRIMETHYLATION OF RIBOSOMAL PROTEIN L11 BY THE JRNL TITL 2 PRMA METHYLTRANSFERASE. JRNL REF STRUCTURE V. 16 1059 2008 JRNL REFN ISSN 0969-2126 JRNL PMID 18611379 JRNL DOI 10.1016/J.STR.2008.03.016 REMARK 2 REMARK 2 RESOLUTION. 2.05 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 27841 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) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1491 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) : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.10 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2035 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.91 REMARK 3 BIN R VALUE (WORKING SET) : 0.2670 REMARK 3 BIN FREE R VALUE SET COUNT : 104 REMARK 3 BIN FREE R VALUE : 0.3100 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2791 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 27 REMARK 3 SOLVENT ATOMS : 328 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) : 51.92 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.33000 REMARK 3 B22 (A**2) : -0.33000 REMARK 3 B33 (A**2) : 0.50000 REMARK 3 B12 (A**2) : -0.17000 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): 0.202 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.194 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.139 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.554 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.908 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2881 ; 0.006 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3927 ; 1.125 ; 1.993 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 363 ; 5.176 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 109 ;30.566 ;22.936 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 444 ;15.590 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;13.497 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 441 ; 0.067 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2185 ; 0.002 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1284 ; 0.177 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1924 ; 0.297 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 266 ; 0.093 ; 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): 47 ; 0.103 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 28 ; 0.111 ; 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): 1881 ; 0.314 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2919 ; 0.557 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1157 ; 0.580 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1008 ; 0.971 ; 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 : 4 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 1 A 54 REMARK 3 ORIGIN FOR THE GROUP (A): 15.1242 -33.7993 14.2761 REMARK 3 T TENSOR REMARK 3 T11: 0.0472 T22: -0.0180 REMARK 3 T33: 0.0494 T12: 0.0752 REMARK 3 T13: 0.5063 T23: -0.2210 REMARK 3 L TENSOR REMARK 3 L11: 10.4200 L22: 14.6259 REMARK 3 L33: 8.8551 L12: -2.6382 REMARK 3 L13: 0.7543 L23: -3.7491 REMARK 3 S TENSOR REMARK 3 S11: -0.2243 S12: -1.3499 S13: 0.5526 REMARK 3 S21: 2.2938 S22: 0.4230 S23: 1.4962 REMARK 3 S31: -1.0932 S32: -0.6329 S33: -0.1987 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 67 A 254 REMARK 3 ORIGIN FOR THE GROUP (A): 50.2902 -38.0915 0.3797 REMARK 3 T TENSOR REMARK 3 T11: -0.0705 T22: -0.0101 REMARK 3 T33: -0.0587 T12: -0.0080 REMARK 3 T13: 0.0016 T23: -0.0233 REMARK 3 L TENSOR REMARK 3 L11: 0.9713 L22: 1.7142 REMARK 3 L33: 1.2331 L12: 0.0231 REMARK 3 L13: 0.1727 L23: -0.1303 REMARK 3 S TENSOR REMARK 3 S11: -0.0272 S12: 0.0080 S13: -0.0183 REMARK 3 S21: 0.0514 S22: 0.0041 S23: 0.1470 REMARK 3 S31: -0.0334 S32: -0.1552 S33: 0.0232 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 70 REMARK 3 ORIGIN FOR THE GROUP (A): 24.9217 -40.8935 0.6663 REMARK 3 T TENSOR REMARK 3 T11: -0.2526 T22: -0.0595 REMARK 3 T33: -0.0588 T12: -0.0288 REMARK 3 T13: 0.0443 T23: -0.1025 REMARK 3 L TENSOR REMARK 3 L11: 5.6825 L22: 7.4822 REMARK 3 L33: 4.2644 L12: 0.8741 REMARK 3 L13: -1.0043 L23: -0.0893 REMARK 3 S TENSOR REMARK 3 S11: 0.1500 S12: -0.5274 S13: 0.2428 REMARK 3 S21: 0.2484 S22: -0.0930 S23: 0.4467 REMARK 3 S31: -0.1330 S32: -0.1551 S33: -0.0571 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 73 B 137 REMARK 3 ORIGIN FOR THE GROUP (A): 13.0327 -18.2487 -4.1355 REMARK 3 T TENSOR REMARK 3 T11: 0.0112 T22: -0.0031 REMARK 3 T33: 0.0150 T12: 0.0405 REMARK 3 T13: 0.0779 T23: 0.0191 REMARK 3 L TENSOR REMARK 3 L11: 13.4799 L22: 19.7455 REMARK 3 L33: 14.2503 L12: 0.3590 REMARK 3 L13: 3.9108 L23: 3.9122 REMARK 3 S TENSOR REMARK 3 S11: 0.0654 S12: 0.9157 S13: 0.4250 REMARK 3 S21: -0.9318 S22: -0.0119 S23: 0.2242 REMARK 3 S31: 0.2066 S32: -0.2233 S33: -0.0534 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 REMARK 4 REMARK 4 3CJR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-MAR-08. REMARK 100 THE DEPOSITION ID IS D_1000046860. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-APR-07 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 : X4A 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 : KOHZU DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR WITH A WATER- REMARK 200 COOLED FLAT FIRST CRYSTAL AND A REMARK 200 SAGITTALLY FOCUSED SECOND REMARK 200 CRYSTAL POSITIONED FOR A FIXED REMARK 200 EXIT BEAM CONDITION. LOCATED ~18 REMARK 200 M FROM SOURCE AND ~6 M FROM REMARK 200 SAMPLE POSITION. REMARK 200 OPTICS : VARIABLE VERTICAL AND FIXED REMARK 200 HORIZONTAL SLITS. KOHZU DOUBLE REMARK 200 CRYSTAL MONOCHROMATOR WITH A REMARK 200 WATER-COOLED FLAT FIRST CRYSTAL REMARK 200 AND A SAGITTALLY FOCUSED SECOND REMARK 200 CRYSTAL POSITIONED FOR A FIXED REMARK 200 EXIT BEAM CONDITION. LOCATED ~18 REMARK 200 M FROM SOURCE AND ~6 M FROM REMARK 200 SAMPLE POSITION. MIRROR SYSTEM REMARK 200 CONSISTING OF TWO VERTICALLY REMARK 200 STACKED, FUSED SILICA, SPHERICAL REMARK 200 MIRRORS, TO PROVIDE VERTICAL REMARK 200 FOCUSING AND HARMONIC REJECTION. REMARK 200 ONE OF THE MIRRORS IS RHODIUM REMARK 200 COATED AND THE OTHER IS REMARK 200 UNCOATED. LOCATED ~19.7 M FROM REMARK 200 SOURCE. REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27841 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.52800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300 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 ENTRIES 2NXC, 2NXN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 170 MM SODIUM ACETATE TRIHYDRATE, 85 REMARK 280 MM TRIS-HCL, 25.5 (W/V) PEG 4000, 15% (V/V) GLYCEROL, 1 MM REMARK 280 SINEFUNGIN, PH 8.5, MICROBATCH UNDER OIL, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.70400 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 15.35200 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 23.02800 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 7.67600 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 38.38000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 GLY A 55 REMARK 465 ASP A 56 REMARK 465 GLU A 57 REMARK 465 ASP A 58 REMARK 465 TRP A 59 REMARK 465 LYS B 80 REMARK 465 ALA B 81 REMARK 465 ALA B 82 REMARK 465 GLY B 83 REMARK 465 LEU B 84 REMARK 465 GLU B 85 REMARK 465 LYS B 86 REMARK 465 GLY B 87 REMARK 465 ALA B 88 REMARK 465 HIS B 89 REMARK 465 LYS B 90 REMARK 465 PRO B 91 REMARK 465 GLY B 92 REMARK 465 ARG B 93 REMARK 465 GLU B 94 REMARK 465 LYS B 95 REMARK 465 VAL B 96 REMARK 465 GLY B 97 REMARK 465 ARG B 98 REMARK 465 VAL B 138 REMARK 465 VAL B 139 REMARK 465 GLY B 140 REMARK 465 ALA B 141 REMARK 465 PRO B 142 REMARK 465 GLU B 143 REMARK 465 VAL B 144 REMARK 465 LYS B 145 REMARK 465 ASP B 146 REMARK 465 ALA B 147 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU A 11 CD REMARK 480 GLU A 32 CG CD OE1 OE2 REMARK 480 MET B 35 CE REMARK 480 ARG B 63 NH2 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 ARG B 63 CZ ARG B 63 NH2 -0.136 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 ARG B 63 NH1 - CZ - NH2 ANGL. DEV. = -11.6 DEGREES REMARK 500 ARG B 63 NE - CZ - NH2 ANGL. DEV. = 11.6 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 ARG A 31 -152.89 -121.82 REMARK 500 GLU A 48 99.35 64.76 REMARK 500 SER A 175 -147.85 -135.38 REMARK 500 LEU A 192 -118.06 -123.76 REMARK 500 LYS B 2 80.59 74.43 REMARK 500 ARG B 63 -5.96 79.41 REMARK 500 PRO B 72 -141.71 -99.71 REMARK 500 TRP B 101 -152.52 -100.15 REMARK 500 PRO B 113 38.26 -90.71 REMARK 500 ASP B 114 -42.79 -140.08 REMARK 500 ALA B 123 -39.93 -148.94 REMARK 500 MET B 126 -30.22 -131.41 REMARK 500 MET B 134 -36.44 -156.64 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 SFG A 255 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2NXC RELATED DB: PDB REMARK 900 APO-FORM OF T. THERMOPHILUS RIBOSOMAL PROTEIN L11 METHYLTRANSFERASE REMARK 900 (PRMA)AT 1.59 A RESOLUTION REMARK 900 RELATED ID: 2NXE RELATED DB: PDB REMARK 900 T. THERMOPHILUS RIBOSOMAL PROTEIN L11 METHYLTRANSFERASE (PRMA) IN REMARK 900 COMPLEX WITH S-ADENOSYL-L-METHIONINE REMARK 900 RELATED ID: 2NXJ RELATED DB: PDB REMARK 900 T.THERMOPHILUS RIBOSOMAL PROTEIN L11 METHYLTRANSFERASE (PRMA) IN REMARK 900 SPACE GROUP P 21 21 2 REMARK 900 RELATED ID: 2NXN RELATED DB: PDB REMARK 900 T. THERMOPHILUS RIBOSOMAL PROTEIN L11 METHYLTRANSFERASE (PRMA) IN REMARK 900 COMPLEX WITH RIBOSOMAL PROTEIN L11 REMARK 900 RELATED ID: 1UFK RELATED DB: PDB REMARK 900 APO-FORM OF T. THERMOPHILUS RIBOSOMAL PROTEIN L11 METHYLTRANSFERASE REMARK 900 (PRMA)AT 1.9 A RESOLUTION REMARK 900 RELATED ID: 3CJQ RELATED DB: PDB REMARK 900 RIBOSOMAL PROTEIN L11 METHYLTRANSFERASE (PRMA) IN COMPLEX WITH REMARK 900 DIMETHYLATED RIBOSOMAL PROTEIN L11 IN SPACE GROUP P212121 REMARK 900 RELATED ID: 3CJS RELATED DB: PDB REMARK 900 RELATED ID: 3CJT RELATED DB: PDB REMARK 900 RELATED ID: 3CJU RELATED DB: PDB DBREF 3CJR A 1 254 UNP Q84BQ9 PRMA_THET8 1 254 DBREF 3CJR B 1 147 UNP P36238 RL11_THETH 1 147 SEQADV 3CJR ALA B 39 UNP P36238 LYS 39 ENGINEERED MUTATION SEQRES 1 A 254 MET TRP VAL TYR ARG LEU LYS GLY THR LEU GLU ALA LEU SEQRES 2 A 254 ASP PRO ILE LEU PRO GLY LEU PHE ASP GLY GLY ALA ARG SEQRES 3 A 254 GLY LEU TRP GLU ARG GLU GLY GLU VAL TRP ALA PHE PHE SEQRES 4 A 254 PRO ALA PRO VAL ASP LEU PRO TYR GLU GLY VAL TRP GLU SEQRES 5 A 254 GLU VAL GLY ASP GLU ASP TRP LEU GLU ALA TRP ARG ARG SEQRES 6 A 254 ASP LEU LYS PRO ALA LEU ALA PRO PRO PHE VAL VAL LEU SEQRES 7 A 254 ALA PRO TRP HIS THR TRP GLU GLY ALA GLU ILE PRO LEU SEQRES 8 A 254 VAL ILE GLU PRO GLY MET ALA PHE GLY THR GLY HIS HIS SEQRES 9 A 254 GLU THR THR ARG LEU ALA LEU LYS ALA LEU ALA ARG HIS SEQRES 10 A 254 LEU ARG PRO GLY ASP LYS VAL LEU ASP LEU GLY THR GLY SEQRES 11 A 254 SER GLY VAL LEU ALA ILE ALA ALA GLU LYS LEU GLY GLY SEQRES 12 A 254 LYS ALA LEU GLY VAL ASP ILE ASP PRO MET VAL LEU PRO SEQRES 13 A 254 GLN ALA GLU ALA ASN ALA LYS ARG ASN GLY VAL ARG PRO SEQRES 14 A 254 ARG PHE LEU GLU GLY SER LEU GLU ALA ALA LEU PRO PHE SEQRES 15 A 254 GLY PRO PHE ASP LEU LEU VAL ALA ASN LEU TYR ALA GLU SEQRES 16 A 254 LEU HIS ALA ALA LEU ALA PRO ARG TYR ARG GLU ALA LEU SEQRES 17 A 254 VAL PRO GLY GLY ARG ALA LEU LEU THR GLY ILE LEU LYS SEQRES 18 A 254 ASP ARG ALA PRO LEU VAL ARG GLU ALA MET ALA GLY ALA SEQRES 19 A 254 GLY PHE ARG PRO LEU GLU GLU ALA ALA GLU GLY GLU TRP SEQRES 20 A 254 VAL LEU LEU ALA TYR GLY ARG SEQRES 1 B 147 MET LYS LYS VAL VAL ALA VAL VAL LYS LEU GLN LEU PRO SEQRES 2 B 147 ALA GLY LYS ALA THR PRO ALA PRO PRO VAL GLY PRO ALA SEQRES 3 B 147 LEU GLY GLN HIS GLY ALA ASN ILE MET GLU PHE VAL ALA SEQRES 4 B 147 ALA PHE ASN ALA ALA THR ALA ASN MET GLY ASP ALA ILE SEQRES 5 B 147 VAL PRO VAL GLU ILE THR ILE TYR ALA ASP ARG SER PHE SEQRES 6 B 147 THR PHE VAL THR LYS THR PRO PRO ALA SER TYR LEU ILE SEQRES 7 B 147 ARG LYS ALA ALA GLY LEU GLU LYS GLY ALA HIS LYS PRO SEQRES 8 B 147 GLY ARG GLU LYS VAL GLY ARG ILE THR TRP GLU GLN VAL SEQRES 9 B 147 LEU GLU ILE ALA LYS GLN LYS MET PRO ASP LEU ASN THR SEQRES 10 B 147 THR ASP LEU GLU ALA ALA ALA ARG MET ILE ALA GLY SER SEQRES 11 B 147 ALA ARG SER MET GLY VAL GLU VAL VAL GLY ALA PRO GLU SEQRES 12 B 147 VAL LYS ASP ALA HET SFG A 255 27 HETNAM SFG SINEFUNGIN HETSYN SFG ADENOSYL-ORNITHINE FORMUL 3 SFG C15 H23 N7 O5 FORMUL 4 HOH *328(H2 O) HELIX 1 1 LEU A 13 PRO A 15 5 3 HELIX 2 2 ILE A 16 GLY A 24 1 9 HELIX 3 3 LEU A 60 ASP A 66 1 7 HELIX 4 4 HIS A 104 LEU A 118 1 15 HELIX 5 5 GLY A 132 LEU A 141 1 10 HELIX 6 6 ASP A 151 MET A 153 5 3 HELIX 7 7 VAL A 154 ASN A 165 1 12 HELIX 8 8 SER A 175 LEU A 180 1 6 HELIX 9 9 PRO A 181 GLY A 183 5 3 HELIX 10 10 TYR A 193 ALA A 207 1 15 HELIX 11 11 ARG A 223 ALA A 234 1 12 HELIX 12 12 PRO B 22 GLN B 29 1 8 HELIX 13 13 ASN B 33 THR B 45 1 13 HELIX 14 14 ALA B 46 GLY B 49 5 4 HELIX 15 15 PRO B 73 ARG B 79 1 7 HELIX 16 16 GLU B 102 LEU B 105 5 4 HELIX 17 17 GLU B 106 LYS B 111 1 6 HELIX 18 18 ALA B 123 SER B 133 1 11 SHEET 1 A 7 VAL A 50 GLU A 52 0 SHEET 2 A 7 TRP A 2 LYS A 7 -1 N ARG A 5 O VAL A 50 SHEET 3 A 7 GLU A 34 PHE A 39 -1 O ALA A 37 N TYR A 4 SHEET 4 A 7 GLY A 27 GLU A 30 -1 N TRP A 29 O TRP A 36 SHEET 5 A 7 VAL B 4 PRO B 13 -1 O GLN B 11 N LEU A 28 SHEET 6 A 7 ILE B 52 TYR B 60 -1 O VAL B 53 N LEU B 12 SHEET 7 A 7 PHE B 65 THR B 69 -1 O THR B 66 N THR B 58 SHEET 1 B 3 ALA A 70 ALA A 72 0 SHEET 2 B 3 PHE A 75 LEU A 78 -1 O VAL A 77 N ALA A 70 SHEET 3 B 3 ILE A 89 VAL A 92 1 O LEU A 91 N LEU A 78 SHEET 1 C 7 ARG A 170 GLU A 173 0 SHEET 2 C 7 LYS A 144 ASP A 149 1 N GLY A 147 O ARG A 170 SHEET 3 C 7 LYS A 123 LEU A 127 1 N ASP A 126 O LEU A 146 SHEET 4 C 7 PHE A 185 ASN A 191 1 O VAL A 189 N LEU A 125 SHEET 5 C 7 LEU A 208 LEU A 220 1 O LEU A 215 N LEU A 188 SHEET 6 C 7 TRP A 247 GLY A 253 -1 O LEU A 250 N LEU A 216 SHEET 7 C 7 ARG A 237 GLU A 244 -1 N ARG A 237 O GLY A 253 CISPEP 1 PRO A 73 PRO A 74 0 8.02 CISPEP 2 GLY A 183 PRO A 184 0 -0.39 CISPEP 3 MET B 1 LYS B 2 0 2.98 CISPEP 4 PRO B 21 PRO B 22 0 6.76 CISPEP 5 THR B 71 PRO B 72 0 -0.61 CISPEP 6 MET B 134 GLY B 135 0 0.26 SITE 1 AC1 19 PHE A 99 GLY A 100 THR A 107 GLY A 128 SITE 2 AC1 19 THR A 129 LEU A 134 ASP A 149 ILE A 150 SITE 3 AC1 19 GLY A 174 SER A 175 ASN A 191 LEU A 192 SITE 4 AC1 19 HOH A 285 HOH A 286 HOH A 314 HOH A 375 SITE 5 AC1 19 HOH A 469 HOH A 473 HOH A 497 CRYST1 132.742 132.742 46.056 90.00 90.00 120.00 P 65 6 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 0.007533 0.004349 0.000000 0.00000 SCALE2 0.000000 0.008699 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021713 0.00000