HEADER PROTEIN FIBRIL 08-APR-18 6G8E TITLE CRYSTAL STRUCTURE OF THE AMYLOID-LIKE VTQVGF SEGMENT FROM THE R5 TITLE 2 REPEAT OF THE E. COLI BIOFILM-ASSOCIATED CSGA CURLI PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAJOR CURLIN SUBUNIT; COMPND 3 CHAIN: B, A; COMPND 4 FRAGMENT: AMYLOID SPINE SEGMENT VTQVGF FROM CSGA (RESIDUES 137-142) COMPND 5 SECRETED BY E. COLI; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 4 ORGANISM_TAXID: 83333; SOURCE 5 OTHER_DETAILS: VTQVGF FROM CSGA, SYNTHESIZED KEYWDS BACTERIAL STERIC-ZIPPER CROSS-BETA AMYLOID FIBRIL FROM E. COLI, KEYWDS 2 PROTEIN FIBRIL EXPDTA X-RAY DIFFRACTION AUTHOR M.LANDAU,S.PEROV REVDAT 3 25-DEC-19 6G8E 1 REMARK REVDAT 2 23-OCT-19 6G8E 1 JRNL REVDAT 1 24-APR-19 6G8E 0 JRNL AUTH S.PEROV,O.LIDOR,N.SALINAS,N.GOLAN,E.TAYEB-FLIGELMAN, JRNL AUTH 2 M.DESHMUKH,D.WILLBOLD,M.LANDAU JRNL TITL STRUCTURAL INSIGHTS INTO CURLI CSGA CROSS-BETA FIBRIL JRNL TITL 2 ARCHITECTURE INSPIRE REPURPOSING OF ANTI-AMYLOID COMPOUNDS JRNL TITL 3 AS ANTI-BIOFILM AGENTS. JRNL REF PLOS PATHOG. V. 15 07978 2019 JRNL REFN ESSN 1553-7374 JRNL PMID 31469892 JRNL DOI 10.1371/JOURNAL.PPAT.1007978 REMARK 2 REMARK 2 RESOLUTION. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.93 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 698 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 + TEST SET) : 0.124 REMARK 3 R VALUE (WORKING SET) : 0.123 REMARK 3 FREE R VALUE : 0.132 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 78 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 92 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 6 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.64 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.47 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.89000 REMARK 3 B22 (A**2) : -0.20000 REMARK 3 B33 (A**2) : -0.58000 REMARK 3 B12 (A**2) : 0.03000 REMARK 3 B13 (A**2) : 0.14000 REMARK 3 B23 (A**2) : -0.36000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.123 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.087 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.058 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.896 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 6G8E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-APR-18. REMARK 100 THE DEPOSITION ID IS D_1200009573. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-SEP-15 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 PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 776 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 19.930 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 6.923 REMARK 200 R MERGE (I) : 0.27500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.0200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.82 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.52 REMARK 200 R MERGE FOR SHELL (I) : 0.44200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.180 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 BETA-STRAND REMARK 200 REMARK 200 REMARK: NEEDLE-LIKE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 13.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RESERVOIR CONTAINED 3.0 M SODIUM REMARK 280 CHLORIDE AND 0.1 M BIS-TRIS PH 5.5, VAPOR DIFFUSION, HANGING REMARK 280 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: OCTADECAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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: B, A REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 4.81000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, A REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 9.62000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, A REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 14.43000 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, A REMARK 350 BIOMT1 5 1.000000 0.000000 0.000000 19.24000 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, A REMARK 350 BIOMT1 6 1.000000 0.000000 0.000000 -4.81000 REMARK 350 BIOMT2 6 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, A REMARK 350 BIOMT1 7 1.000000 0.000000 0.000000 -9.62000 REMARK 350 BIOMT2 7 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 7 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, A REMARK 350 BIOMT1 8 1.000000 0.000000 0.000000 -14.43000 REMARK 350 BIOMT2 8 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 8 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, A REMARK 350 BIOMT1 9 1.000000 0.000000 0.000000 -19.24000 REMARK 350 BIOMT2 9 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 9 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 103 O HOH A 103 1664 2.19 REMARK 500 REMARK 500 REMARK: NULL DBREF 6G8E B 1 6 UNP P28307 CSGA_ECOLI 137 142 DBREF 6G8E A 1 6 UNP P28307 CSGA_ECOLI 137 142 SEQRES 1 B 6 VAL THR GLN VAL GLY PHE SEQRES 1 A 6 VAL THR GLN VAL GLY PHE FORMUL 3 HOH *6(H2 O) CRYST1 4.810 19.340 21.900 65.82 83.72 83.20 P 1 2 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 0.207900 -0.024776 -0.014096 0.00000 SCALE2 0.000000 0.052072 -0.022853 0.00000 SCALE3 0.000000 0.000000 0.050167 0.00000