HEADER RIBOSOMAL PROTEIN 20-FEB-97 1AD2 TITLE RIBOSOMAL PROTEIN L1 MUTANT WITH SERINE 179 REPLACED BY CYSTEINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSOMAL PROTEIN L1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TL2; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 274; SOURCE 4 STRAIN: VK-1; SOURCE 5 ORGANELLE: RIBOSOME; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PACA-L1 KEYWDS RIBOSOMAL PROTEIN, RNA BINDING, PROTEIN SYNTHESIS, MUTANT EXPDTA X-RAY DIFFRACTION AUTHOR J.UNGE,S.AL-KARADAGHI,A.LILJAS,B.-H.JONSSON,I.ELISEIKINA,N.OSSINA, AUTHOR 2 N.NEVSKAYA,N.FOMENKOVA,M.GARBER,S.NIKONOV REVDAT 4 07-FEB-24 1AD2 1 REMARK REVDAT 3 03-NOV-21 1AD2 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1AD2 1 VERSN REVDAT 1 15-MAY-97 1AD2 0 JRNL AUTH J.UNGE,S.AL-KARADAGHI,A.LILJAS,B.H.JONSSON,I.ELISEIKINA, JRNL AUTH 2 N.OSSINA,N.NEVSKAYA,N.FOMENKOVA,M.GARBER,S.NIKONOV JRNL TITL A MUTANT FORM OF THE RIBOSOMAL PROTEIN L1 REVEALS JRNL TITL 2 CONFORMATIONAL FLEXIBILITY. JRNL REF FEBS LETT. V. 411 53 1997 JRNL REFN ISSN 0014-5793 JRNL PMID 9247141 JRNL DOI 10.1016/S0014-5793(97)00611-X REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 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)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 100000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.1000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 17136 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) : 0.203 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1710 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 1712 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 122 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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) : 0.013 REMARK 3 BOND ANGLES (DEGREES) : 1.850 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.14 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.670 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : PARAM11.WAT REMARK 3 PARAMETER FILE 3 : PAR.MPD REMARK 3 PARAMETER FILE 4 : PAR.SULPH REMARK 3 PARAMETER FILE 5 : PARAMNEW.ION REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH11.WAT REMARK 3 TOPOLOGY FILE 3 : TOP.MPD REMARK 3 TOPOLOGY FILE 4 : TOP.SULPH REMARK 3 TOPOLOGY FILE 5 : TOPNEW.ION REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1AD2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000170668. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NOV-95 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : COLLIMATOR 0.3X0.3 REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24181 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 12.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05900 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) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.32000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 8.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: NAT L1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: DROPS CONTAINING: APPR. 15 MG/ML L1 50 REMARK 280 MM GLYCINE, INITIALLY AT PH 10 5% (V/V) METHANE PENTANEDIOL 1.2 REMARK 280 M AMMONIUM SULFATE EQUILIBRATED AGAINST 2.4 M AMMONIUM SULFATE 7% REMARK 280 (V/V) METHANE PENTANEDIOL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 38.05000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.70000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 38.05000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.70000 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 PRO A 1 REMARK 465 LYS A 2 REMARK 465 HIS A 3 REMARK 465 GLY A 4 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 6 47.63 -167.78 REMARK 500 TYR A 7 20.52 -167.03 REMARK 500 ALA A 33 35.39 -89.60 REMARK 500 PHE A 37 -168.86 46.37 REMARK 500 MET A 108 23.27 -152.99 REMARK 500 ASP A 109 45.83 -81.30 REMARK 500 ASN A 148 59.16 -91.70 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HG A 900 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 42 OE2 REMARK 620 2 HIS A 172 NE2 87.4 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 800 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG A 900 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD A 700 DBREF 1AD2 A 1 228 UNP P27150 RL1_THETH 1 228 SEQADV 1AD2 CYS A 179 UNP P27150 SER 179 ENGINEERED MUTATION SEQRES 1 A 228 PRO LYS HIS GLY LYS ARG TYR ARG ALA LEU LEU GLU LYS SEQRES 2 A 228 VAL ASP PRO ASN LYS ILE TYR THR ILE ASP GLU ALA ALA SEQRES 3 A 228 HIS LEU VAL LYS GLU LEU ALA THR ALA LYS PHE ASP GLU SEQRES 4 A 228 THR VAL GLU VAL HIS ALA LYS LEU GLY ILE ASP PRO ARG SEQRES 5 A 228 ARG SER ASP GLN ASN VAL ARG GLY THR VAL SER LEU PRO SEQRES 6 A 228 HIS GLY LEU GLY LYS GLN VAL ARG VAL LEU ALA ILE ALA SEQRES 7 A 228 LYS GLY GLU LYS ILE LYS GLU ALA GLU GLU ALA GLY ALA SEQRES 8 A 228 ASP TYR VAL GLY GLY GLU GLU ILE ILE GLN LYS ILE LEU SEQRES 9 A 228 ASP GLY TRP MET ASP PHE ASP ALA VAL VAL ALA THR PRO SEQRES 10 A 228 ASP VAL MET GLY ALA VAL GLY SER LYS LEU GLY ARG ILE SEQRES 11 A 228 LEU GLY PRO ARG GLY LEU LEU PRO ASN PRO LYS ALA GLY SEQRES 12 A 228 THR VAL GLY PHE ASN ILE GLY GLU ILE ILE ARG GLU ILE SEQRES 13 A 228 LYS ALA GLY ARG ILE GLU PHE ARG ASN ASP LYS THR GLY SEQRES 14 A 228 ALA ILE HIS ALA PRO VAL GLY LYS ALA CYS PHE PRO PRO SEQRES 15 A 228 GLU LYS LEU ALA ASP ASN ILE ARG ALA PHE ILE ARG ALA SEQRES 16 A 228 LEU GLU ALA HIS LYS PRO GLU GLY ALA LYS GLY THR PHE SEQRES 17 A 228 LEU ARG SER VAL TYR VAL THR THR THR MET GLY PRO SER SEQRES 18 A 228 VAL ARG ILE ASN PRO HIS SER HET SO4 A 800 5 HET SO4 A 801 5 HET SO4 A 803 5 HET HG A 900 1 HET MRD A 700 8 HETNAM SO4 SULFATE ION HETNAM HG MERCURY (II) ION HETNAM MRD (4R)-2-METHYLPENTANE-2,4-DIOL FORMUL 2 SO4 3(O4 S 2-) FORMUL 5 HG HG 2+ FORMUL 6 MRD C6 H14 O2 FORMUL 7 HOH *122(H2 O) HELIX 1 1 ILE A 22 GLU A 31 1 10 HELIX 2 2 SER A 54 GLN A 56 5 3 HELIX 3 3 GLY A 80 GLU A 88 5 9 HELIX 4 4 GLU A 97 LEU A 104 5 8 HELIX 5 5 PRO A 117 ARG A 134 5 18 HELIX 6 6 ILE A 149 LYS A 157 1 9 HELIX 7 7 PRO A 182 HIS A 199 1 18 SHEET 1 A 2 ARG A 59 SER A 63 0 SHEET 2 A 2 ARG A 160 ARG A 164 -1 N PHE A 163 O GLY A 60 SHEET 1 B 3 ALA A 112 ALA A 115 0 SHEET 2 B 3 VAL A 74 ILE A 77 1 N LEU A 75 O ALA A 112 SHEET 3 B 3 TYR A 93 GLY A 95 1 N TYR A 93 O ALA A 76 SHEET 1 C 4 VAL A 222 ILE A 224 0 SHEET 2 C 4 LEU A 209 THR A 215 -1 N VAL A 214 O VAL A 222 SHEET 3 C 4 THR A 40 LEU A 47 -1 N LYS A 46 O ARG A 210 SHEET 4 C 4 ALA A 170 LYS A 177 -1 N GLY A 176 O VAL A 41 LINK OE2 GLU A 42 HG HG A 900 1555 1555 3.53 LINK NE2 HIS A 172 HG HG A 900 1555 1555 2.88 SITE 1 AC1 3 LYS A 18 THR A 61 HIS A 199 SITE 1 AC2 4 HIS A 66 GLY A 67 GLN A 71 LYS A 184 SITE 1 AC3 5 GLU A 88 LYS A 141 ASP A 166 LYS A 167 SITE 2 AC3 5 HOH A 683 SITE 1 AC4 2 GLU A 42 HIS A 172 SITE 1 AC5 3 GLY A 67 GLY A 176 LYS A 177 CRYST1 76.100 61.400 46.100 90.00 90.00 90.00 P 21 21 2 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 0.013141 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016287 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021692 0.00000