HEADER RIBOSOME 19-APR-99 1CJS TITLE CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN L1 FROM METHANOCOCCUS TITLE 2 JANNASCHII 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; SOURCE 10 EXPRESSION_SYSTEM_GENE: MJAL1 KEYWDS RIBOSOMAL PROTEIN, PRIMARY RRNA-BINDING PROTEIN, TRANSLATIONAL KEYWDS 2 REPRESSOR, RIBOSOME EXPDTA X-RAY DIFFRACTION AUTHOR N.NEVSKAYA,S.TISHCHENKO,R.FEDOROV,S.AL-KARADAGHI,A.LILJAS,A.KRAFT, AUTHOR 2 W.PIENDL,M.GARBER,S.NIKONOV REVDAT 6 27-DEC-23 1CJS 1 REMARK REVDAT 5 07-MAR-18 1CJS 1 REMARK REVDAT 4 24-FEB-09 1CJS 1 VERSN REVDAT 3 01-APR-03 1CJS 1 JRNL REVDAT 2 07-MAR-01 1CJS 1 REMARK REVDAT 1 31-MAY-00 1CJS 0 JRNL AUTH N.NEVSKAYA,S.TISCHENKO,R.FEDOROV,S.AL-KARADAGHI,A.LILJAS, JRNL AUTH 2 A.KRAFT,W.PIENDL,M.GARBER,S.NIKONOV JRNL TITL ARCHAEAL RIBOSOMAL PROTEIN L1: THE STRUCTURE PROVIDES NEW JRNL TITL 2 INSIGHTS INTO RNA BINDING OF THE L1 PROTEIN FAMILY. JRNL REF STRUCTURE FOLD.DES. V. 8 363 2000 JRNL REFN ISSN 0969-2126 JRNL PMID 10801481 JRNL DOI 10.1016/S0969-2126(00)00116-7 REMARK 2 REMARK 2 RESOLUTION. 2.30 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.2000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 89.1 REMARK 3 NUMBER OF REFLECTIONS : 11079 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.271 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 531 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.40 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 77.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1112 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 : 1683 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 70 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.87 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) : 0.018 REMARK 3 BOND ANGLES (DEGREES) : 3.090 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.95 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.370 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 : NULL REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPH19X.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1CJS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-APR-99. REMARK 100 THE DEPOSITION ID IS D_1000000876. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-98 REMARK 200 TEMPERATURE (KELVIN) : 293.0 REMARK 200 PH : 7.50 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) : 1.0009 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11387 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.1 REMARK 200 DATA REDUNDANCY : 2.100 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.4 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: X-PLOR, CCP4 REMARK 200 STARTING MODEL: NULL 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: PH 7.50, VAPOR DIFFUSION 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 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 213 CA C O CB CG CD CE REMARK 470 LYS A 213 NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 HIS A 52 NE2 HIS A 52 CD2 -0.074 REMARK 500 HIS A 102 NE2 HIS A 102 CD2 -0.077 REMARK 500 REMARK 500 REMARK: NULL 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 3 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 14 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 81 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 93 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 96 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 117 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES REMARK 500 MET A 119 CG - SD - CE ANGL. DEV. = 9.8 DEGREES REMARK 500 ARG A 126 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 MET A 129 CG - SD - CE ANGL. DEV. = 9.8 DEGREES REMARK 500 ARG A 155 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 MET A 205 CG - SD - CE ANGL. DEV. = 9.8 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 33.17 -84.14 REMARK 500 ARG A 155 -124.92 70.10 REMARK 500 PRO A 158 58.60 -91.35 REMARK 500 LYS A 202 140.88 -176.96 REMARK 500 LYS A 212 -8.71 114.78 REMARK 500 REMARK 500 REMARK: NULL DBREF 1CJS 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 FORMUL 2 HOH *70(H2 O) HELIX 1 H1 ARG A 3 LEU A 16 1 14 HELIX 2 H2 PRO A 40 ASN A 42 5 3 HELIX 3 H3 ASP A 67 GLU A 74 1 8 HELIX 4 H4 GLU A 84 GLY A 89 1 6 HELIX 5 H5 LYS A 92 LYS A 100 1 9 HELIX 6 H6 ALA A 109 LEU A 111 5 3 HELIX 7 H7 MET A 112 LEU A 123 1 12 HELIX 8 H8 GLY A 124 ARG A 126 5 3 HELIX 9 H9 LYS A 140 LEU A 146 1 7 HELIX 10 H10 ASP A 171 LYS A 188 1 18 SHEET 1 A 2 LYS A 45 VAL A 49 0 SHEET 2 A 2 THR A 149 ASN A 153 -1 N ILE A 152 O THR A 46 SHEET 1 B 4 THR A 78 ARG A 81 0 SHEET 2 B 4 ILE A 60 GLY A 64 1 N VAL A 62 O THR A 78 SHEET 3 B 4 PHE A 104 GLN A 108 1 N PHE A 104 O ALA A 61 SHEET 4 B 4 LYS A 131 VAL A 133 1 N LYS A 131 O ALA A 107 SHEET 1 C 3 TYR A 159 ASN A 166 0 SHEET 2 C 3 SER A 25 LEU A 32 -1 N ALA A 30 O PHE A 160 SHEET 3 C 3 ILE A 196 LEU A 203 -1 N LYS A 202 O GLU A 27 CRYST1 34.407 39.910 55.634 83.03 80.25 74.68 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 0.029064 -0.007962 -0.004367 0.00000 SCALE2 0.000000 0.025979 -0.002100 0.00000 SCALE3 0.000000 0.000000 0.018297 0.00000