HEADER RNA BINDING PROTEIN 02-OCT-98 1BXE TITLE RIBOSOMAL PROTEIN L22 FROM THERMUS THERMOPHILUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (RIBOSOMAL PROTEIN L22); COMPND 3 CHAIN: A; 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 CELLULAR_LOCATION: RIBOSOME; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RIBOSOMAL PROTEIN, PROTEIN SYNTHESIS, RNA BINDING, ANTIBIOTICS KEYWDS 2 RESISTANCE, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.UNGE,A.ABERG,S.AL-KARADAGHI,A.NIKULIN,S.NIKONOV,N.DAVYDOVA, AUTHOR 2 N.NEVSKAYA,M.GARBER,A.LILJAS REVDAT 6 14-MAR-18 1BXE 1 SEQADV REVDAT 5 07-MAR-18 1BXE 1 REMARK REVDAT 4 24-FEB-09 1BXE 1 VERSN REVDAT 3 01-APR-03 1BXE 1 JRNL REVDAT 2 22-DEC-99 1BXE 4 HEADER COMPND REMARK JRNL REVDAT 2 2 4 ATOM SOURCE SEQRES REVDAT 1 07-OCT-98 1BXE 0 JRNL AUTH J.UNGE,A.BERG,S.AL-KHARADAGHI,A.NIKULIN,S.NIKONOV, JRNL AUTH 2 N.DAVYDOVA,N.NEVSKAYA,M.GARBER,A.LILJAS JRNL TITL THE CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN L22 FROM THERMUS JRNL TITL 2 THERMOPHILUS: INSIGHTS INTO THE MECHANISM OF ERYTHROMYCIN JRNL TITL 3 RESISTANCE. JRNL REF STRUCTURE V. 6 1577 1998 JRNL REFN ISSN 0969-2126 JRNL PMID 9862810 JRNL DOI 10.1016/S0969-2126(98)00155-5 REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 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) (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 15976 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) : 0.189 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.99 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1336 REMARK 3 BIN R VALUE (WORKING SET) : 0.2600 REMARK 3 BIN FREE R VALUE : 0.3100 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 69 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 876 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 63 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.340 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.32 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.710 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL 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 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 : PARAMETER.ELEMENTS REMARK 3 PARAMETER FILE 3 : PARAM19.SOL REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1BXE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB. REMARK 100 THE DEPOSITION ID IS D_1000008134. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 287 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX II REMARK 200 BEAMLINE : I711 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.012 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12173 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.05300 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) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.15900 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: CCP4 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7 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 16.32000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.91500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.96500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.91500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.32000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.96500 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 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 HIS A 111 REMARK 465 GLY A 112 REMARK 465 LYS A 113 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 263 O HOH A 273 2.01 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 CL A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 903 DBREF 1BXE A 1 113 UNP P48286 RL22_THETH 1 113 SEQADV 1BXE MSE A 1 UNP P48286 MET 1 ENGINEERED MUTATION SEQADV 1BXE MSE A 64 UNP P48286 MET 64 ENGINEERED MUTATION SEQRES 1 A 113 MSE GLU ALA LYS ALA ILE ALA ARG TYR VAL ARG ILE SER SEQRES 2 A 113 PRO ARG LYS VAL ARG LEU VAL VAL ASP LEU ILE ARG GLY SEQRES 3 A 113 LYS SER LEU GLU GLU ALA ARG ASN ILE LEU ARG TYR THR SEQRES 4 A 113 ASN LYS ARG GLY ALA TYR PHE VAL ALA LYS VAL LEU GLU SEQRES 5 A 113 SER ALA ALA ALA ASN ALA VAL ASN ASN HIS ASP MSE LEU SEQRES 6 A 113 GLU ASP ARG LEU TYR VAL LYS ALA ALA TYR VAL ASP GLU SEQRES 7 A 113 GLY PRO ALA LEU LYS ARG VAL LEU PRO ARG ALA ARG GLY SEQRES 8 A 113 ARG ALA ASP ILE ILE LYS LYS ARG THR SER HIS ILE THR SEQRES 9 A 113 VAL ILE LEU GLY GLU LYS HIS GLY LYS MODRES 1BXE MSE A 1 MET SELENOMETHIONINE MODRES 1BXE MSE A 64 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 64 8 HET CL A 901 1 HET CL A 902 1 HET CL A 903 1 HETNAM MSE SELENOMETHIONINE HETNAM CL CHLORIDE ION FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 2 CL 3(CL 1-) FORMUL 5 HOH *63(H2 O) HELIX 1 1 PRO A 14 ILE A 24 1 11 HELIX 2 2 LEU A 29 TYR A 38 1 10 HELIX 3 3 ALA A 44 ASN A 60 1 17 HELIX 4 4 GLU A 66 ARG A 68 5 3 SHEET 1 A 2 LEU A 82 LEU A 86 0 SHEET 2 A 2 ASP A 94 LYS A 98 -1 N LYS A 98 O LEU A 82 LINK C MSE A 1 N GLU A 2 1555 1555 1.33 LINK C ASP A 63 N MSE A 64 1555 1555 1.33 LINK C MSE A 64 N LEU A 65 1555 1555 1.33 SITE 1 AC1 5 ARG A 18 TYR A 75 VAL A 76 ARG A 88 SITE 2 AC1 5 GLY A 91 SITE 1 AC2 3 ARG A 18 GLU A 66 ARG A 88 SITE 1 AC3 3 ARG A 8 TYR A 9 HIS A 102 CRYST1 32.640 65.930 67.830 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 0.030637 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015168 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014743 0.00000 HETATM 1 N MSE A 1 20.522 42.474 20.428 1.00 44.21 N HETATM 2 CA MSE A 1 20.300 41.032 20.153 1.00 42.98 C HETATM 3 C MSE A 1 21.011 40.128 21.166 1.00 39.68 C HETATM 4 O MSE A 1 22.180 40.338 21.506 1.00 38.60 O HETATM 5 CB MSE A 1 20.787 40.689 18.742 1.00 48.08 C HETATM 6 CG MSE A 1 19.673 40.368 17.752 1.00 59.81 C HETATM 7 SE MSE A 1 18.546 39.024 18.273 1.00 76.77 SE HETATM 8 CE MSE A 1 17.177 39.964 18.996 1.00 71.95 C