PDB Short entry for 1I4J HEADER RNA BINDING PROTEIN 22-FEB-01 1I4J TITLE CRYSTAL STRUCTURE OF L22 RIBOSOMAL PROTEIN MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: 50S RIBOSOMAL PROTEIN L22; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 274; SOURCE 4 GENE: RPL22; 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: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PTTHL22 KEYWDS RIBOSOMAL PROTEIN, MUTANT, ERYTHROMYCIN RESISTANCE, RNA BINDING, RNA KEYWDS 2 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.L.DAVYDOVA,V.A.STRELTSOV,R.FEDOROV,M.WILCE,A.LILJAS,M.GARDER REVDAT 4 09-AUG-23 1I4J 1 SEQADV REVDAT 3 04-OCT-17 1I4J 1 REMARK REVDAT 2 24-FEB-09 1I4J 1 VERSN REVDAT 1 11-SEP-02 1I4J 0 JRNL AUTH N.DAVYDOVA,V.STRELTSOV,M.WILCE,A.LILJAS,M.GARBER JRNL TITL L22 RIBOSOMAL PROTEIN AND EFFECT OF ITS MUTATION ON RIBOSOME JRNL TITL 2 RESISTANCE TO ERYTHROMYCIN. JRNL REF J.MOL.BIOL. V. 322 635 2002 JRNL REFN ISSN 0022-2836 JRNL PMID 12225755 JRNL DOI 10.1016/S0022-2836(02)00772-6 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.17 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 85.6 REMARK 3 NUMBER OF REFLECTIONS : 16162 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) : 0.209 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1619 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 47.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1334 REMARK 3 BIN R VALUE (WORKING SET) : 0.2824 REMARK 3 BIN FREE R VALUE : 0.2823 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 141 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.024 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1738 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 37 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.62000 REMARK 3 B22 (A**2) : -0.88000 REMARK 3 B33 (A**2) : -2.74000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.50000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.14 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) : 0.27 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.12 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.270 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.06 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.770 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : CNS BULK SOLVENT MODEL USED REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 59.43 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER.PARAM REMARK 3 PARAMETER FILE 4 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1I4J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-FEB-01. REMARK 100 THE DEPOSITION ID IS D_1000012894. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-00 REMARK 200 TEMPERATURE (KELVIN) : 298.0 REMARK 200 PH : NULL 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54179 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MONOCHROMATOR AND MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16162 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 23.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.6 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 74.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 47.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.38300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 71.30 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1BXE WITH REMOVED BETA-LOOP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.9M SODIUM CHLORIDE, 3% ETHANOL, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 43.29500 REMARK 290 SMTRY3 2 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: DIMERIC 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 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 GLU A 2 -72.21 -68.48 REMARK 500 ASN A 40 51.69 -110.31 REMARK 500 LYS A 110 -139.24 15.01 REMARK 500 HIS A 111 140.86 -12.31 REMARK 500 ALA B 89 -103.33 43.81 REMARK 500 ARG B 92 61.55 24.49 REMARK 500 ALA B 93 -127.43 -98.26 REMARK 500 HIS B 111 116.71 66.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BXE RELATED DB: PDB REMARK 900 1BXE IS RIBOSOMAL PROTEIN L22 FROM THERMUS THERMOPHILUS DBREF 1I4J A 1 113 UNP P48286 RL22_THETH 1 113 DBREF 1I4J B 1 113 UNP P48286 RL22_THETH 1 113 SEQADV 1I4J A UNP P48286 LEU 82 DELETION SEQADV 1I4J A UNP P48286 LYS 83 DELETION SEQADV 1I4J A UNP P48286 ARG 84 DELETION SEQADV 1I4J B UNP P48286 LEU 82 DELETION SEQADV 1I4J B UNP P48286 LYS 83 DELETION SEQADV 1I4J B UNP P48286 ARG 84 DELETION SEQRES 1 A 110 MET GLU ALA LYS ALA ILE ALA ARG TYR VAL ARG ILE SER SEQRES 2 A 110 PRO ARG LYS VAL ARG LEU VAL VAL ASP LEU ILE ARG GLY SEQRES 3 A 110 LYS SER LEU GLU GLU ALA ARG ASN ILE LEU ARG TYR THR SEQRES 4 A 110 ASN LYS ARG GLY ALA TYR PHE VAL ALA LYS VAL LEU GLU SEQRES 5 A 110 SER ALA ALA ALA ASN ALA VAL ASN ASN HIS ASP ALA LEU SEQRES 6 A 110 GLU ASP ARG LEU TYR VAL LYS ALA ALA TYR VAL ASP GLU SEQRES 7 A 110 GLY PRO ALA VAL LEU PRO ARG ALA ARG GLY ARG ALA ASP SEQRES 8 A 110 ILE ILE LYS LYS ARG THR SER HIS ILE THR VAL ILE LEU SEQRES 9 A 110 GLY GLU LYS HIS GLY LYS SEQRES 1 B 110 MET GLU ALA LYS ALA ILE ALA ARG TYR VAL ARG ILE SER SEQRES 2 B 110 PRO ARG LYS VAL ARG LEU VAL VAL ASP LEU ILE ARG GLY SEQRES 3 B 110 LYS SER LEU GLU GLU ALA ARG ASN ILE LEU ARG TYR THR SEQRES 4 B 110 ASN LYS ARG GLY ALA TYR PHE VAL ALA LYS VAL LEU GLU SEQRES 5 B 110 SER ALA ALA ALA ASN ALA VAL ASN ASN HIS ASP ALA LEU SEQRES 6 B 110 GLU ASP ARG LEU TYR VAL LYS ALA ALA TYR VAL ASP GLU SEQRES 7 B 110 GLY PRO ALA VAL LEU PRO ARG ALA ARG GLY ARG ALA ASP SEQRES 8 B 110 ILE ILE LYS LYS ARG THR SER HIS ILE THR VAL ILE LEU SEQRES 9 B 110 GLY GLU LYS HIS GLY LYS FORMUL 3 HOH *37(H2 O) HELIX 1 1 SER A 13 ARG A 25 1 13 HELIX 2 2 SER A 28 THR A 39 1 12 HELIX 3 3 GLY A 43 ASN A 61 1 19 HELIX 4 4 LEU A 65 ASP A 67 5 3 HELIX 5 5 SER B 13 ARG B 25 1 13 HELIX 6 6 SER B 28 THR B 39 1 12 HELIX 7 7 GLY B 43 HIS B 62 1 20 SHEET 1 A 3 ALA A 3 VAL A 10 0 SHEET 2 A 3 LYS A 98 GLU A 109 -1 O SER A 101 N VAL A 10 SHEET 3 A 3 LEU A 69 VAL A 85 -1 N TYR A 70 O GLY A 108 SHEET 1 B 3 ALA B 3 VAL B 10 0 SHEET 2 B 3 SER B 101 GLU B 109 -1 O SER B 101 N VAL B 10 SHEET 3 B 3 LEU B 69 GLU B 78 -1 N TYR B 70 O GLY B 108 CRYST1 31.880 86.590 38.960 90.00 104.47 90.00 P 1 21 1 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 0.031368 0.000000 0.008095 0.00000 SCALE2 0.000000 0.011549 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026508 0.00000