HEADER TRANSFERASE/RIBOSOMAL PROTEIN 11-SEP-08 3EGV TITLE RIBOSOMAL PROTEIN L11 METHYLTRANSFERASE (PRMA) IN COMPLEX WITH TITLE 2 TRIMETHYLATED RIBOSOMAL PROTEIN L11 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 HB8; SOURCE 3 ORGANISM_TAXID: 300852; SOURCE 4 STRAIN: HB8; SOURCE 5 GENE: PRMA, TTHA0656; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 DE3 STAR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET30B; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS HB8; SOURCE 13 ORGANISM_TAXID: 300852; SOURCE 14 STRAIN: HB8; SOURCE 15 GENE: RPL11, RPLK, TTHA0247; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21 DE3 PRMA::TC; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS POST-TRANSLATIONAL MODIFICATION, MULTIPLE METHYLTRANSFERASE, KEYWDS 2 METHYLTRANSFERASE, TRANSFERASE, METHYLATION, RIBONUCLEOPROTEIN, KEYWDS 3 RIBOSOMAL PROTEIN, RNA-BINDING, RRNA-BINDING, TRANSFERASE-RIBOSOMAL KEYWDS 4 PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.DEMIRCI,S.T.GREGORY,A.E.DAHLBERG,G.JOGL REVDAT 7 15-NOV-23 3EGV 1 LINK ATOM REVDAT 6 30-AUG-23 3EGV 1 REMARK SEQADV LINK REVDAT 5 01-MAR-17 3EGV 1 DBREF HETATM REMARK SEQRES REVDAT 4 18-JAN-17 3EGV 1 DBREF HETATM REMARK REVDAT 3 13-JUL-11 3EGV 1 VERSN REVDAT 2 24-FEB-09 3EGV 1 VERSN REVDAT 1 23-SEP-08 3EGV 0 SPRSDE 23-SEP-08 3EGV 3CJU 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. 1.75 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 48051 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) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2577 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) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.79 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3478 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.45 REMARK 3 BIN R VALUE (WORKING SET) : 0.2900 REMARK 3 BIN FREE R VALUE SET COUNT : 198 REMARK 3 BIN FREE R VALUE : 0.3220 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2530 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 52 REMARK 3 SOLVENT ATOMS : 415 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) : 33.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.20000 REMARK 3 B22 (A**2) : -0.20000 REMARK 3 B33 (A**2) : 0.30000 REMARK 3 B12 (A**2) : -0.10000 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): 0.094 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.095 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.063 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.550 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2648 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3610 ; 1.503 ; 2.002 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 329 ; 5.888 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 103 ;29.819 ;22.913 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 389 ;13.062 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;21.081 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 396 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2015 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1261 ; 0.207 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1727 ; 0.306 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 296 ; 0.159 ; 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 ; 0.165 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 31 ; 0.222 ; 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): 1670 ; 0.762 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2644 ; 1.187 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1095 ; 2.002 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 966 ; 3.173 ; 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 : 3 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): -11.5454 -39.0477 -6.5994 REMARK 3 T TENSOR REMARK 3 T11: -0.1986 T22: 0.0207 REMARK 3 T33: 0.0516 T12: -0.0445 REMARK 3 T13: 0.1218 T23: -0.1728 REMARK 3 L TENSOR REMARK 3 L11: 7.2815 L22: 4.3161 REMARK 3 L33: 1.9690 L12: -2.4438 REMARK 3 L13: -2.1922 L23: 1.8574 REMARK 3 S TENSOR REMARK 3 S11: -0.0103 S12: -0.0599 S13: 0.6951 REMARK 3 S21: -0.1442 S22: 0.3339 S23: -0.6175 REMARK 3 S31: -0.1332 S32: 0.4539 S33: -0.3236 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): -52.0935 -35.9421 11.2867 REMARK 3 T TENSOR REMARK 3 T11: -0.0479 T22: -0.0471 REMARK 3 T33: -0.0793 T12: 0.0308 REMARK 3 T13: -0.0149 T23: -0.0400 REMARK 3 L TENSOR REMARK 3 L11: 1.7067 L22: 1.5108 REMARK 3 L33: 1.3502 L12: -0.3241 REMARK 3 L13: 0.2645 L23: -0.1360 REMARK 3 S TENSOR REMARK 3 S11: -0.1283 S12: -0.1213 S13: 0.0700 REMARK 3 S21: 0.1164 S22: 0.1152 S23: -0.1628 REMARK 3 S31: -0.1013 S32: -0.0126 S33: 0.0131 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 2 B 70 REMARK 3 ORIGIN FOR THE GROUP (A): -29.7161 -36.8826 -4.3478 REMARK 3 T TENSOR REMARK 3 T11: -0.1041 T22: -0.0353 REMARK 3 T33: 0.0427 T12: 0.0054 REMARK 3 T13: 0.0609 T23: -0.0140 REMARK 3 L TENSOR REMARK 3 L11: 5.2127 L22: 0.9772 REMARK 3 L33: 2.8685 L12: -0.1398 REMARK 3 L13: -2.1103 L23: 0.5594 REMARK 3 S TENSOR REMARK 3 S11: 0.0831 S12: 0.3279 S13: 0.4781 REMARK 3 S21: -0.1914 S22: 0.0818 S23: -0.2154 REMARK 3 S31: -0.1306 S32: 0.0110 S33: -0.1649 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 3EGV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-SEP-08. REMARK 100 THE DEPOSITION ID IS D_1000049306. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-SEP-06 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 : 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 : 48051 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 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 (%) : 97.2 REMARK 200 DATA REDUNDANCY : 1.700 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.8 REMARK 200 DATA REDUNDANCY IN SHELL : 1.60 REMARK 200 R MERGE FOR SHELL (I) : 0.33400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 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 (%): 58.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 160 MM CALCIUM ACETATE HYDRATE, 80 MM REMARK 280 SODIUM CACODYLATE, 14.4% W/V PEG8000, 20% V/V GLYCEROL, 4MM REMARK 280 ADOMET, PH 6.5, MICROBATCH TECHNIQUE UNDER OIL, TEMPERATURE REMARK 280 277.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 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 REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 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 32.62933 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 16.31467 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 0.00000 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 32.62933 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 16.31467 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: 4460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 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 ARG B 79 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 ILE B 99 REMARK 465 THR B 100 REMARK 465 TRP B 101 REMARK 465 GLU B 102 REMARK 465 GLN B 103 REMARK 465 VAL B 104 REMARK 465 LEU B 105 REMARK 465 GLU B 106 REMARK 465 ILE B 107 REMARK 465 ALA B 108 REMARK 465 LYS B 109 REMARK 465 GLN B 110 REMARK 465 LYS B 111 REMARK 465 MET B 112 REMARK 465 PRO B 113 REMARK 465 ASP B 114 REMARK 465 LEU B 115 REMARK 465 ASN B 116 REMARK 465 THR B 117 REMARK 465 THR B 118 REMARK 465 ASP B 119 REMARK 465 LEU B 120 REMARK 465 GLU B 121 REMARK 465 ALA B 122 REMARK 465 ALA B 123 REMARK 465 ALA B 124 REMARK 465 ARG B 125 REMARK 465 MET B 126 REMARK 465 ILE B 127 REMARK 465 ALA B 128 REMARK 465 GLY B 129 REMARK 465 SER B 130 REMARK 465 ALA B 131 REMARK 465 ARG B 132 REMARK 465 SER B 133 REMARK 465 MET B 134 REMARK 465 GLY B 135 REMARK 465 VAL B 136 REMARK 465 GLU B 137 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 612 O HOH A 614 1.98 REMARK 500 O HOH A 630 O HOH A 668 2.02 REMARK 500 O HOH A 625 O HOH A 702 2.06 REMARK 500 O GLY A 233 O HOH A 421 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 O3 GOL A 303 O HOH A 612 2454 1.91 REMARK 500 REMARK 500 REMARK: NULL 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 TYR A 47 CG TYR A 47 CD2 0.150 REMARK 500 TYR A 47 CG TYR A 47 CD1 0.080 REMARK 500 TYR A 47 CE1 TYR A 47 CZ 0.133 REMARK 500 TYR A 47 CZ TYR A 47 CE2 0.078 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 HIS A 103 43.15 -95.11 REMARK 500 SER A 175 -149.81 -117.79 REMARK 500 LEU A 239 -143.19 -103.50 REMARK 500 ARG B 63 -10.40 87.69 REMARK 500 TYR B 76 -80.63 -37.13 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 306 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) 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: 3CJU RELATED DB: PDB REMARK 900 RIBOSOMAL PROTEIN L11 METHYLTRANSFERASE (PRMA) IN COMPLEX WITH REMARK 900 TRIMETHYLATED RIBOSOMAL PROTEIN L11 REMARK 900 RELATED ID: 3CJS RELATED DB: PDB REMARK 900 MINIMAL RECOGNITION COMPLEX BETWEEN PRMA AND RIBOSOMAL PROTEIN L11 REMARK 900 RELATED ID: 3CJR RELATED DB: PDB REMARK 900 RIBOSOMAL PROTEIN L11 METHYLTRANSFERASE (PRMA) IN COMPLEX WITH REMARK 900 RIBOSOMAL PROTEIN L11 (K39A) AND INHIBITOR SINEFUNGIN. 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: 3CJT RELATED DB: PDB REMARK 900 RIBOSOMAL PROTEIN L11 METHYLTRANSFERASE (PRMA) IN COMPLEX WITH REMARK 900 DIMETHYLATED 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) DBREF 3EGV A 1 254 UNP Q84BQ9 PRMA_THET8 1 254 DBREF 3EGV B 1 147 UNP Q5SLP6 RL11_THET8 1 147 SEQADV 3EGV ALA B 16 UNP Q5SLP6 LYS 16 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 4MM LYS LYS VAL VAL ALA VAL VAL LYS LEU GLN LEU PRO SEQRES 2 B 147 ALA GLY ALA 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 LYS 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 MODRES 3EGV 4MM B 1 MET N,N,N-TRIMETHYLMETHIONINE HET 4MM B 1 11 HET SAH A 301 26 HET GOL A 302 6 HET GOL A 303 6 HET GOL A 304 6 HET GOL A 305 6 HET CL A 306 1 HET IOD B 201 1 HETNAM 4MM N,N,N-TRIMETHYLMETHIONINE HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM GOL GLYCEROL HETNAM CL CHLORIDE ION HETNAM IOD IODIDE ION HETSYN 4MM (1S)-1-CARBOXY-N,N,N-TRIMETHYL-3-(METHYLSULFANYL) HETSYN 2 4MM PROPAN-1-AMINIUM HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 4MM C8 H18 N O2 S 1+ FORMUL 3 SAH C14 H20 N6 O5 S FORMUL 4 GOL 4(C3 H8 O3) FORMUL 8 CL CL 1- FORMUL 9 IOD I 1- FORMUL 10 HOH *415(H2 O) HELIX 1 1 THR A 9 ASP A 14 1 6 HELIX 2 2 ILE A 16 GLY A 23 1 8 HELIX 3 3 ASP A 58 LEU A 67 1 10 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 PRO B 73 ILE B 78 1 6 SHEET 1 A 7 VAL A 50 GLU A 53 0 SHEET 2 A 7 TRP A 2 LYS A 7 -1 N VAL A 3 O GLU A 52 SHEET 3 A 7 GLU A 34 PHE A 39 -1 O PHE A 39 N TRP A 2 SHEET 4 A 7 GLY A 27 ARG A 31 -1 N ARG A 31 O GLU A 34 SHEET 5 A 7 VAL B 4 PRO B 13 -1 O LYS B 9 N GLU A 30 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 LINK C 4MM B 1 N LYS B 2 1555 1555 1.69 CISPEP 1 PRO A 73 PRO A 74 0 10.29 CISPEP 2 GLY A 183 PRO A 184 0 7.77 CISPEP 3 PRO B 21 PRO B 22 0 3.93 SITE 1 AC1 22 PHE A 99 GLY A 100 THR A 107 GLY A 128 SITE 2 AC1 22 THR A 129 GLY A 130 LEU A 134 ASP A 149 SITE 3 AC1 22 ILE A 150 ASP A 151 SER A 175 ASN A 191 SITE 4 AC1 22 LEU A 192 LEU A 196 HOH A 572 HOH A 721 SITE 5 AC1 22 HOH A 723 HOH A 732 HOH A 738 HOH A 739 SITE 6 AC1 22 HOH A 746 4MM B 1 SITE 1 AC2 8 PRO A 120 GLU A 159 ARG A 170 PHE A 171 SITE 2 AC2 8 HOH A 503 HOH A 628 HOH A 656 HOH A 668 SITE 1 AC3 11 ALA A 115 ARG A 116 LEU A 118 LYS A 123 SITE 2 AC3 11 ALA A 145 LEU A 146 ARG A 170 PHE A 182 SITE 3 AC3 11 HOH A 612 HOH A 614 HOH A 728 SITE 1 AC4 10 ARG A 116 HIS A 117 GLY A 183 PRO A 184 SITE 2 AC4 10 ASP A 186 VAL A 209 GLU A 240 HOH A 532 SITE 3 AC4 10 HOH A 607 HOH A 609 SITE 1 AC5 7 ARG A 65 LYS A 68 PRO A 69 HIS A 82 SITE 2 AC5 7 THR A 83 HOH A 745 HOH A 755 SITE 1 AC6 1 HOH A 465 CRYST1 134.547 134.547 48.944 90.00 90.00 120.00 P 62 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 0.007432 0.004291 0.000000 0.00000 SCALE2 0.000000 0.008582 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020432 0.00000