HEADER PROTEIN FIBRIL 24-JAN-07 2ONW TITLE STRUCTURE OF SSTSSA, A FIBRIL FORMING PEPTIDE FROM BOVINE PANCREATIC TITLE 2 RIBONUCLEASE (RNASE A, RESIDUES 15-20) COMPND MOL_ID: 1; COMPND 2 MOLECULE: FIBRIL FORMING PEPTIDE FROM BOVINE PANCREATIC RIBONUCLEASE COMPND 3 (RNASE A); COMPND 4 CHAIN: X; COMPND 5 FRAGMENT: HINGE LOOP REGION (RESIDUES 15-20); COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE PEPTIDE SSTSAA WAS COMMERCIALLY SYNTHESIZED. KEYWDS PARALLEL FACE-TO-FACE-UP/UP BETA SHEETS, STERIC ZIPPER, PROTEIN KEYWDS 2 FIBRIL EXPDTA X-RAY DIFFRACTION AUTHOR S.SAMBASHIVAN,M.R.SAWAYA,D.EISENBERG REVDAT 4 18-OCT-17 2ONW 1 REMARK REVDAT 3 24-FEB-09 2ONW 1 VERSN REVDAT 2 05-JUN-07 2ONW 1 JRNL REVDAT 1 06-FEB-07 2ONW 0 JRNL AUTH M.R.SAWAYA,S.SAMBASHIVAN,R.NELSON,M.I.IVANOVA,S.A.SIEVERS, JRNL AUTH 2 M.I.APOSTOL,M.J.THOMPSON,M.BALBIRNIE,J.J.WILTZIUS, JRNL AUTH 3 H.T.MCFARLANE,A.O.MADSEN,C.RIEKEL,D.EISENBERG JRNL TITL ATOMIC STRUCTURES OF AMYLOID CROSS-BETA SPINES REVEAL VARIED JRNL TITL 2 STERIC ZIPPERS. JRNL REF NATURE V. 447 453 2007 JRNL REFN ISSN 0028-0836 JRNL PMID 17468747 JRNL DOI 10.1038/NATURE05695 REMARK 2 REMARK 2 RESOLUTION. 1.51 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.51 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.6 REMARK 3 NUMBER OF REFLECTIONS : 458 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) : 0.159 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 21 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.51 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.55 REMARK 3 REFLECTION IN BIN (WORKING SET) : 25 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 66.67 REMARK 3 BIN R VALUE (WORKING SET) : 0.2490 REMARK 3 BIN FREE R VALUE SET COUNT : 1 REMARK 3 BIN FREE R VALUE : 0.7230 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 36 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 1 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 6.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 5.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.97000 REMARK 3 B22 (A**2) : -0.02000 REMARK 3 B33 (A**2) : 0.99000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.151 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.102 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.040 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.481 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.973 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.903 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 35 ; 0.004 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 30 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 47 ; 1.087 ; 1.983 REMARK 3 BOND ANGLES OTHERS (DEGREES): 70 ; 0.693 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 5 ; 5.242 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 4 ; 5.467 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 7 ; 0.064 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 39 ; 0.001 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 5 ; 0.000 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): 11 ; 0.207 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 16 ; 0.122 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 23 ; 0.093 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 5 ; 0.053 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 9 ; 0.307 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 1 ; 0.060 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 36 ; 0.488 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 14 ; 0.164 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 46 ; 0.615 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 5 ; 0.243 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1 ; 0.137 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 71 ; 0.409 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 1 ; 0.344 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 66 ; 0.714 ; 3.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2ONW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JAN-07. REMARK 100 THE DEPOSITION ID IS D_1000041368. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID13 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9466 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 474 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 80.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.17400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.62 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.43400 REMARK 200 R SYM FOR SHELL (I) : NULL 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: X-PLOR REMARK 200 STARTING MODEL: 5 RESIDUE BETA STRAND SSTSA WITH THE C-TERMINAL REMARK 200 ALANINE ABSENT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEPTIDE CONCENTRATION: 30 MG/ML, REMARK 280 RESERVOIR: 0.1M HEPES-NA, PH 7.5, 10% V/V ISOPROPANOL, 20% REMARK 280 PEG4000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 21.00400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 6.44400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 2.41500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 6.44400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.00400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 2.41500 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 300 REMARK: THE BIOLOGICAL UNIT IS A PAIR OF SHEETS. EACH SHEET IS REMARK 300 COMPRISED OF BETA STRANDS GENERATED BY UNIT CELL TRANSLATIONS ALONG REMARK 300 THE Y-AXIS. THE SECOND SHEET IN THE PAIR-OF-SHEET STRUCTURES IS REMARK 300 GENERATED BY APPLYING THE OPERATOR -X+1, Y+1/2, -Z+1/2. IN THE REMARK 300 SECOND SHEET ALSO, BETA STRANDS ARE GENERATED BY UNIT CELL REMARK 300 TRANSLATIONS ALONG THE Y-AXIS. 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: X 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 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 4.83000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 42.00800 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 2.41500 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 6.44400 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 42.00800 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 7.24500 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 6.44400 DBREF 2ONW X 1 6 PDB 2ONW 2ONW 1 6 SEQRES 1 X 6 SER SER THR SER ALA ALA FORMUL 2 HOH *(H2 O) CRYST1 42.008 4.830 12.888 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 0.023805 0.000000 0.000000 0.00000 SCALE2 0.000000 0.207039 0.000000 0.00000 SCALE3 0.000000 0.000000 0.077592 0.00000 MASTER 250 0 0 0 0 0 0 6 0 0 0 1 END