HEADER RIBOSOMAL PROTEIN 08-AUG-97 1HUS TITLE RIBOSOMAL PROTEIN S7 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSOMAL PROTEIN S7; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 1422; SOURCE 4 CELL_LINE: BL21; SOURCE 5 GENE: S7; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) LYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET-22B; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: BL21; SOURCE 12 EXPRESSION_SYSTEM_GENE: S7 KEYWDS RIBOSOMAL PROTEIN, RNA-BINDING PROTEIN, DECODING CENTER EXPDTA X-RAY DIFFRACTION AUTHOR H.HOSAKA,A.NAKAGAWA,I.TANAKA REVDAT 3 16-OCT-24 1HUS 1 SEQADV LINK REVDAT 2 24-FEB-09 1HUS 1 VERSN REVDAT 1 28-JAN-98 1HUS 0 JRNL AUTH H.HOSAKA,A.NAKAGAWA,I.TANAKA,N.HARADA,K.SANO,M.KIMURA,M.YAO, JRNL AUTH 2 S.WAKATSUKI JRNL TITL RIBOSOMAL PROTEIN S7: A NEW RNA-BINDING MOTIF WITH JRNL TITL 2 STRUCTURAL SIMILARITIES TO A DNA ARCHITECTURAL FACTOR. JRNL REF STRUCTURE V. 5 1199 1997 JRNL REFN ISSN 0969-2126 JRNL PMID 9331423 JRNL DOI 10.1016/S0969-2126(97)00270-0 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH N.HARADA,K.SANO,M.KIMURA,H.HOSAKA,A.NAKAGAWA,I.TANAKA REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY CRYSTALLOGRAPHIC STUDY REMARK 1 TITL 2 OF THE RIBOSOMAL PROTEIN S7 FROM BACILLUS STEAROTHERMOPHILUS REMARK 1 REF J.STRUCT.BIOL. V. 120 112 1997 REMARK 1 REFN ISSN 1047-8477 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 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) (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 7305 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) : 0.216 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 715 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.61 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 769 REMARK 3 BIN R VALUE (WORKING SET) : 0.3530 REMARK 3 BIN FREE R VALUE : 0.3390 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 81 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.038 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1120 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 25 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.40 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) : 0.29 REMARK 3 ESD FROM SIGMAA (A) : 0.37 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) : 0.37 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.36 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.020 REMARK 3 BOND ANGLES (DEGREES) : 2.000 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.120 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) : 8.230 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 10.570; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 11.450; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 16.270; 2.500 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: REFMAC (G.N.MURSHUDOV ET AL.) WAS ALSO REMARK 3 USED DURING THE REFINEMENT CYCLE. PARAMETERS OF SE-MET WAS REMARK 3 DERIVED FROM THOSE OF METHIONINE. REMARK 4 REMARK 4 1HUS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000174035. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : MAR-97 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 8.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.90007 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : COLLIMATING AND FOCUSING MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : PRINCETON 2K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7586 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 18.700 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.13800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD WITH SE-MET MUTANT REMARK 200 SOFTWARE USED: SHARP, X-PLOR 3.851 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED FROM 0.1M NA REMARK 280 HEPES BUFFER(PH8.2) WITH 4%(V/V) 2-PROPANOL AND 2.0M AMMONIUM REMARK 280 SULFATE. 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 27.20000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 65.51000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.20000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 65.51000 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 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 PRO A 1 REMARK 465 ARG A 2 REMARK 465 ARG A 3 REMARK 465 GLY A 4 REMARK 465 PRO A 5 REMARK 465 VAL A 6 REMARK 465 ALA A 7 REMARK 465 LYS A 8 REMARK 465 LYS A 148 REMARK 465 ALA A 149 REMARK 465 PHE A 150 REMARK 465 ALA A 151 REMARK 465 HIS A 152 REMARK 465 TYR A 153 REMARK 465 ARG A 154 REMARK 465 TRP A 155 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 159 O HOH A 165 2.09 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 ARG A 77 88.71 -154.70 REMARK 500 GLN A 85 103.38 -55.13 REMARK 500 ARG A 110 178.80 -56.29 REMARK 500 REMARK 500 REMARK: NULL DBREF 1HUS A 1 155 UNP P22744 RS7_BACST 1 155 SEQADV 1HUS MSE A 30 UNP P22744 MET 30 MODIFIED RESIDUE SEQADV 1HUS MSE A 58 UNP P22744 MET 58 MODIFIED RESIDUE SEQADV 1HUS MSE A 69 UNP P22744 MET 69 MODIFIED RESIDUE SEQADV 1HUS MSE A 115 UNP P22744 MET 115 MODIFIED RESIDUE SEQADV 1HUS MSE A 124 UNP P22744 MET 124 MODIFIED RESIDUE SEQADV 1HUS MSE A 143 UNP P22744 MET 143 MODIFIED RESIDUE SEQRES 1 A 155 PRO ARG ARG GLY PRO VAL ALA LYS ARG ASP VAL LEU PRO SEQRES 2 A 155 ASP PRO ILE TYR ASN SER LYS LEU VAL THR ARG LEU ILE SEQRES 3 A 155 ASN LYS ILE MSE ILE ASP GLY LYS LYS SER LYS ALA GLN SEQRES 4 A 155 LYS ILE LEU TYR THR ALA PHE ASP ILE ILE ARG GLU ARG SEQRES 5 A 155 THR GLY LYS ASP PRO MSE GLU VAL PHE GLU GLN ALA LEU SEQRES 6 A 155 LYS ASN VAL MSE PRO VAL LEU GLU VAL ARG ALA ARG ARG SEQRES 7 A 155 VAL GLY GLY ALA ASN TYR GLN VAL PRO VAL GLU VAL ARG SEQRES 8 A 155 PRO ASP ARG ARG VAL SER LEU GLY LEU ARG TRP LEU VAL SEQRES 9 A 155 GLN TYR ALA ARG LEU ARG ASN GLU LYS THR MSE GLU GLU SEQRES 10 A 155 ARG LEU ALA ASN GLU ILE MSE ASP ALA ALA ASN ASN THR SEQRES 11 A 155 GLY ALA ALA VAL LYS LYS ARG GLU ASP THR HIS LYS MSE SEQRES 12 A 155 ALA GLU ALA ASN LYS ALA PHE ALA HIS TYR ARG TRP MODRES 1HUS MSE A 30 MET SELENOMETHIONINE MODRES 1HUS MSE A 58 MET SELENOMETHIONINE MODRES 1HUS MSE A 69 MET SELENOMETHIONINE MODRES 1HUS MSE A 115 MET SELENOMETHIONINE MODRES 1HUS MSE A 124 MET SELENOMETHIONINE MODRES 1HUS MSE A 143 MET SELENOMETHIONINE HET MSE A 30 8 HET MSE A 58 8 HET MSE A 69 8 HET MSE A 115 8 HET MSE A 124 8 HET MSE A 143 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 2 HOH *25(H2 O) HELIX 1 1 LYS A 20 LYS A 28 1 9 HELIX 2 2 LYS A 35 THR A 53 1 19 HELIX 3 3 PRO A 57 ASN A 67 5 11 HELIX 4 4 PRO A 92 LEU A 109 1 18 HELIX 5 5 GLU A 117 ASN A 128 1 12 HELIX 6 6 ALA A 132 GLU A 145 1 14 SHEET 1 A 2 LEU A 72 ARG A 75 0 SHEET 2 A 2 VAL A 86 GLU A 89 -1 N VAL A 88 O GLU A 73 LINK C ILE A 29 N MSE A 30 1555 1555 1.33 LINK C MSE A 30 N ILE A 31 1555 1555 1.33 LINK C PRO A 57 N MSE A 58 1555 1555 1.31 LINK C MSE A 58 N GLU A 59 1555 1555 1.32 LINK C VAL A 68 N MSE A 69 1555 1555 1.32 LINK C MSE A 69 N PRO A 70 1555 1555 1.35 LINK C THR A 114 N MSE A 115 1555 1555 1.34 LINK C MSE A 115 N GLU A 116 1555 1555 1.33 LINK C ILE A 123 N MSE A 124 1555 1555 1.32 LINK C MSE A 124 N ASP A 125 1555 1555 1.33 LINK C LYS A 142 N MSE A 143 1555 1555 1.33 LINK C MSE A 143 N ALA A 144 1555 1555 1.32 CRYST1 54.400 131.020 29.150 90.00 90.00 90.00 P 21 21 2 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 0.018382 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007632 0.000000 0.00000 SCALE3 0.000000 0.000000 0.034305 0.00000