HEADER RIBOSOME 08-DEC-22 8BXA TITLE CRYSTAL STRUCTURE OF RIBOSOME BINDING FACTOR A (RBFA) FROM S. AUREUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSOME-BINDING FACTOR A; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS NCTC 8325; SOURCE 3 ORGANISM_TAXID: 93061; SOURCE 4 GENE: RBFA, SAOUHSC_01247; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS RIBOSOME, MATURATION, 30S SUBUNIT, S. AUREUS EXPDTA X-RAY DIFFRACTION AUTHOR B.FATKHULLIN,A.BIKMULLIN,A.GABDULKHAKOV,I.KHUSAINOV,S.VALIDOV, AUTHOR 2 K.USACHEV,M.YUSUPOV REVDAT 1 22-FEB-23 8BXA 0 JRNL AUTH A.G.BIKMULLIN,B.FATKHULLIN,A.STETSENKO,A.GABDULKHAKOV, JRNL AUTH 2 N.GARAEVA,L.NURULLINA,E.KLOCHKOVA,A.GOLUBEV,I.KHUSAINOV, JRNL AUTH 3 N.TRACHTMANN,D.BLOKHIN,A.GUSKOV,S.VALIDOV,K.USACHEV, JRNL AUTH 4 M.YUSUPOV JRNL TITL YET ANOTHER SIMILARITY BETWEEN MITOCHONDRIAL AND BACTERIAL JRNL TITL 2 RIBOSOMAL SMALL SUBUNIT BIOGENESIS OBTAINED BY STRUCTURAL JRNL TITL 3 CHARACTERIZATION OF RBFA FROM S. AUREUS. JRNL REF INT J MOL SCI V. 24 2023 JRNL REFN ESSN 1422-0067 JRNL PMID 36768442 JRNL DOI 10.3390/IJMS24032118 REMARK 2 REMARK 2 RESOLUTION. 2.22 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.22 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 5909 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 296 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 46.1800 - 2.8000 1.00 2856 151 0.1865 0.2287 REMARK 3 2 2.8000 - 2.2200 1.00 2757 145 0.2516 0.3297 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.580 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 49.47 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.79 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 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 : 0.009 848 REMARK 3 ANGLE : 1.006 1137 REMARK 3 CHIRALITY : 0.053 130 REMARK 3 PLANARITY : 0.005 147 REMARK 3 DIHEDRAL : 16.314 343 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 8BXA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-DEC-22. REMARK 100 THE DEPOSITION ID IS D_1292127210. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-OCT-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.991872 REMARK 200 MONOCHROMATOR : M REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5910 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.220 REMARK 200 RESOLUTION RANGE LOW (A) : 46.180 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.05850 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.22 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.78280 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.440 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES PH 6.5, 80 MM MANGANESE(II) REMARK 280 CHLORIDE, 15% PEG 20000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 13.64350 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 6.82175 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 20.46525 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 TYR A 100 REMARK 465 GLY A 101 REMARK 465 ASN A 102 REMARK 465 LYS A 103 REMARK 465 ILE A 104 REMARK 465 GLU A 105 REMARK 465 ARG A 106 REMARK 465 MET A 107 REMARK 465 ILE A 108 REMARK 465 GLN A 109 REMARK 465 ASP A 110 REMARK 465 LEU A 111 REMARK 465 HIS A 112 REMARK 465 LYS A 113 REMARK 465 GLN A 114 REMARK 465 ASP A 115 REMARK 465 ARG A 116 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 SER A 2 86.36 -156.81 REMARK 500 REMARK 500 REMARK: NULL DBREF 8BXA A 1 116 UNP Q2G2Q4 RBFA_STAA8 1 116 SEQRES 1 A 116 MET SER SER MET ARG ALA GLU ARG VAL GLY GLU GLN MET SEQRES 2 A 116 LYS LYS GLU LEU MET ASP ILE ILE ASN ASN LYS VAL LYS SEQRES 3 A 116 ASP PRO ARG VAL GLY PHE ILE THR ILE THR ASP VAL VAL SEQRES 4 A 116 LEU THR ASN ASP LEU SER GLN ALA LYS VAL PHE LEU THR SEQRES 5 A 116 VAL LEU GLY ASN ASP LYS GLU VAL GLU ASN THR PHE LYS SEQRES 6 A 116 ALA LEU ASP LYS ALA LYS GLY PHE ILE LYS SER GLU LEU SEQRES 7 A 116 GLY SER ARG MET ARG LEU ARG ILE MET PRO GLU LEU MET SEQRES 8 A 116 TYR GLU TYR ASP GLN SER ILE GLU TYR GLY ASN LYS ILE SEQRES 9 A 116 GLU ARG MET ILE GLN ASP LEU HIS LYS GLN ASP ARG FORMUL 2 HOH *14(H2 O) HELIX 1 AA1 SER A 3 VAL A 25 1 23 HELIX 2 AA2 ASN A 56 ALA A 70 1 15 HELIX 3 AA3 ALA A 70 SER A 80 1 11 SHEET 1 AA1 3 THR A 34 LEU A 40 0 SHEET 2 AA1 3 GLN A 46 THR A 52 -1 O LYS A 48 N VAL A 39 SHEET 3 AA1 3 GLU A 89 TYR A 94 1 O MET A 91 N VAL A 49 CRYST1 65.315 65.315 27.287 90.00 90.00 90.00 P 41 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 0.015310 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015310 0.000000 0.00000 SCALE3 0.000000 0.000000 0.036647 0.00000