PDB Short entry for 1SEI HEADER RIBOSOMAL PROTEIN 14-AUG-96 1SEI TITLE STRUCTURE OF 30S RIBOSOMAL PROTEIN S8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSOMAL PROTEIN S8; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 1422; SOURCE 4 GENE: BACILLUS STEAROTHERMOPHILUS; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: T7; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET13; SOURCE 10 EXPRESSION_SYSTEM_GENE: BACILLUS STEAROTHERMOPHILUS; SOURCE 11 OTHER_DETAILS: T7 EXPRESSION SYSTEM INDUCIBLE BY ISOPROPYL- SOURCE 12 BETA-D-THIOGALACTOPYRANOSIDE (IPTG). ALSO SEE MEDLINE SOURCE 13 IDENTIFIER 92110431. KEYWDS PROKARYOTIC, RIBOSOMAL PROTEIN, RRNA-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR C.DAVIES,V.RAMAKRISHNAN,S.W.WHITE REVDAT 2 24-FEB-09 1SEI 1 VERSN REVDAT 1 12-MAR-97 1SEI 0 JRNL AUTH C.DAVIES,V.RAMAKRISHNAN,S.W.WHITE JRNL TITL STRUCTURAL EVIDENCE FOR SPECIFIC S8-RNA AND JRNL TITL 2 S8-PROTEIN INTERACTIONS WITHIN THE 30S RIBOSOMAL JRNL TITL 3 SUBUNIT: RIBOSOMAL PROTEIN S8 FROM BACILLUS JRNL TITL 4 STEAROTHERMOPHILUS AT 1.9 A RESOLUTION. JRNL REF STRUCTURE V. 4 1093 1996 JRNL REFN ISSN 0969-2126 JRNL PMID 8805594 JRNL DOI 10.1016/S0969-2126(96)00115-3 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 21545 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) : 0.222 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL 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 : 2058 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 117 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.70 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) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.77 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.47 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) : 1.000 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : 1.500 ; 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 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1SEI COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUN-96 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21973 REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 5.050 REMARK 200 R MERGE (I) : 0.08300 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 40.08000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.98000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 40.08000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.98000 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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: 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 LEU A 104 CA - CB - CG ANGL. DEV. = 14.4 DEGREES REMARK 500 LEU B 104 CA - CB - CG ANGL. DEV. = 16.6 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 ASP A 47 -179.37 -173.88 REMARK 500 PRO A 67 81.30 -59.08 REMARK 500 ASN A 68 -26.87 80.96 REMARK 500 ILE A 78 -79.58 -99.52 REMARK 500 LEU A 83 62.50 -158.07 REMARK 500 PRO B 67 76.36 -51.19 REMARK 500 ASN B 68 -27.28 89.08 REMARK 500 ILE B 78 -83.43 -97.99 REMARK 500 LEU B 83 69.39 -152.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 132 DISTANCE = 8.05 ANGSTROMS REMARK 525 HOH A 135 DISTANCE = 7.65 ANGSTROMS REMARK 525 HOH A 149 DISTANCE = 5.31 ANGSTROMS REMARK 525 HOH B 164 DISTANCE = 6.66 ANGSTROMS REMARK 525 HOH A 182 DISTANCE = 5.77 ANGSTROMS REMARK 525 HOH A 187 DISTANCE = 5.58 ANGSTROMS DBREF 1SEI A 1 130 UNP P56209 RS8_BACST 1 130 DBREF 1SEI B 1 130 UNP P56209 RS8_BACST 1 130 SEQRES 1 A 130 VAL MET THR ASP PRO ILE ALA ASP MET LEU THR ALA ILE SEQRES 2 A 130 ARG ASN ALA ASN MET VAL ARG HIS GLU LYS LEU GLU VAL SEQRES 3 A 130 PRO ALA SER LYS ILE LYS ARG GLU ILE ALA GLU ILE LEU SEQRES 4 A 130 LYS ARG GLU GLY PHE ILE ARG ASP TYR GLU TYR ILE GLU SEQRES 5 A 130 ASP ASN LYS GLN GLY ILE LEU ARG ILE PHE LEU LYS TYR SEQRES 6 A 130 GLY PRO ASN GLU ARG VAL ILE THR GLY LEU LYS ARG ILE SEQRES 7 A 130 SER LYS PRO GLY LEU ARG VAL TYR VAL LYS ALA HIS GLU SEQRES 8 A 130 VAL PRO ARG VAL LEU ASN GLY LEU GLY ILE ALA ILE LEU SEQRES 9 A 130 SER THR SER GLN GLY VAL LEU THR ASP LYS GLU ALA ARG SEQRES 10 A 130 GLN LYS GLY THR GLY GLY GLU ILE ILE ALA TYR VAL ILE SEQRES 1 B 130 VAL MET THR ASP PRO ILE ALA ASP MET LEU THR ALA ILE SEQRES 2 B 130 ARG ASN ALA ASN MET VAL ARG HIS GLU LYS LEU GLU VAL SEQRES 3 B 130 PRO ALA SER LYS ILE LYS ARG GLU ILE ALA GLU ILE LEU SEQRES 4 B 130 LYS ARG GLU GLY PHE ILE ARG ASP TYR GLU TYR ILE GLU SEQRES 5 B 130 ASP ASN LYS GLN GLY ILE LEU ARG ILE PHE LEU LYS TYR SEQRES 6 B 130 GLY PRO ASN GLU ARG VAL ILE THR GLY LEU LYS ARG ILE SEQRES 7 B 130 SER LYS PRO GLY LEU ARG VAL TYR VAL LYS ALA HIS GLU SEQRES 8 B 130 VAL PRO ARG VAL LEU ASN GLY LEU GLY ILE ALA ILE LEU SEQRES 9 B 130 SER THR SER GLN GLY VAL LEU THR ASP LYS GLU ALA ARG SEQRES 10 B 130 GLN LYS GLY THR GLY GLY GLU ILE ILE ALA TYR VAL ILE FORMUL 3 HOH *117(H2 O) HELIX 1 1 ASP A 4 MET A 18 1 15 HELIX 2 2 LYS A 30 ARG A 41 1 12 HELIX 3 3 ALA A 89 GLU A 91 5 3 HELIX 4 4 ASP A 113 LYS A 119 1 7 HELIX 5 5 THR B 3 MET B 18 1 16 HELIX 6 6 LYS B 30 ARG B 41 1 12 HELIX 7 7 ALA B 89 GLU B 91 5 3 HELIX 8 8 ASP B 113 LYS B 119 1 7 SHEET 1 A 3 LYS A 23 PRO A 27 0 SHEET 2 A 3 GLY A 57 LEU A 63 -1 N ILE A 61 O LEU A 24 SHEET 3 A 3 ILE A 45 GLU A 52 -1 N ILE A 51 O ILE A 58 SHEET 1 B 4 LEU A 75 ARG A 77 0 SHEET 2 B 4 GLU A 124 VAL A 129 -1 N TYR A 128 O LYS A 76 SHEET 3 B 4 ILE A 101 THR A 106 -1 N SER A 105 O GLU A 124 SHEET 4 B 4 GLY A 109 THR A 112 -1 N LEU A 111 O LEU A 104 SHEET 1 C 3 LYS B 23 PRO B 27 0 SHEET 2 C 3 GLN B 56 LEU B 63 -1 N ILE B 61 O LEU B 24 SHEET 3 C 3 ILE B 45 ASP B 53 -1 N ASP B 53 O GLN B 56 SHEET 1 D 4 LEU B 75 ARG B 77 0 SHEET 2 D 4 GLU B 124 VAL B 129 -1 N TYR B 128 O LYS B 76 SHEET 3 D 4 ILE B 101 THR B 106 -1 N SER B 105 O GLU B 124 SHEET 4 D 4 GLY B 109 THR B 112 -1 N LEU B 111 O LEU B 104 CRYST1 80.160 85.960 39.590 90.00 90.00 90.00 P 21 21 2 8 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 0.012475 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011633 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025259 0.00000 MTRIX1 1 -0.998700 0.049130 0.013450 77.66786 1 MTRIX2 1 0.049320 0.998690 0.013690 -2.45282 1 MTRIX3 1 -0.012760 0.014330 -0.999820 19.76353 1