HEADER RIBOSOME 07-AUG-01 1IQV TITLE CRYSTAL STRUCTURE ANALYSIS OF THE ARCHAEBACTERIAL RIBOSOMAL PROTEIN S7 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSOMAL PROTEIN S7; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 30S RIBOSOMAL PROTEIN S7P; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 3 ORGANISM_TAXID: 53953; SOURCE 4 GENE: PH1541; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS(DE3)-RIL; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS RIBOSOMAL PROTEIN, RNA-BINDING, DECODING CENTER, HELIX-TURN-HELIX, KEYWDS 2 RIBOSOME EXPDTA X-RAY DIFFRACTION AUTHOR H.HOSAKA,M.YAO,M.KIMURA,I.TANAKA REVDAT 6 25-OCT-23 1IQV 1 REMARK REVDAT 5 23-OCT-19 1IQV 1 JRNL REVDAT 4 24-FEB-09 1IQV 1 VERSN REVDAT 3 14-JAN-03 1IQV 1 REMARK REVDAT 2 06-FEB-02 1IQV 1 JRNL REVDAT 1 29-AUG-01 1IQV 0 JRNL AUTH H.HOSAKA,M.YAO,M.KIMURA,I.TANAKA JRNL TITL THE STRUCTURE OF THE ARCHAEBACTERIAL RIBOSOMAL PROTEIN S7 JRNL TITL 2 AND ITS POSSIBLE INTERACTION WITH 16S RRNA. JRNL REF J.BIOCHEM. V. 130 695 2001 JRNL REFN ISSN 0021-924X JRNL PMID 11686933 JRNL DOI 10.1093/OXFORDJOURNALS.JBCHEM.A003036 REMARK 2 REMARK 2 RESOLUTION. 2.10 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 13999 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) : 0.196 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.140 REMARK 3 FREE R VALUE TEST SET COUNT : 1420 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 : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.17 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1213 REMARK 3 BIN R VALUE (WORKING SET) : 0.2430 REMARK 3 BIN FREE R VALUE : 0.2650 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 138 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 : 1318 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 131 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.54200 REMARK 3 B22 (A**2) : -3.54200 REMARK 3 B33 (A**2) : 7.08400 REMARK 3 B12 (A**2) : -2.81200 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM SIGMAA (A) : 0.18 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) : 0.30 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.17 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.030 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 19.56 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.767 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.757 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.732 ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : 2.948 ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.292 ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : 0.44 REMARK 3 BSOL : 66.80 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 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1IQV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-AUG-01. REMARK 100 THE DEPOSITION ID IS D_1000005195. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAR-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : MONOCHROMATOR + MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : OXFORD PX210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14407 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 31.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 9.700 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : 0.07700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.2000 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) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 0.26200 REMARK 200 R SYM FOR SHELL (I) : 0.24300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1HUS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3000, SODIUM CHLORIDE, PH 7.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 78.73333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 39.36667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 39.36667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 78.73333 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 MET A 1 REMARK 465 LYS A 2 REMARK 465 GLU A 3 REMARK 465 VAL A 4 REMARK 465 ALA A 5 REMARK 465 LYS A 6 REMARK 465 PRO A 7 REMARK 465 LEU A 8 REMARK 465 GLN A 9 REMARK 465 GLU A 10 REMARK 465 ARG A 11 REMARK 465 PHE A 12 REMARK 465 PHE A 13 REMARK 465 ILE A 14 REMARK 465 PRO A 15 REMARK 465 HIS A 16 REMARK 465 GLU A 17 REMARK 465 LEU A 46 REMARK 465 LEU A 47 REMARK 465 PRO A 48 REMARK 465 HIS A 49 REMARK 465 THR A 50 REMARK 465 HIS A 51 REMARK 465 GLY A 52 REMARK 465 ARG A 53 REMARK 465 HIS A 54 REMARK 465 ALA A 55 REMARK 465 LYS A 56 REMARK 465 LYS A 57 REMARK 465 HIS A 58 REMARK 465 PHE A 59 REMARK 465 GLY A 60 REMARK 465 LYS A 61 REMARK 465 ALA A 62 REMARK 465 ASN A 63 REMARK 465 HIS A 81 REMARK 465 TYR A 82 REMARK 465 LYS A 83 REMARK 465 VAL A 84 REMARK 465 ALA A 85 REMARK 465 GLY A 86 REMARK 465 HIS A 87 REMARK 465 PHE A 88 REMARK 465 MET A 89 REMARK 465 ARG A 90 REMARK 465 ARG A 91 REMARK 465 GLU A 92 REMARK 465 HIS A 93 REMARK 465 ARG A 94 REMARK 465 SER A 95 REMARK 465 LEU A 96 REMARK 465 ASN A 97 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 ARG A 23 -44.95 -146.34 REMARK 500 SER A 77 -77.65 -102.03 REMARK 500 LYS A 180 32.75 -97.83 REMARK 500 SER A 217 39.09 -98.30 REMARK 500 REMARK 500 REMARK: NULL DBREF 1IQV A 1 218 UNP O59230 RS7_PYRHO 1 218 SEQRES 1 A 218 MET LYS GLU VAL ALA LYS PRO LEU GLN GLU ARG PHE PHE SEQRES 2 A 218 ILE PRO HIS GLU ILE LYS VAL MET GLY ARG TRP SER THR SEQRES 3 A 218 GLU ASP VAL GLU VAL LYS ASP PRO SER LEU LYS PRO TYR SEQRES 4 A 218 ILE ASN LEU GLU PRO ARG LEU LEU PRO HIS THR HIS GLY SEQRES 5 A 218 ARG HIS ALA LYS LYS HIS PHE GLY LYS ALA ASN VAL HIS SEQRES 6 A 218 ILE VAL GLU ARG LEU ILE ASN LYS VAL MET ARG SER GLY SEQRES 7 A 218 GLY SER HIS TYR LYS VAL ALA GLY HIS PHE MET ARG ARG SEQRES 8 A 218 GLU HIS ARG SER LEU ASN SER LYS LYS VAL ARG ALA TYR SEQRES 9 A 218 GLU VAL VAL LYS GLU ALA PHE LYS ILE ILE GLU LYS ARG SEQRES 10 A 218 THR GLY LYS ASN PRO ILE GLN VAL LEU VAL TRP ALA ILE SEQRES 11 A 218 GLU ASN ALA ALA PRO ARG GLU ASP THR THR SER VAL MET SEQRES 12 A 218 PHE GLY GLY ILE ARG TYR HIS VAL ALA VAL ASP ILE SER SEQRES 13 A 218 PRO LEU ARG ARG LEU ASP VAL ALA LEU ARG ASN ILE ALA SEQRES 14 A 218 LEU GLY ALA SER ALA LYS CYS TYR ARG THR LYS MET SER SEQRES 15 A 218 PHE ALA GLU ALA LEU ALA GLU GLU ILE ILE LEU ALA ALA SEQRES 16 A 218 ASN LYS ASP PRO LYS SER TYR ALA TYR SER LYS LYS LEU SEQRES 17 A 218 GLU ILE GLU ARG ILE ALA GLU SER SER ARG FORMUL 2 HOH *131(H2 O) HELIX 1 1 MET A 21 ARG A 23 5 3 HELIX 2 2 LEU A 36 ILE A 40 5 5 HELIX 3 3 HIS A 65 ARG A 76 1 12 HELIX 4 4 SER A 98 GLY A 119 1 22 HELIX 5 5 ASN A 121 ALA A 134 1 14 HELIX 6 6 SER A 156 THR A 179 1 24 HELIX 7 7 SER A 182 ASN A 196 1 15 HELIX 8 8 SER A 201 SER A 217 1 17 SHEET 1 A 2 ASP A 138 PHE A 144 0 SHEET 2 A 2 ILE A 147 VAL A 153 -1 N ILE A 147 O PHE A 144 CRYST1 58.900 58.900 118.100 90.00 90.00 120.00 P 32 2 1 6 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 0.016978 0.009802 0.000000 0.00000 SCALE2 0.000000 0.019604 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008467 0.00000