HEADER PROTEIN FIBRIL 09-JAN-18 6FG4 TITLE CRYSTAL STRUCTURE OF THE AMYLOID-LIKE IIKVIK SEGMENT FROM THE S. TITLE 2 AUREUS BIOFILM-ASSOCIATED PSMALPHA1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHENOL-SOLUBLE MODULIN ALPHA 1 PEPTIDE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: AMYLOID SPINE SEGMENT IIKVIK FROM PSMALPHA1 (RESIDUES 7-12) COMPND 5 SECRETED BY S. AUREUS; COMPND 6 SYNONYM: PSM ALPHA-1; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 4 ORGANISM_TAXID: 1280; SOURCE 5 OTHER_DETAILS: IIKVIK FROM PSMALPHA1, SYNTHESIZED KEYWDS STERIC-ZIPPER, CROSS-BETA, BACTERIAL AMYLOID FIBRIL, S. AUREUS, PSM, KEYWDS 2 PROTEIN FIBRIL EXPDTA X-RAY DIFFRACTION AUTHOR M.LANDAU,J.-P.COLLETIER REVDAT 4 30-MAR-22 6FG4 1 REMARK REVDAT 3 25-DEC-19 6FG4 1 REMARK REVDAT 2 12-SEP-18 6FG4 1 JRNL REVDAT 1 08-AUG-18 6FG4 0 JRNL AUTH N.SALINAS,J.P.COLLETIER,A.MOSHE,M.LANDAU JRNL TITL EXTREME AMYLOID POLYMORPHISM IN STAPHYLOCOCCUS AUREUS JRNL TITL 2 VIRULENT PSM ALPHA PEPTIDES. JRNL REF NAT COMMUN V. 9 3512 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 30158633 JRNL DOI 10.1038/S41467-018-05490-0 REMARK 2 REMARK 2 RESOLUTION. 1.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.38 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 3 NUMBER OF REFLECTIONS : 1863 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 207 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 50 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 2 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.35 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.93 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.27000 REMARK 3 B22 (A**2) : 0.05000 REMARK 3 B33 (A**2) : 0.07000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.20000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.048 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.046 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.029 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.313 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6FG4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1200008248. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-OCT-14 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 : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8729 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2070 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 18.380 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 200 DATA REDUNDANCY : 11.16 REMARK 200 R MERGE (I) : 0.13300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.1300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.13 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.44 REMARK 200 R MERGE FOR SHELL (I) : 0.75200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.140 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: IDEAL POLY-ALA BETA-STRAND REMARK 200 REMARK 200 REMARK: NEEDLE LIKE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 25.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RESERVOIR CONTAINED 15% POLYETHYLENE REMARK 280 GLYCOL 8,000: 0.5M LITHIUM SULFATE, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 22.63500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 2.40000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 22.63500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 2.40000 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: OCTADECAMERIC 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 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 -4.80000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 -9.60000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 -14.40000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 5 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 -19.20000 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 6 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 6 0.000000 1.000000 0.000000 4.80000 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 7 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 7 0.000000 1.000000 0.000000 9.60000 REMARK 350 BIOMT3 7 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 8 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 8 0.000000 1.000000 0.000000 14.40000 REMARK 350 BIOMT3 8 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 9 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 9 0.000000 1.000000 0.000000 19.20000 REMARK 350 BIOMT3 9 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 10 -1.000000 0.000000 0.000000 22.63500 REMARK 350 BIOMT2 10 0.000000 1.000000 0.000000 2.40000 REMARK 350 BIOMT3 10 0.000000 0.000000 -1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 11 -1.000000 0.000000 0.000000 22.63500 REMARK 350 BIOMT2 11 0.000000 1.000000 0.000000 -2.40000 REMARK 350 BIOMT3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 12 -1.000000 0.000000 0.000000 22.63500 REMARK 350 BIOMT2 12 0.000000 1.000000 0.000000 -7.20000 REMARK 350 BIOMT3 12 0.000000 0.000000 -1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 13 -1.000000 0.000000 0.000000 22.63500 REMARK 350 BIOMT2 13 0.000000 1.000000 0.000000 -12.00000 REMARK 350 BIOMT3 13 0.000000 0.000000 -1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 14 -1.000000 0.000000 0.000000 22.63500 REMARK 350 BIOMT2 14 0.000000 1.000000 0.000000 -16.80000 REMARK 350 BIOMT3 14 0.000000 0.000000 -1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 15 -1.000000 0.000000 0.000000 22.63500 REMARK 350 BIOMT2 15 0.000000 1.000000 0.000000 7.20000 REMARK 350 BIOMT3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 16 -1.000000 0.000000 0.000000 22.63500 REMARK 350 BIOMT2 16 0.000000 1.000000 0.000000 12.00000 REMARK 350 BIOMT3 16 0.000000 0.000000 -1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 17 -1.000000 0.000000 0.000000 22.63500 REMARK 350 BIOMT2 17 0.000000 1.000000 0.000000 16.80000 REMARK 350 BIOMT3 17 0.000000 0.000000 -1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 18 -1.000000 0.000000 0.000000 22.63500 REMARK 350 BIOMT2 18 0.000000 1.000000 0.000000 21.60000 REMARK 350 BIOMT3 18 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 O3 SO4 A 101 LIES ON A SPECIAL POSITION. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 102 DBREF 6FG4 A 1 6 UNP H9BRQ5 H9BRQ5_STAAU 7 12 SEQRES 1 A 6 ILE ILE LYS VAL ILE LYS HET SO4 A 101 5 HET SO4 A 102 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 HOH *2(H2 O) SITE 1 AC1 3 ILE A 1 LYS A 3 LYS A 6 SITE 1 AC2 3 ILE A 1 LYS A 6 HOH A 201 CRYST1 45.270 4.800 22.900 90.00 107.65 90.00 C 1 2 1 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 0.022090 0.000000 0.007028 0.00000 SCALE2 0.000000 0.208333 0.000000 0.00000 SCALE3 0.000000 0.000000 0.045825 0.00000