HEADER PROTEIN FIBRIL 24-DEC-17 6BZM TITLE GFGNFGTS FROM LOW-COMPLEXITY/FG REPEAT DOMAIN OF NUP98, RESIDUES 116- TITLE 2 123 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEAR PORE COMPLEX PROTEIN NUP98-NUP96; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 116-123; 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 KEYWDS AMYLOID, LARKS, REVERSIBLE-AMYLOID, LOW-COMPLEXITY, FG REPEAT, KEYWDS 2 PROTEIN FIBRIL EXPDTA ELECTRON CRYSTALLOGRAPHY AUTHOR M.P.HUGHES,J.A.RODRIGUEZ,M.R.SAWAYA,D.CASCIO,L.CHONG,T.GONEN, AUTHOR 2 D.S.EISENBERG REVDAT 6 13-MAR-24 6BZM 1 REMARK REVDAT 5 30-JUN-21 6BZM 1 REMARK REVDAT 4 20-NOV-19 6BZM 1 REMARK REVDAT 3 06-NOV-19 6BZM 1 REMARK REVDAT 2 25-APR-18 6BZM 1 REMARK REVDAT 1 04-APR-18 6BZM 0 JRNL AUTH M.P.HUGHES,M.R.SAWAYA,D.R.BOYER,L.GOLDSCHMIDT,J.A.RODRIGUEZ, JRNL AUTH 2 D.CASCIO,L.CHONG,T.GONEN,D.S.EISENBERG JRNL TITL ATOMIC STRUCTURES OF LOW-COMPLEXITY PROTEIN SEGMENTS REVEAL JRNL TITL 2 KINKED BETA SHEETS THAT ASSEMBLE NETWORKS. JRNL REF SCIENCE V. 359 698 2018 JRNL REFN ESSN 1095-9203 JRNL PMID 29439243 JRNL DOI 10.1126/SCIENCE.AAN6398 REMARK 2 REMARK 2 RESOLUTION. 0.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.36 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.9 REMARK 3 NUMBER OF REFLECTIONS : 5799 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) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 580 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 5 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 0.90 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.01 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 72.26 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 1365 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2228 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1229 REMARK 3 BIN R VALUE (WORKING SET) : 0.2200 REMARK 3 BIN FREE R VALUE : 0.2473 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.96 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 136 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 112 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 2 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 3.45 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 8.02 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.28920 REMARK 3 B22 (A**2) : 0.64220 REMARK 3 B33 (A**2) : -1.93140 REMARK 3 B12 (A**2) : -0.61760 REMARK 3 B13 (A**2) : -0.30920 REMARK 3 B23 (A**2) : -0.33550 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.190 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.030 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.033 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.032 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.035 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.911 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.895 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 202 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 346 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 32 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 4 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 34 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 202 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 12 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 237 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 BOND ANGLES (DEGREES) : 1.16 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.45 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 13.01 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): 1.4694 9.4609 17.6099 REMARK 3 T TENSOR REMARK 3 T11: -0.0233 T22: -0.0093 REMARK 3 T33: 0.0014 T12: 0.0042 REMARK 3 T13: 0.0072 T23: 0.0010 REMARK 3 L TENSOR REMARK 3 L11: -0.0139 L22: 0.0118 REMARK 3 L33: 0.0046 L12: 0.0483 REMARK 3 L13: 0.0103 L23: 0.0273 REMARK 3 S TENSOR REMARK 3 S11: 0.0006 S12: 0.0051 S13: -0.0047 REMARK 3 S21: -0.0022 S22: 0.0006 S23: 0.0006 REMARK 3 S31: -0.0003 S32: -0.0011 S33: -0.0012 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { B|* } REMARK 3 ORIGIN FOR THE GROUP (A): -0.2721 10.0436 29.4641 REMARK 3 T TENSOR REMARK 3 T11: -0.0338 T22: -0.0135 REMARK 3 T33: -0.0033 T12: 0.0040 REMARK 3 T13: 0.0023 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: -0.0033 L22: 0.0047 REMARK 3 L33: -0.0014 L12: 0.0251 REMARK 3 L13: -0.0290 L23: 0.0126 REMARK 3 S TENSOR REMARK 3 S11: 0.0004 S12: -0.0091 S13: -0.0028 REMARK 3 S21: 0.0040 S22: -0.0006 S23: -0.0004 REMARK 3 S31: -0.0014 S32: 0.0032 S33: 0.0003 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6BZM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1000231824. REMARK 240 REMARK 240 EXPERIMENTAL DETAILS REMARK 240 RECONSTRUCTION METHOD : CRYSTALLOGRAPHY REMARK 240 SAMPLE TYPE : 3D ARRAY REMARK 240 SPECIMEN TYPE : NULL REMARK 240 DATA ACQUISITION REMARK 240 DATE OF DATA COLLECTION : 23-MAR-17 REMARK 240 TEMPERATURE (KELVIN) : 100.0 REMARK 240 PH : 9.50 REMARK 240 NUMBER OF CRYSTALS USED : NULL REMARK 240 MICROSCOPE MODEL : FEI TECNAI 20 REMARK 240 DETECTOR TYPE : TVIPS TEMCAM-F415 (4K X 4K) REMARK 240 ACCELERATION VOLTAGE (KV) : 200 REMARK 240 NUMBER OF UNIQUE REFLECTIONS : 5800 REMARK 240 RESOLUTION RANGE HIGH (A) : 0.900 REMARK 240 RESOLUTION RANGE LOW (A) : 26.360 REMARK 240 DATA SCALING SOFTWARE : XSCALE REMARK 240 COMPLETENESS FOR RANGE (%) : 88.0 REMARK 240 DATA REDUNDANCY : 5.461 REMARK 240 IN THE HIGHEST RESOLUTION SHELL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :0.90 REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :0.92 REMARK 240 COMPLETENESS FOR SHELL (%) : 47.8 REMARK 240 DATA REDUNDANCY IN SHELL : 2.80 REMARK 240 R MERGE FOR SHELL (I) : 0.58800 REMARK 240 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING REMARK 240 SOFTWARE USED : NULL REMARK 240 STARTING MODEL : NULL 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: DECAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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, B REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 4.79000 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: A, B REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 -4.79000 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: A, B REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 9.58000 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: A, B REMARK 350 BIOMT1 5 1.000000 0.000000 0.000000 -9.58000 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 DBREF 6BZM A 1 8 UNP P52948 NUP98_HUMAN 116 123 DBREF 6BZM B 1 8 UNP P52948 NUP98_HUMAN 116 123 SEQRES 1 A 8 GLY PHE GLY ASN PHE GLY THR SER SEQRES 1 B 8 GLY PHE GLY ASN PHE GLY THR SER FORMUL 3 HOH *2(H2 O) CRYST1 4.790 18.240 26.440 93.14 92.73 97.15 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 0.208768 0.026188 0.011581 0.00000 SCALE2 0.000000 0.055254 0.003391 0.00000 SCALE3 0.000000 0.000000 0.037936 0.00000