HEADER RIBOSOMAL PROTEIN 20-FEB-18 6FSW TITLE STRUCTURE OF ARCHAEOGLOBUS FULGIDUS SBDS PROTEIN AT 1.9 ANGSTROM COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSOME MATURATION PROTEIN SDO1-LIKE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARCHAEOGLOBUS FULGIDUS; SOURCE 3 ORGANISM_TAXID: 2234; SOURCE 4 GENE: XD40_1041, XD48_1723; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SBDS, CONFORMATIONAL FLEXIBILITY, RIBOSOMAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.MAZZORANA,J.FOADI,D.SILIQI,N.SANCHEZ-PUIG REVDAT 2 17-JAN-24 6FSW 1 REMARK REVDAT 1 21-MAR-18 6FSW 0 JRNL AUTH D.SILIQI,J.FOADI,M.MAZZORANA,D.ALTAMURA,A.MENDEZ GODOY, JRNL AUTH 2 N.SANCHEZ PUIG JRNL TITL CONFORMATIONAL FLEXIBILITY OF PROTEINS INVOLVED IN RIBOSOME JRNL TITL 2 BIOGENESIS: INVESTIGATIONS VIA SMALL ANGLE X-RAY SCATTERING JRNL TITL 3 (SAXS) JRNL REF CRYSTALS V. 8 109 2018 JRNL REFN ESSN 2073-4352 JRNL DOI 10.3390/CRYST8030109 REMARK 2 REMARK 2 RESOLUTION. 1.90 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 21716 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.760 REMARK 3 FREE R VALUE TEST SET COUNT : 1034 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 36.7149 - 3.6336 0.97 3033 132 0.1522 0.1689 REMARK 3 2 3.6336 - 2.8844 0.97 2999 148 0.2135 0.2485 REMARK 3 3 2.8844 - 2.5199 0.96 2973 158 0.2289 0.2865 REMARK 3 4 2.5199 - 2.2896 0.96 2965 140 0.2318 0.2795 REMARK 3 5 2.2896 - 2.1255 0.94 2922 150 0.2504 0.2833 REMARK 3 6 2.1255 - 2.0002 0.93 2892 163 0.2471 0.2820 REMARK 3 7 2.0002 - 1.9000 0.94 2898 143 0.2699 0.3091 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.580 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.008 1896 REMARK 3 ANGLE : 0.824 2545 REMARK 3 CHIRALITY : 0.054 283 REMARK 3 PLANARITY : 0.005 331 REMARK 3 DIHEDRAL : 8.113 1674 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 5 THROUGH 49 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.5542 11.1137 7.8944 REMARK 3 T TENSOR REMARK 3 T11: 0.2140 T22: 0.3418 REMARK 3 T33: 0.2803 T12: -0.0013 REMARK 3 T13: 0.0165 T23: -0.0436 REMARK 3 L TENSOR REMARK 3 L11: 0.9837 L22: 1.3637 REMARK 3 L33: 0.9449 L12: 0.6806 REMARK 3 L13: 0.1525 L23: 0.5874 REMARK 3 S TENSOR REMARK 3 S11: -0.0677 S12: -0.0926 S13: 0.2126 REMARK 3 S21: -0.0336 S22: -0.0201 S23: 0.0388 REMARK 3 S31: -0.0697 S32: -0.0221 S33: 0.0001 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 50 THROUGH 90 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.3023 13.4073 10.0893 REMARK 3 T TENSOR REMARK 3 T11: 0.2829 T22: 0.3426 REMARK 3 T33: 0.2825 T12: -0.0308 REMARK 3 T13: -0.0123 T23: -0.0097 REMARK 3 L TENSOR REMARK 3 L11: 1.7137 L22: 0.2060 REMARK 3 L33: 0.5800 L12: 1.1839 REMARK 3 L13: 0.3839 L23: 0.1306 REMARK 3 S TENSOR REMARK 3 S11: -0.0319 S12: 0.2508 S13: -0.1889 REMARK 3 S21: 0.0102 S22: 0.1721 S23: -0.1276 REMARK 3 S31: -0.0810 S32: 0.1892 S33: -0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 91 THROUGH 155 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.9960 -3.3123 -10.1117 REMARK 3 T TENSOR REMARK 3 T11: 0.3522 T22: 0.2880 REMARK 3 T33: 0.3130 T12: -0.0224 REMARK 3 T13: -0.0410 T23: 0.0153 REMARK 3 L TENSOR REMARK 3 L11: 0.7692 L22: 1.7965 REMARK 3 L33: 1.4538 L12: 0.3210 REMARK 3 L13: -0.0638 L23: 0.3911 REMARK 3 S TENSOR REMARK 3 S11: 0.1962 S12: -0.2321 S13: -0.2385 REMARK 3 S21: -0.1409 S22: -0.0151 S23: 0.1845 REMARK 3 S31: 0.2330 S32: -0.1797 S33: -0.0001 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 156 THROUGH 236 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.8595 12.5626 -25.1209 REMARK 3 T TENSOR REMARK 3 T11: 0.3406 T22: 0.2413 REMARK 3 T33: 0.3473 T12: 0.0385 REMARK 3 T13: 0.0614 T23: 0.0496 REMARK 3 L TENSOR REMARK 3 L11: 0.1325 L22: 1.9490 REMARK 3 L33: 2.1547 L12: -0.9007 REMARK 3 L13: 1.7831 L23: -0.1679 REMARK 3 S TENSOR REMARK 3 S11: -0.1476 S12: 0.0566 S13: -0.1803 REMARK 3 S21: 0.3290 S22: 0.1164 S23: 0.3493 REMARK 3 S31: -0.1803 S32: -0.0810 S33: 0.0012 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 6FSW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-FEB-18. REMARK 100 THE DEPOSITION ID IS D_1200008133. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-FEB-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9686 REMARK 200 MONOCHROMATOR : NULL 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 : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28569 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.730 REMARK 200 RESOLUTION RANGE LOW (A) : 36.710 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 200 DATA REDUNDANCY : 1.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.17800 REMARK 200 FOR THE DATA SET : 5.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.73 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.77 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) : 0.64800 REMARK 200 FOR SHELL : NULL 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: 1T95 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.02M 1,6-HEXANEDIOL; 0.02M 1-BUTANOL; REMARK 280 0.02M 1,2-PROPANEDIOL; 0.02M 2- PROPANOL; 0.02M 1,4-BUTANEDIOL; REMARK 280 0.02M 1,3-PROPANEDIOL;0.05 M IMIDAZOLE; 0.05 M MES; 12.5% V/V REMARK 280 MPD; 12.5% PEG 1000; 12.5% W/V PEG 3350, PH 6.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: 280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 2.0 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 GLY A 1 REMARK 465 HIS A 2 REMARK 465 MET A 3 REMARK 465 VAL A 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 301 DBREF1 6FSW A 3 236 UNP A0A101DZV9_ARCFL DBREF2 6FSW A A0A101DZV9 1 234 SEQADV 6FSW GLY A 1 UNP A0A101DZV EXPRESSION TAG SEQADV 6FSW HIS A 2 UNP A0A101DZV EXPRESSION TAG SEQADV 6FSW VAL A 62 UNP A0A101DZV ALA 60 CONFLICT SEQADV 6FSW ALA A 78 UNP A0A101DZV VAL 76 CONFLICT SEQRES 1 A 236 GLY HIS MET VAL SER LEU ASP LYS ALA VAL ILE ALA ARG SEQRES 2 A 236 LEU ARG LYS GLY GLY GLU GLU PHE GLU VAL LEU VAL ASP SEQRES 3 A 236 PRO TYR LEU ALA ARG ASP LEU LYS GLU GLY LYS GLU VAL SEQRES 4 A 236 ASN PHE GLU ASP LEU LEU ALA ALA GLU GLU VAL PHE LYS SEQRES 5 A 236 ASP ALA LYS LYS GLY GLU ARG ALA SER VAL ASP GLU LEU SEQRES 6 A 236 ARG LYS ILE PHE GLY THR ASP ASP VAL PHE GLU ILE ALA SEQRES 7 A 236 ARG LYS ILE ILE LEU GLU GLY GLU VAL GLN ILE THR ALA SEQRES 8 A 236 GLU GLN ARG ARG GLU MET LEU GLU ALA LYS ARG LYS GLN SEQRES 9 A 236 ILE ILE ASN PHE ILE SER ARG ASN THR ILE ASP PRO ARG SEQRES 10 A 236 THR ASN ALA PRO HIS PRO PRO SER ARG ILE GLU ARG ALA SEQRES 11 A 236 LEU GLU GLU ALA LYS VAL HIS ILE ASP ILE PHE LYS SER SEQRES 12 A 236 VAL GLU ALA GLN VAL LYS ASP ILE VAL LYS ALA LEU LYS SEQRES 13 A 236 PRO ILE LEU PRO LEU LYS PHE GLU GLU MET GLU ILE ALA SEQRES 14 A 236 ILE LYS ILE PRO PRO GLU HIS THR GLY ARG ALA ILE SER SEQRES 15 A 236 ALA LEU TYR ASN PHE GLY GLY VAL THR ARG GLU GLU TRP SEQRES 16 A 236 GLN ARG ASP GLY SER TRP ILE CYS VAL MET ARG ILE PRO SEQRES 17 A 236 SER GLY MET TYR GLY ASP LEU MET ASP LEU LEU GLY LYS SEQRES 18 A 236 VAL ALA LYS GLY GLU ALA LEU THR LYS VAL LEU ARG ARG SEQRES 19 A 236 ILE GLY HET PEG A 301 7 HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 2 PEG C4 H10 O3 FORMUL 3 HOH *81(H2 O) HELIX 1 AA1 ASP A 26 GLY A 36 1 11 HELIX 2 AA2 ASN A 40 LEU A 45 1 6 HELIX 3 AA3 SER A 61 GLY A 70 1 10 HELIX 4 AA4 ASP A 73 GLY A 85 1 13 HELIX 5 AA5 THR A 90 ASN A 112 1 23 HELIX 6 AA6 PRO A 123 LYS A 135 1 13 HELIX 7 AA7 SER A 143 LYS A 156 1 14 HELIX 8 AA8 PRO A 173 GLU A 175 5 3 HELIX 9 AA9 HIS A 176 GLY A 188 1 13 HELIX 10 AB1 MET A 211 LYS A 224 1 14 SHEET 1 AA1 3 GLU A 19 VAL A 25 0 SHEET 2 AA1 3 VAL A 10 LYS A 16 -1 N LYS A 16 O GLU A 19 SHEET 3 AA1 3 GLU A 86 VAL A 87 -1 O GLU A 86 N ARG A 13 SHEET 1 AA2 2 PHE A 51 ASP A 53 0 SHEET 2 AA2 2 GLU A 58 ARG A 59 -1 O GLU A 58 N LYS A 52 SHEET 1 AA3 2 THR A 113 ILE A 114 0 SHEET 2 AA3 2 LYS A 162 PHE A 163 -1 O LYS A 162 N ILE A 114 SHEET 1 AA4 4 VAL A 190 TRP A 195 0 SHEET 2 AA4 4 TRP A 201 PRO A 208 -1 O VAL A 204 N THR A 191 SHEET 3 AA4 4 GLU A 165 ILE A 172 -1 N ILE A 168 O MET A 205 SHEET 4 AA4 4 LEU A 228 ILE A 235 -1 O ILE A 235 N GLU A 165 SITE 1 AC1 3 ALA A 169 LEU A 228 LYS A 230 CRYST1 33.810 44.520 54.710 75.08 84.52 69.72 P 1 1 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 0.029577 -0.010929 -0.000218 0.00000 SCALE2 0.000000 0.023946 -0.005928 0.00000 SCALE3 0.000000 0.000000 0.018916 0.00000