HEADER RIBOSOMAL PROTEIN 17-JUL-13 4LQ4 TITLE CRYSTAL STRUCTURE OF MUTANT RIBOSOMAL PROTEIN L1 FROM METHANOCOCCUS TITLE 2 JANNASCHII WITH DELETION OF 8 RESIDUES FROM C-TERMINUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: 50S RIBOSOMAL PROTEIN L1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII; SOURCE 3 ORGANISM_TAXID: 243232; SOURCE 4 STRAIN: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440; SOURCE 5 GENE: MJ0510, RPL1, RPLA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET11A-PL; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET11A-PL-MJAL1 KEYWDS BETA-ALPHA-BETA, STRUCTURAL CONSTITUENT OF RIBOSOME, RRNA BINDING, KEYWDS 2 REGULATION OF TRANSLATION, TRANSLATION, RIBOSOMAL RNA, MRNA, KEYWDS 3 RIBOSOMAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.G.GABDULKHAKOV,S.V.TISHCHENKO,A.A.SHKLIAEVA,M.B.GARBER,S.V.NIKONOV, AUTHOR 2 A.V.SARSKIKH REVDAT 1 02-JUL-14 4LQ4 0 JRNL AUTH A.V.SARSKIKH,A.G.GABDULKHAKOV,O.S.KOSTAREVA,A.A.SHKLIAEVA, JRNL AUTH 2 S.V.TISHCHENKO JRNL TITL CRYSTAL STRUCTURE OF A MUTANT OF ARCHAEAL RIBOSOMAL PROTEIN JRNL TITL 2 L1 FROM METHANOCOCCUS JANNASCHII JRNL REF CRYSTALLOGRAPHY REPORTS V. 59 394 2014 JRNL REFN ISSN 1063-7745 JRNL DOI 10.1134/S1063774514030158 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_1389) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.190 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.6 REMARK 3 NUMBER OF REFLECTIONS : 26039 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 2365 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 32.8662 - 4.4961 1.00 2895 169 0.1326 0.1795 REMARK 3 2 4.4961 - 3.5701 1.00 2899 163 0.1391 0.1824 REMARK 3 3 3.5701 - 3.1192 0.99 2862 169 0.1690 0.2457 REMARK 3 4 3.1192 - 2.8342 0.99 2867 160 0.1865 0.2413 REMARK 3 5 2.8342 - 2.6311 0.99 2905 147 0.1888 0.2331 REMARK 3 6 2.6311 - 2.4761 0.99 2865 168 0.1689 0.1987 REMARK 3 7 2.4761 - 2.3521 0.98 2873 140 0.1580 0.2374 REMARK 3 8 2.3521 - 2.2497 0.96 2739 142 0.1497 0.1946 REMARK 3 9 2.2497 - 2.1632 0.93 2745 165 0.1400 0.2086 REMARK 3 10 2.1632 - 2.0885 0.91 2684 110 0.1501 0.2102 REMARK 3 11 2.0885 - 2.0232 0.88 2560 117 0.1592 0.2096 REMARK 3 12 2.0232 - 1.9654 0.86 2489 142 0.1770 0.2770 REMARK 3 13 1.9654 - 1.9137 0.83 2424 106 0.1812 0.2373 REMARK 3 14 1.9137 - 1.8670 0.78 2282 92 0.1955 0.2513 REMARK 3 15 1.8670 - 1.8245 0.76 2228 140 0.2020 0.2494 REMARK 3 16 1.8245 - 1.7857 0.72 2005 120 0.2321 0.2797 REMARK 3 17 1.7857 - 1.7500 0.66 1981 115 0.2921 0.3411 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.490 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.34 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 1715 REMARK 3 ANGLE : 1.051 2304 REMARK 3 CHIRALITY : 0.073 265 REMARK 3 PLANARITY : 0.005 295 REMARK 3 DIHEDRAL : 12.661 687 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4LQ4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-AUG-13. REMARK 100 THE RCSB ID CODE IS RCSB080944. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-APR-10 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 7.5 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 : BRUKER AXS MICROSTAR REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54189 REMARK 200 MONOCHROMATOR : MONTEL 200 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER PLATINUM 135 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PROTEUM PLUS REMARK 200 DATA SCALING SOFTWARE : PROTEUM PLUS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26074 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.4 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1I2A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG4000, 10% ISOPROPANOL, 0.1 M REMARK 280 HEPES-NAOH, 0.5 MKL 0.8 KNA-TARTRATE, PH 7.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 277K 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 52.62750 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 300 REMARK: PART OF RIBOSOME 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 ASN A 21 43.47 -82.18 REMARK 500 ARG A 155 -133.78 47.63 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 TLA A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IPA A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 305 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1U63 RELATED DB: PDB REMARK 900 THE STRUCTURE OF A RIBOSOMAL PROTEIN L1-MRNA COMPLEX REMARK 900 RELATED ID: 1CJS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN L1 FROM REMARK 900 METHANOCOCCUS JANNASCHII REMARK 900 RELATED ID: 1I2A RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF L1 RIBOSOMAL PROTEIN FROM REMARK 900 METHANOCOCCUS JANNASCHII WITH 1.85A RESOLUTION DBREF 4LQ4 A 1 211 UNP P54050 RL1_METJA 1 211 SEQRES 1 A 211 MET ASP ARG GLU ALA LEU LEU GLN ALA VAL LYS GLU ALA SEQRES 2 A 211 ARG GLU LEU ALA LYS PRO ARG ASN PHE THR GLN SER PHE SEQRES 3 A 211 GLU PHE ILE ALA THR LEU LYS GLU ILE ASP MET ARG LYS SEQRES 4 A 211 PRO GLU ASN ARG ILE LYS THR GLU VAL VAL LEU PRO HIS SEQRES 5 A 211 GLY ARG GLY LYS GLU ALA LYS ILE ALA VAL ILE GLY THR SEQRES 6 A 211 GLY ASP LEU ALA LYS GLN ALA GLU GLU LEU GLY LEU THR SEQRES 7 A 211 VAL ILE ARG LYS GLU GLU ILE GLU GLU LEU GLY LYS ASN SEQRES 8 A 211 LYS ARG LYS LEU ARG LYS ILE ALA LYS ALA HIS ASP PHE SEQRES 9 A 211 PHE ILE ALA GLN ALA ASP LEU MET PRO LEU ILE GLY ARG SEQRES 10 A 211 TYR MET GLY VAL ILE LEU GLY PRO ARG GLY LYS MET PRO SEQRES 11 A 211 LYS PRO VAL PRO ALA ASN ALA ASN ILE LYS PRO LEU VAL SEQRES 12 A 211 GLU ARG LEU LYS LYS THR VAL VAL ILE ASN THR ARG ASP SEQRES 13 A 211 LYS PRO TYR PHE GLN VAL LEU VAL GLY ASN GLU LYS MET SEQRES 14 A 211 THR ASP GLU GLN ILE VAL ASP ASN ILE GLU ALA VAL LEU SEQRES 15 A 211 ASN VAL VAL ALA LYS LYS TYR GLU LYS GLY LEU TYR HIS SEQRES 16 A 211 ILE LYS ASP ALA TYR VAL LYS LEU THR MET GLY PRO ALA SEQRES 17 A 211 VAL LYS VAL HET TLA A 301 10 HET IPA A 302 4 HET CL A 303 1 HET CL A 304 1 HET CL A 305 1 HETNAM TLA L(+)-TARTARIC ACID HETNAM IPA ISOPROPYL ALCOHOL HETNAM CL CHLORIDE ION HETSYN IPA 2-PROPANOL FORMUL 2 TLA C4 H6 O6 FORMUL 3 IPA C3 H8 O FORMUL 4 CL 3(CL 1-) FORMUL 7 HOH *219(H2 O) HELIX 1 1 ASP A 2 ALA A 17 1 16 HELIX 2 2 LYS A 39 ARG A 43 5 5 HELIX 3 3 THR A 65 LEU A 75 1 11 HELIX 4 4 ARG A 81 ASN A 91 1 11 HELIX 5 5 ASN A 91 HIS A 102 1 12 HELIX 6 6 LEU A 111 MET A 119 1 9 HELIX 7 7 MET A 119 GLY A 124 1 6 HELIX 8 8 PRO A 125 GLY A 127 5 3 HELIX 9 9 ILE A 139 LYS A 147 1 9 HELIX 10 10 THR A 170 TYR A 189 1 20 HELIX 11 11 LYS A 191 TYR A 194 5 4 SHEET 1 A 4 TYR A 159 ASN A 166 0 SHEET 2 A 4 SER A 25 LEU A 32 -1 N PHE A 28 O VAL A 162 SHEET 3 A 4 ILE A 196 LEU A 203 -1 O LYS A 202 N GLU A 27 SHEET 4 A 4 VAL A 209 LYS A 210 -1 O VAL A 209 N VAL A 201 SHEET 1 B 2 LYS A 45 VAL A 49 0 SHEET 2 B 2 THR A 149 ASN A 153 -1 O VAL A 150 N VAL A 48 SHEET 1 C 4 THR A 78 ILE A 80 0 SHEET 2 C 4 ILE A 60 ILE A 63 1 N VAL A 62 O ILE A 80 SHEET 3 C 4 PHE A 104 GLN A 108 1 O ILE A 106 N ILE A 63 SHEET 4 C 4 LYS A 131 VAL A 133 1 O LYS A 131 N PHE A 105 SITE 1 AC1 11 LYS A 39 GLU A 41 ASN A 42 LYS A 100 SITE 2 AC1 11 LYS A 140 TYR A 189 GLU A 190 HOH A 404 SITE 3 AC1 11 HOH A 419 HOH A 585 HOH A 617 SITE 1 AC2 2 PRO A 141 ARG A 145 SITE 1 AC3 2 VAL A 48 VAL A 49 SITE 1 AC4 2 ARG A 126 LYS A 128 SITE 1 AC5 6 THR A 170 ASP A 171 GLU A 172 HOH A 451 SITE 2 AC5 6 HOH A 536 HOH A 584 CRYST1 33.868 105.255 38.526 90.00 104.01 90.00 P 1 21 1 2 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 0.029526 0.000000 0.007368 0.00000 SCALE2 0.000000 0.009501 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026752 0.00000 MASTER 250 0 5 11 10 0 8 6 0 0 0 17 END