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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END
