HEADER RIBOSOMAL PROTEIN 11-FEB-11 3QOY TITLE CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN L1 FROM AQUIFEX AEOLICUS 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: AQUIFEX AEOLICUS; SOURCE 3 ORGANISM_TAXID: 63363; SOURCE 4 GENE: AQ_1935, RPLA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET11A-PL-AAEL1 KEYWDS BETA-ALPHA-BETA, STRUCTURAL CONSTITUENT OF RIBOSOME, RRNA BINDING, KEYWDS 2 REGULATION OF TRANSLATION, TRANSLATION, RIBOSOMAL RNA, MRNA, KEYWDS 3 RIBOSOMAL PROTEINS, RIBOSOMAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.G.GABDULKHAKOV,S.V.TISHCHENKO,E.U.NIKONOVA,A.A.SHKLIAEVA, AUTHOR 2 M.B.GARBER,S.V.NIKONOV,N.A.NEVSKAYA REVDAT 2 13-SEP-23 3QOY 1 REMARK REVDAT 1 28-DEC-11 3QOY 0 JRNL AUTH E.YU.NIKONOVA,S.V.TISHCHENKO,A.G.GABDULKHAKOV,A.A.SHKLYAEVA, JRNL AUTH 2 M.B.GARBER,S.V.NIKONOV,N.A.NEVSKAYA JRNL TITL CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN L1 FROM THE BACTERIUM JRNL TITL 2 AQUIFEX AEOLICUS JRNL REF CRYSTALLOGRAPHY REPORTS V. 56 603 2011 JRNL REFN ISSN 1063-7745 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.4_486) 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.65 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.040 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.2 REMARK 3 NUMBER OF REFLECTIONS : 12219 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 611 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 19.6537 - 3.3296 0.96 3067 162 0.1725 0.2122 REMARK 3 2 3.3296 - 2.6448 0.95 2962 156 0.2013 0.2640 REMARK 3 3 2.6448 - 2.3111 0.93 2879 151 0.2068 0.2826 REMARK 3 4 2.3111 - 2.1000 0.88 2700 142 0.2189 0.2941 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.83 REMARK 3 K_SOL : 0.37 REMARK 3 B_SOL : 23.55 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.14610 REMARK 3 B22 (A**2) : -3.44970 REMARK 3 B33 (A**2) : 1.30350 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.09700 REMARK 3 B23 (A**2) : 0.00000 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 : 0.008 1955 REMARK 3 ANGLE : 1.146 2634 REMARK 3 CHIRALITY : 0.073 297 REMARK 3 PLANARITY : 0.004 337 REMARK 3 DIHEDRAL : 16.894 777 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 3QOY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-FEB-11. REMARK 100 THE DEPOSITION ID IS D_1000063919. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JAN-11 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 4.6 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 : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12221 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 28.670 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 200 DATA REDUNDANCY : 3.390 REMARK 200 R MERGE (I) : 0.11600 REMARK 200 R SYM (I) : 0.09800 REMARK 200 FOR THE DATA SET : 11.9400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.3 REMARK 200 DATA REDUNDANCY IN SHELL : 1.36 REMARK 200 R MERGE FOR SHELL (I) : 0.33200 REMARK 200 R SYM FOR SHELL (I) : 0.28900 REMARK 200 FOR SHELL : 2.850 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: PDB ENTRY 1AD2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25 % PEG4000, 100MM ACETATE BUFFER, REMARK 280 200MM AMMONIUM SULPHATE, PH 4.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 285K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 53.74500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.76000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 53.74500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.76000 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 315 LIES ON A SPECIAL POSITION. 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 ALA A 2 14.46 -67.27 REMARK 500 PRO A 55 1.17 -66.11 REMARK 500 ALA A 241 -79.76 -119.04 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 SO4 A 243 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 244 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS A 245 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 246 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AD2 RELATED DB: PDB REMARK 900 RIBOSOMAL PROTEIN L1 MUTANT WITH SERINE 179 REPLACED BY CYSTEINE 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: 1ZHO RELATED DB: PDB REMARK 900 THE STRUCTURE OF A RIBOSOMAL PROTEIN L1 IN COMPLEX WITH MRNA REMARK 900 RELATED ID: 1MZP RELATED DB: PDB REMARK 900 STRUCTURE OF THE L1 PROTUBERANCE IN THE RIBOSOME DBREF 3QOY A 1 242 UNP O67759 RL1_AQUAE 1 242 SEQRES 1 A 242 MET ALA ARG ARG GLY LYS LYS TYR ILE GLU ALA SER LYS SEQRES 2 A 242 LEU VAL ASP ARG ASN LYS ARG TYR THR LEU GLU GLU ALA SEQRES 3 A 242 VAL ASP LEU LEU LYS LYS MET GLU GLU VAL LEU GLN ARG SEQRES 4 A 242 ARG PHE ASP GLU THR VAL GLU LEU ALA MET ARG LEU ASN SEQRES 5 A 242 VAL ASP PRO ARG TYR ALA ASP GLN MET VAL ARG GLY SER SEQRES 6 A 242 VAL VAL LEU PRO HIS GLY LEU GLY LYS PRO ILE LYS VAL SEQRES 7 A 242 VAL VAL PHE ALA GLU GLY GLU TYR ALA LYS LYS ALA GLU SEQRES 8 A 242 GLU ALA GLY ALA ASP TYR VAL GLY GLY ASP GLU LEU ILE SEQRES 9 A 242 ASN LYS ILE LEU LYS GLU GLU TRP THR ASP PHE ASP VAL SEQRES 10 A 242 ALA ILE ALA THR PRO GLU MET MET PRO LYS VAL ALA LYS SEQRES 11 A 242 LEU GLY ARG ILE LEU GLY PRO ARG GLY LEU MET PRO SER SEQRES 12 A 242 PRO LYS THR GLY THR VAL THR THR ASN VAL GLU GLN ALA SEQRES 13 A 242 ILE LYS ASP ALA LYS ARG GLY ARG VAL GLU PHE LYS VAL SEQRES 14 A 242 ASP LYS ALA GLY ASN VAL HIS MET PRO VAL GLY LYS ILE SEQRES 15 A 242 SER PHE GLU LYS GLU LYS LEU ILE ASP ASN LEU TYR ALA SEQRES 16 A 242 ALA ILE ASP ALA VAL VAL ARG ALA LYS PRO PRO GLY ALA SEQRES 17 A 242 LYS GLY GLN TYR ILE LYS ASN MET ALA VAL SER LEU THR SEQRES 18 A 242 MET SER PRO SER VAL LYS LEU ASP ILE ASN GLU VAL LEU SEQRES 19 A 242 LYS LYS LEU GLN GLU LYS ALA ALA HET SO4 A 243 5 HET SO4 A 244 5 HET TRS A 245 8 HET ACY A 246 4 HETNAM SO4 SULFATE ION HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM ACY ACETIC ACID HETSYN TRS TRIS BUFFER FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 TRS C4 H12 N O3 1+ FORMUL 5 ACY C2 H4 O2 FORMUL 6 HOH *77(H2 O) HELIX 1 1 ARG A 3 LEU A 14 1 12 HELIX 2 2 THR A 22 GLN A 38 1 17 HELIX 3 3 TYR A 57 MET A 61 5 5 HELIX 4 4 GLU A 83 ALA A 93 1 11 HELIX 5 5 GLY A 100 GLU A 111 1 12 HELIX 6 6 MET A 124 ALA A 129 1 6 HELIX 7 7 LEU A 131 GLY A 136 1 6 HELIX 8 8 PRO A 137 GLY A 139 5 3 HELIX 9 9 SER A 143 GLY A 147 5 5 HELIX 10 10 ASN A 152 ARG A 162 1 11 HELIX 11 11 GLU A 185 ALA A 203 1 19 HELIX 12 12 ASP A 229 LYS A 240 1 12 SHEET 1 A 4 ASN A 174 LYS A 181 0 SHEET 2 A 4 THR A 44 LEU A 51 -1 N VAL A 45 O GLY A 180 SHEET 3 A 4 ILE A 213 LEU A 220 -1 O SER A 219 N GLU A 46 SHEET 4 A 4 VAL A 226 LYS A 227 -1 O VAL A 226 N VAL A 218 SHEET 1 B 2 ARG A 63 VAL A 67 0 SHEET 2 B 2 ARG A 164 LYS A 168 -1 O VAL A 165 N VAL A 66 SHEET 1 C 3 TYR A 97 GLY A 99 0 SHEET 2 C 3 VAL A 78 PHE A 81 1 N VAL A 80 O TYR A 97 SHEET 3 C 3 VAL A 117 ALA A 120 1 O VAL A 117 N VAL A 79 CISPEP 1 LYS A 74 PRO A 75 0 9.26 SITE 1 AC1 5 LYS A 161 LYS A 171 ACY A 246 HOH A 250 SITE 2 AC1 5 HOH A 319 SITE 1 AC2 4 PRO A 75 ASP A 170 LYS A 171 HOH A 307 SITE 1 AC3 7 ARG A 50 PRO A 69 HIS A 70 GLY A 71 SITE 2 AC3 7 LYS A 188 LYS A 214 HOH A 321 SITE 1 AC4 6 ASP A 54 ARG A 56 LYS A 74 LYS A 161 SITE 2 AC4 6 ARG A 162 SO4 A 243 CRYST1 107.490 37.520 58.970 90.00 110.32 90.00 C 1 2 1 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 0.009303 0.000000 0.003446 0.00000 SCALE2 0.000000 0.026652 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018084 0.00000