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 2 20-SEP-23 4LQ4 1 REMARK 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-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER 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 13-AUG-13. REMARK 100 THE DEPOSITION ID IS D_1000080944. 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 PLUS REMARK 200 DATA SCALING SOFTWARE : PROTEUM PLUS 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 METHANOCOCCUS REMARK 900 JANNASCHII REMARK 900 RELATED ID: 1I2A RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF L1 RIBOSOMAL PROTEIN FROM METHANOCOCCUS REMARK 900 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