HEADER RIBOSOMAL PROTEIN/RNA 17-APR-14 4PDB TITLE CRYSTAL STRUCTURE OF BACILLUS ANTHRACIS RIBOSOMAL PROTEIN S8 IN TITLE 2 COMPLEX WITH AN RNA APTAMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: 30S RIBOSOMAL PROTEIN S8; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: SELEX RNA APTAMER; COMPND 7 CHAIN: I; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS ANTHRACIS; SOURCE 3 ORGANISM_TAXID: 260799; SOURCE 4 STRAIN: STERNE; SOURCE 5 GENE: RPSH; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-GOLD(DE3)PLYSS AG; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-28B; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630 KEYWDS PROTEIN-RNA COMPLEX SELEX BASE TRIPLE TRANSLATION, RIBOSOMAL PROTEIN- KEYWDS 2 RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.DAVLIEVA,Y.SHAMOO,E.P.NIKONOWICZ REVDAT 6 27-DEC-23 4PDB 1 REMARK REVDAT 5 11-DEC-19 4PDB 1 REMARK REVDAT 4 17-JUL-19 4PDB 1 REMARK REVDAT 3 27-SEP-17 4PDB 1 SOURCE JRNL REMARK REVDAT 2 01-OCT-14 4PDB 1 JRNL REVDAT 1 03-SEP-14 4PDB 0 JRNL AUTH M.DAVLIEVA,J.DONARSKI,J.WANG,Y.SHAMOO,E.P.NIKONOWICZ JRNL TITL STRUCTURE ANALYSIS OF FREE AND BOUND STATES OF AN RNA JRNL TITL 2 APTAMER AGAINST RIBOSOMAL PROTEIN S8 FROM BACILLUS JRNL TITL 3 ANTHRACIS. JRNL REF NUCLEIC ACIDS RES. V. 42 10795 2014 JRNL REFN ESSN 1362-4962 JRNL PMID 25140011 JRNL DOI 10.1093/NAR/GKU743 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.22 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 9325 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.810 REMARK 3 FREE R VALUE TEST SET COUNT : 471 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 3.7482 - 2.9761 1.00 3059 160 0.2171 0.2951 REMARK 3 2 2.9761 - 2.6002 1.00 3049 148 0.2828 0.3784 REMARK 3 3 2.6660 - 2.5990 1.00 3211 163 0.1544 0.2230 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.197 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.950 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.43 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -13.52000 REMARK 3 B22 (A**2) : 6.95000 REMARK 3 B33 (A**2) : 6.57000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 1937 REMARK 3 ANGLE : 1.260 2796 REMARK 3 CHIRALITY : 0.051 350 REMARK 3 PLANARITY : 0.005 216 REMARK 3 DIHEDRAL : 17.174 859 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4PDB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-APR-14. REMARK 100 THE DEPOSITION ID IS D_1000201180. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-AUG-09 REMARK 200 TEMPERATURE (KELVIN) : 103 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 4.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976 REMARK 200 MONOCHROMATOR : ROSENBAUM-ROCK DOUBLE CRYSTAL REMARK 200 SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NOIR-1 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9796 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.080 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.73 REMARK 200 R MERGE FOR SHELL (I) : 0.64300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.3 M DI-AMMONIUM HYDROGEN CITRATE, REMARK 280 100 MM SODIUM CHLORIDE, 16% PEG 3350, 10 MM SPERMIDINE, PH 7.0, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 283K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 27.70500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.12500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.63500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.12500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.70500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.63500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, I 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 GLY A 2 REMARK 465 SER A 3 REMARK 465 SER A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 HIS A 8 REMARK 465 HIS A 9 REMARK 465 HIS A 10 REMARK 465 SER A 11 REMARK 465 SER A 12 REMARK 465 GLY A 13 REMARK 465 LEU A 14 REMARK 465 VAL A 15 REMARK 465 PRO A 16 REMARK 465 ARG A 17 REMARK 465 GLY A 18 REMARK 465 SER A 19 REMARK 465 HIS A 20 REMARK 465 MET A 21 REMARK 465 ALA A 22 REMARK 465 SER A 23 REMARK 465 MET A 24 REMARK 465 VAL A 25 REMARK 465 MET A 26 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 211 O HOH A 212 2.19 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 77 13.04 -156.79 REMARK 500 ASN A 78 12.95 50.13 REMARK 500 LYS A 79 -111.38 -105.72 REMARK 500 ASN A 92 62.91 -100.79 REMARK 500 ILE A 103 -80.31 -103.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2LUN RELATED DB: PDB REMARK 900 CONTAINS THE SOLUTION NMR STRUCTURE OF THE RNA APTAMER DBREF 4PDB A 24 155 UNP W0CSD8 W0CSD8_BACAN 1 132 DBREF 4PDB I 1 38 PDB 4PDB 4PDB 1 38 SEQADV 4PDB MET A 1 UNP W0CSD8 EXPRESSION TAG SEQADV 4PDB GLY A 2 UNP W0CSD8 EXPRESSION TAG SEQADV 4PDB SER A 3 UNP W0CSD8 EXPRESSION TAG SEQADV 4PDB SER A 4 UNP W0CSD8 EXPRESSION TAG SEQADV 4PDB HIS A 5 UNP W0CSD8 EXPRESSION TAG SEQADV 4PDB HIS A 6 UNP W0CSD8 EXPRESSION TAG SEQADV 4PDB HIS A 7 UNP W0CSD8 EXPRESSION TAG SEQADV 4PDB HIS A 8 UNP W0CSD8 EXPRESSION TAG SEQADV 4PDB HIS A 9 UNP W0CSD8 EXPRESSION TAG SEQADV 4PDB HIS A 10 UNP W0CSD8 EXPRESSION TAG SEQADV 4PDB SER A 11 UNP W0CSD8 EXPRESSION TAG SEQADV 4PDB SER A 12 UNP W0CSD8 EXPRESSION TAG SEQADV 4PDB GLY A 13 UNP W0CSD8 EXPRESSION TAG SEQADV 4PDB LEU A 14 UNP W0CSD8 EXPRESSION TAG SEQADV 4PDB VAL A 15 UNP W0CSD8 EXPRESSION TAG SEQADV 4PDB PRO A 16 UNP W0CSD8 EXPRESSION TAG SEQADV 4PDB ARG A 17 UNP W0CSD8 EXPRESSION TAG SEQADV 4PDB GLY A 18 UNP W0CSD8 EXPRESSION TAG SEQADV 4PDB SER A 19 UNP W0CSD8 EXPRESSION TAG SEQADV 4PDB HIS A 20 UNP W0CSD8 EXPRESSION TAG SEQADV 4PDB MET A 21 UNP W0CSD8 EXPRESSION TAG SEQADV 4PDB ALA A 22 UNP W0CSD8 EXPRESSION TAG SEQADV 4PDB SER A 23 UNP W0CSD8 EXPRESSION TAG SEQRES 1 A 155 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 155 LEU VAL PRO ARG GLY SER HIS MET ALA SER MET VAL MET SEQRES 3 A 155 THR ASP PRO ILE ALA ASP MET LEU THR ARG ILE ARG ASN SEQRES 4 A 155 ALA ASN MET VAL ARG HIS GLU LYS LEU GLU VAL PRO ALA SEQRES 5 A 155 SER LYS ILE LYS LYS GLU ILE ALA GLU LEU LEU LYS ARG SEQRES 6 A 155 GLU GLY PHE ILE ARG ASP VAL GLU TYR ILE GLU ASP ASN SEQRES 7 A 155 LYS GLN GLY ILE LEU ARG ILE PHE LEU LYS TYR GLY ALA SEQRES 8 A 155 ASN ASN GLU ARG VAL ILE THR GLY LEU LYS ARG ILE SER SEQRES 9 A 155 LYS PRO GLY LEU ARG VAL TYR ALA LYS ALA ASP GLU VAL SEQRES 10 A 155 PRO ARG VAL LEU ASN GLY LEU GLY ILE ALA LEU VAL SER SEQRES 11 A 155 THR SER LYS GLY VAL MET THR ASP LYS ASP ALA ARG GLN SEQRES 12 A 155 LEU GLN THR GLY GLY GLU VAL VAL ALA TYR VAL TRP SEQRES 1 I 38 G G G A U G C U C A G U G SEQRES 2 I 38 A U C C U U C G G G A U A SEQRES 3 I 38 U C A G G G C A U C C C FORMUL 3 HOH *17(H2 O) HELIX 1 AA1 ASP A 28 VAL A 43 1 16 HELIX 2 AA2 SER A 53 GLU A 66 1 14 HELIX 3 AA3 VAL A 120 LEU A 124 5 5 HELIX 4 AA4 THR A 137 GLN A 145 1 9 SHEET 1 AA1 3 LYS A 47 PRO A 51 0 SHEET 2 AA1 3 ILE A 82 LEU A 87 -1 O LEU A 83 N VAL A 50 SHEET 3 AA1 3 ILE A 69 ILE A 75 -1 N ASP A 71 O PHE A 86 SHEET 1 AA2 3 LEU A 100 ARG A 102 0 SHEET 2 AA2 3 GLY A 148 VAL A 154 -1 O TYR A 153 N LYS A 101 SHEET 3 AA2 3 TYR A 111 ALA A 112 -1 N ALA A 112 O GLY A 148 SHEET 1 AA3 4 LEU A 100 ARG A 102 0 SHEET 2 AA3 4 GLY A 148 VAL A 154 -1 O TYR A 153 N LYS A 101 SHEET 3 AA3 4 ILE A 126 THR A 131 -1 N ILE A 126 O VAL A 154 SHEET 4 AA3 4 GLY A 134 MET A 136 -1 O MET A 136 N VAL A 129 CRYST1 55.410 59.270 92.250 90.00 90.00 90.00 P 21 21 21 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 0.018047 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016872 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010840 0.00000