HEADER RIBOSOME 07-FEB-01 1I2A TITLE CRYSTAL STRUCTURE OF L1 RIBOSOMAL PROTEIN FROM METHANOCOCCUS TITLE 2 JANNASCHII WITH 1.85A RESOLUTION. COMPND MOL_ID: 1; COMPND 2 MOLECULE: 50S RIBOSOMAL PROTEIN L1P; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII; SOURCE 3 ORGANISM_TAXID: 2190; SOURCE 4 GENE: RPLA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET11A-MJAL1 KEYWDS RIBOSOMAL PROTEIN, PRIMARY RRNA-BINDING PROTEIN, TRANSLATIONAL KEYWDS 2 REPRESSOR, RIBOSOME EXPDTA X-RAY DIFFRACTION AUTHOR Y.SMOLINSKAYA,S.V.NIKONOV REVDAT 7 09-AUG-23 1I2A 1 REMARK REVDAT 6 07-MAR-18 1I2A 1 REMARK REVDAT 5 12-MAR-14 1I2A 1 REMARK REVDAT 4 31-AUG-11 1I2A 1 HETATM VERSN REVDAT 3 24-FEB-09 1I2A 1 VERSN REVDAT 2 20-JAN-04 1I2A 1 JRNL REVDAT 1 09-DEC-03 1I2A 0 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH N.NEVSKAYA,S.TISCHENKO,R.FEDOROV,S.AL-KARADAGHI,A.LILJAS, REMARK 1 AUTH 2 A.KRAFT,W.PIENDL,M.GARBER,S.NIKONOV REMARK 1 TITL ARCHAEAL RIBOSOMAL PROTEIN L1: THE STRUCTURE PROVIDES NEW REMARK 1 TITL 2 INSIGHTS INTO RNA BINDING OF THE L1 PROTEIN FAMILY. REMARK 1 REF STRUCTURE V. 8 363 2000 REMARK 1 REFN ISSN 0969-2126 REMARK 1 PMID 10801481 REMARK 1 DOI 10.1016/S0969-2126(00)00116-7 REMARK 1 REFERENCE 2 REMARK 1 AUTH N.NEVSKAYA,S.TISHCHENKO,M.PAVELIEV,Y.SMOLINSKAYA,R.FEDOROV, REMARK 1 AUTH 2 W.PIENDL,Y.NAKAMURA,T.TOYODA,M.GARBER,S.NIKONOV REMARK 1 TITL STRUCTURE OF RIBOSOMAL PROTEIN L1 FROM METHANOCOCCUS REMARK 1 TITL 2 THERMOLITHOTROPHICUS. FUNCTIONALLY IMPORTANT STRUCTURAL REMARK 1 TITL 3 INVARIANTS ON THE L1 SURFACE. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 58 1023 2002 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 12037305 REMARK 1 DOI 10.1107/S0907444902006157 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.83 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 673607.520 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 22327 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) : 0.222 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1078 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3541 REMARK 3 BIN R VALUE (WORKING SET) : 0.2980 REMARK 3 BIN FREE R VALUE : 0.2790 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 166 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.022 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1682 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 185 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.18000 REMARK 3 B22 (A**2) : 2.27000 REMARK 3 B33 (A**2) : -3.45000 REMARK 3 B12 (A**2) : 1.85000 REMARK 3 B13 (A**2) : -0.83000 REMARK 3 B23 (A**2) : 0.48000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.20 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.28 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.17 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.850 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 3.210 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.860 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 5.760 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 8.510 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 56.13 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ALD_OLD.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ALD.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1I2A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-FEB-01. REMARK 100 THE DEPOSITION ID IS D_1000012813. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : 1.009 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23155 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.825 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 (%) : 94.8 REMARK 200 DATA REDUNDANCY : 3.520 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.83 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.41 REMARK 200 R MERGE FOR SHELL (I) : 0.30900 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: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1CJS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 10000, HEPES-HCL, PH 7.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 301.5K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 LYS A 213 REMARK 465 GLU A 214 REMARK 465 LYS A 215 REMARK 465 ALA A 216 REMARK 465 LYS A 217 REMARK 465 LYS A 218 REMARK 465 LYS A 219 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 54 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 155 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 37.58 -79.68 REMARK 500 LYS A 45 77.72 -151.33 REMARK 500 ASN A 91 70.87 -115.92 REMARK 500 ARG A 155 -138.24 55.26 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 PTL A 220 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1CJS RELATED DB: PDB REMARK 900 1CJS IS THE L1 PROTEIN WITH LOWER RESOLUTION. DBREF 1I2A A 1 219 UNP P54050 RL1_METJA 14 232 SEQRES 1 A 219 MET ASP ARG GLU ALA LEU LEU GLN ALA VAL LYS GLU ALA SEQRES 2 A 219 ARG GLU LEU ALA LYS PRO ARG ASN PHE THR GLN SER PHE SEQRES 3 A 219 GLU PHE ILE ALA THR LEU LYS GLU ILE ASP MET ARG LYS SEQRES 4 A 219 PRO GLU ASN ARG ILE LYS THR GLU VAL VAL LEU PRO HIS SEQRES 5 A 219 GLY ARG GLY LYS GLU ALA LYS ILE ALA VAL ILE GLY THR SEQRES 6 A 219 GLY ASP LEU ALA LYS GLN ALA GLU GLU LEU GLY LEU THR SEQRES 7 A 219 VAL ILE ARG LYS GLU GLU ILE GLU GLU LEU GLY LYS ASN SEQRES 8 A 219 LYS ARG LYS LEU ARG LYS ILE ALA LYS ALA HIS ASP PHE SEQRES 9 A 219 PHE ILE ALA GLN ALA ASP LEU MET PRO LEU ILE GLY ARG SEQRES 10 A 219 TYR MET GLY VAL ILE LEU GLY PRO ARG GLY LYS MET PRO SEQRES 11 A 219 LYS PRO VAL PRO ALA ASN ALA ASN ILE LYS PRO LEU VAL SEQRES 12 A 219 GLU ARG LEU LYS LYS THR VAL VAL ILE ASN THR ARG ASP SEQRES 13 A 219 LYS PRO TYR PHE GLN VAL LEU VAL GLY ASN GLU LYS MET SEQRES 14 A 219 THR ASP GLU GLN ILE VAL ASP ASN ILE GLU ALA VAL LEU SEQRES 15 A 219 ASN VAL VAL ALA LYS LYS TYR GLU LYS GLY LEU TYR HIS SEQRES 16 A 219 ILE LYS ASP ALA TYR VAL LYS LEU THR MET GLY PRO ALA SEQRES 17 A 219 VAL LYS VAL LYS LYS GLU LYS ALA LYS LYS LYS HET PTL A 220 6 HETNAM PTL PENTANAL FORMUL 2 PTL C5 H10 O FORMUL 3 HOH *185(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 GLU A 83 ASN A 91 1 9 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 148 1 10 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 O PHE A 26 N VAL A 164 SHEET 3 A 4 ILE A 196 LEU A 203 -1 N LYS A 197 O THR A 31 SHEET 4 A 4 VAL A 209 LYS A 210 -1 N VAL A 209 O 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 O ILE A 60 N THR A 78 SHEET 3 C 4 PHE A 104 GLN A 108 1 O PHE A 104 N ALA A 61 SHEET 4 C 4 LYS A 131 VAL A 133 1 N LYS A 131 O PHE A 105 SITE 1 AC1 6 ARG A 20 ASN A 21 LYS A 33 TYR A 194 SITE 2 AC1 6 ILE A 196 LYS A 197 CRYST1 33.577 38.881 54.936 83.32 80.14 74.72 P 1 1 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 0.029782 -0.008137 -0.004581 0.00000 SCALE2 0.000000 0.026662 -0.002001 0.00000 SCALE3 0.000000 0.000000 0.018528 0.00000