HEADER PROTEIN FIBRIL 08-JUL-10 3NVF TITLE IIHFGS SEGMENT 138-143 FROM HUMAN PRION COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAJOR PRION PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PRP, PRP27-30, PRP33-35C, ASCR; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606; SOURCE 6 OTHER_DETAILS: IIHFGS (UNP RESIDUES 138-143) FROM HUMAN PRION KEYWDS AMYLOID-LIKE PROTOFIBRIL, PROTEIN FIBRIL EXPDTA X-RAY DIFFRACTION AUTHOR M.I.APOSTOL,M.R.SAWAYA,D.EISENBERG REVDAT 3 21-FEB-24 3NVF 1 REMARK REVDAT 2 13-APR-11 3NVF 1 JRNL REVDAT 1 02-MAR-11 3NVF 0 JRNL AUTH M.I.APOSTOL,J.J.WILTZIUS,M.R.SAWAYA,D.CASCIO,D.EISENBERG JRNL TITL ATOMIC STRUCTURES SUGGEST DETERMINANTS OF TRANSMISSION JRNL TITL 2 BARRIERS IN MAMMALIAN PRION DISEASE. JRNL REF BIOCHEMISTRY V. 50 2456 2011 JRNL REFN ISSN 0006-2960 JRNL PMID 21323366 JRNL DOI 10.1021/BI101803K REMARK 2 REMARK 2 RESOLUTION. 1.80 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 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.4 REMARK 3 NUMBER OF REFLECTIONS : 433 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) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.200 REMARK 3 FREE R VALUE TEST SET COUNT : 40 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 5 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.01 REMARK 3 REFLECTION IN BIN (WORKING SET) : 87 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 72.22 REMARK 3 BIN R VALUE (WORKING SET) : 0.3820 REMARK 3 BIN FREE R VALUE SET COUNT : 4 REMARK 3 BIN FREE R VALUE : 0.3300 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 48 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.82 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.00000 REMARK 3 B22 (A**2) : -0.04000 REMARK 3 B33 (A**2) : -0.95000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.167 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.111 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.009 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 56 ; 0.009 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 35 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 75 ; 1.657 ; 2.043 REMARK 3 BOND ANGLES OTHERS (DEGREES): 84 ; 0.693 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 5 ; 9.100 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 2 ;52.201 ;20.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 7 ;10.817 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 8 ; 0.053 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 52 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 12 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 29 ; 0.523 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 12 ; 0.157 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 46 ; 0.853 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 27 ; 1.220 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 29 ; 1.673 ; 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): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL 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 3NVF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JUL-10. REMARK 100 THE DEPOSITION ID IS D_1000060327. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 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) : 0.8726 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 443 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 90.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.4 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.21600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 67.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.70 REMARK 200 R MERGE FOR SHELL (I) : 0.39500 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: PHASER 1.3.2 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 19.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM TRIS PH 7.4, 25% MPD, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 13.77300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.50850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 13.77300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 15.50850 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: DECAMERIC 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 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 9.60800 REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 4.80400 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 -4.80400 REMARK 350 BIOMT1 5 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 -9.60800 REMARK 350 BIOMT1 6 -1.000000 0.000000 0.000000 27.54600 REMARK 350 BIOMT2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 9.60800 REMARK 350 BIOMT1 7 -1.000000 0.000000 0.000000 27.54600 REMARK 350 BIOMT2 7 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 7 0.000000 0.000000 1.000000 4.80400 REMARK 350 BIOMT1 8 -1.000000 0.000000 0.000000 27.54600 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 BIOMT1 9 -1.000000 0.000000 0.000000 27.54600 REMARK 350 BIOMT2 9 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 9 0.000000 0.000000 1.000000 -4.80400 REMARK 350 BIOMT1 10 -1.000000 0.000000 0.000000 27.54600 REMARK 350 BIOMT2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 10 0.000000 0.000000 1.000000 -9.60800 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 7 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3NVE RELATED DB: PDB REMARK 900 MMHFGN HEXAPEPTIDE (RESIDUES 138-143) FROM GOLDEN HAMSTER PRION REMARK 900 PROTEIN REMARK 900 RELATED ID: 3NVG RELATED DB: PDB REMARK 900 MIHFGN HEXAPEPTIDE (RESIDUES 137-142) FROM MOUSE PRION PROTEIN REMARK 900 RELATED ID: 3NVH RELATED DB: PDB REMARK 900 MIHFGND (RESIDUES 137-143) FROM MOUSE PRION PROTEIN DBREF 3NVF A 1 6 UNP P04156 PRIO_HUMAN 138 143 SEQRES 1 A 6 ILE ILE HIS PHE GLY SER HET MPD A 7 8 HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 2 MPD C6 H14 O2 SITE 1 AC1 4 ILE A 1 ILE A 2 HIS A 3 PHE A 4 CRYST1 27.546 31.017 4.804 90.00 90.00 90.00 P 21 21 2 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 0.036303 0.000000 0.000000 0.00000 SCALE2 0.000000 0.032240 0.000000 0.00000 SCALE3 0.000000 0.000000 0.208160 0.00000