HEADER RNA BINDING PROTEIN 14-JAN-99 1RL6 TITLE RIBOSOMAL PROTEIN L6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (RIBOSOMAL PROTEIN L6); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: LOCATED IN THE LARGE 50S RIBOSOMAL SUBUNIT BELOW THE COMPND 6 L7/L12 STALK AND CLOSE TO THE GTPASE CENTER SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 1422; SOURCE 4 CELLULAR_LOCATION: RIBOSOME; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VIRUS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: T7; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-13A KEYWDS RNA-BINDING PROTEIN, GENTAMICIN RESISTANCE, RIBOSOMAL PROTEIN, KEYWDS 2 ALPHA/BETA PROTEIN, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.L.GOLDEN,C.DAVIES,V.RAMAKRISHNAN,S.W.WHITE REVDAT 6 27-DEC-23 1RL6 1 REMARK REVDAT 5 30-OCT-19 1RL6 1 KEYWDS JRNL REVDAT 4 24-FEB-09 1RL6 1 VERSN REVDAT 3 01-APR-03 1RL6 1 JRNL REVDAT 2 27-MAR-00 1RL6 1 DBREF REVDAT 1 02-FEB-99 1RL6 0 JRNL AUTH B.L.GOLDEN,V.RAMAKRISHNAN,S.W.WHITE JRNL TITL RIBOSOMAL PROTEIN L6: STRUCTURAL EVIDENCE OF GENE JRNL TITL 2 DUPLICATION FROM A PRIMITIVE RNA BINDING PROTEIN. JRNL REF EMBO J. V. 12 4901 1993 JRNL REFN ISSN 0261-4189 JRNL PMID 8262035 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.DAVIES,D.E.BUSSIERE,B.L.GOLDEN,S.J.PORTER,V.RAMAKRISHNAN, REMARK 1 AUTH 2 S.W.WHITE REMARK 1 TITL RIBOSOMAL PROTEINS S5 AND L6: HIGH-RESOLUTION CRYSTAL REMARK 1 TITL 2 STRUCTURES AND ROLES IN PROTEIN SYNTHESIS AND ANTIBIOTIC REMARK 1 TITL 3 RESISTANCE. REMARK 1 REF J.MOL.BIOL. V. 279 873 1998 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 9642068 REMARK 1 DOI 10.1006/JMBI.1998.1780 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 18251945.800 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 13142 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 SET) : 0.257 REMARK 3 FREE R VALUE : 0.302 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1288 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1893 REMARK 3 BIN R VALUE (WORKING SET) : 0.3450 REMARK 3 BIN FREE R VALUE : 0.4100 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 186 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1251 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 140 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.07000 REMARK 3 B22 (A**2) : -0.07000 REMARK 3 B33 (A**2) : 0.13000 REMARK 3 B12 (A**2) : -1.85000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.33 REMARK 3 ESD FROM SIGMAA (A) : 0.36 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.40 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.36 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.430 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.040 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.280 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 5.020 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 7.120 ; 2.500 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PARAM19X.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPH19X.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1RL6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JAN-99. REMARK 100 THE DEPOSITION ID IS D_1000000397. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 7.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : COLLIMATOR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13166 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: MUTANT V124C WAS CONSTRUCTED FOR THE MERCURY DERIVATIVE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.6 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 41.50000 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 83.00000 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 62.25000 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 103.75000 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 20.75000 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 41.50000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 83.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 103.75000 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 62.25000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 20.75000 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 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 400 REMARK 400 COMPOUND REMARK 400 THE PROTEIN CONTAINS TWO DOMAINS OF APPROXIMATELY EQUAL REMARK 400 SIZE. THE DOMAINS HAVE VERY SIMILAR ALPHA BETA STRUCTURES REMARK 400 AND SECONDARY STRUCTURE TOPOLOGIES AND APPEAR TO HAVE REMARK 400 ARISEN BY GENE DUPLICATION. EACH DOMAIN IS ALSO HOMOLOGOUS REMARK 400 TO THE RNA RECOGNITION MOTIF (RRM), WITH THE C-TERMINAL REMARK 400 DOMAIN BEING THE MOST SIMILAR. 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 1 REMARK 465 ARG A 2 REMARK 465 VAL A 3 REMARK 465 GLY A 4 REMARK 465 LYS A 5 REMARK 465 LYS A 6 REMARK 465 LYS A 171 REMARK 465 GLU A 172 REMARK 465 GLY A 173 REMARK 465 LYS A 174 REMARK 465 THR A 175 REMARK 465 GLY A 176 REMARK 465 LYS A 177 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 151 84.30 -160.13 REMARK 500 REMARK 500 REMARK: NULL DBREF 1RL6 A 1 177 UNP P02391 RL6_BACST 1 177 SEQRES 1 A 177 SER ARG VAL GLY LYS LYS PRO ILE GLU ILE PRO ALA GLY SEQRES 2 A 177 VAL THR VAL THR VAL ASN GLY ASN THR VAL THR VAL LYS SEQRES 3 A 177 GLY PRO LYS GLY GLU LEU THR ARG THR PHE HIS PRO ASP SEQRES 4 A 177 MET THR ILE THR VAL GLU GLY ASN VAL ILE THR VAL THR SEQRES 5 A 177 ARG PRO SER ASP GLU LYS HIS HIS ARG ALA LEU HIS GLY SEQRES 6 A 177 THR THR ARG SER LEU LEU ALA ASN MET VAL GLU GLY VAL SEQRES 7 A 177 SER LYS GLY TYR GLU LYS ALA LEU GLU LEU VAL GLY VAL SEQRES 8 A 177 GLY TYR ARG ALA SER LYS GLN GLY LYS LYS LEU VAL LEU SEQRES 9 A 177 SER VAL GLY TYR SER HIS PRO VAL GLU ILE GLU PRO GLU SEQRES 10 A 177 GLU GLY LEU GLU ILE GLU VAL PRO SER GLN THR LYS ILE SEQRES 11 A 177 ILE VAL LYS GLY ALA ASP LYS GLN ARG VAL GLY GLU LEU SEQRES 12 A 177 ALA ALA ASN ILE ARG ALA VAL ARG PRO PRO GLU PRO TYR SEQRES 13 A 177 LYS GLY LYS GLY ILE ARG TYR GLU GLY GLU LEU VAL ARG SEQRES 14 A 177 LEU LYS GLU GLY LYS THR GLY LYS FORMUL 2 HOH *140(H2 O) HELIX 1 1 LYS A 58 SER A 79 1 22 HELIX 2 2 LYS A 137 VAL A 150 1 14 SHEET 1 A 3 THR A 15 ASN A 19 0 SHEET 2 A 3 THR A 22 GLY A 27 -1 N LYS A 26 O THR A 15 SHEET 3 A 3 GLY A 30 THR A 35 -1 N ARG A 34 O VAL A 23 SHEET 1 B 2 MET A 40 GLU A 45 0 SHEET 2 B 2 VAL A 48 ARG A 53 -1 N THR A 52 O THR A 41 SHEET 1 C 4 GLY A 160 TYR A 163 0 SHEET 2 C 4 TYR A 82 VAL A 89 -1 N VAL A 89 O GLY A 160 SHEET 3 C 4 LYS A 129 GLY A 134 -1 N GLY A 134 O TYR A 82 SHEET 4 C 4 LEU A 120 GLU A 123 -1 N GLU A 123 O ILE A 131 SHEET 1 D 3 ARG A 94 GLN A 98 0 SHEET 2 D 3 LYS A 101 SER A 105 -1 N SER A 105 O ARG A 94 SHEET 3 D 3 VAL A 112 GLU A 115 -1 N ILE A 114 O LEU A 102 CRYST1 71.800 71.800 124.500 90.00 90.00 120.00 P 61 2 2 12 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 0.013927 0.008041 0.000000 0.00000 SCALE2 0.000000 0.016082 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008032 0.00000