HEADER PROTEIN FIBRIL 29-MAY-21 7N2K TITLE MICROED STRUCTURE OF SEQUENCE VARIANT OF REPEAT SEGMENT OF THE YEAST TITLE 2 PRION NEW1P PHASED BY ARCIMBOLDO-BORGES COMPND MOL_ID: 1; COMPND 2 MOLECULE: PRION NEW1P; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: REPEAT SEGMENT; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 4 ORGANISM_TAXID: 4932 KEYWDS AMYLOID, MICROED, PRION, YEAST, NEW1P, PROTEIN FIBRIL EXPDTA ELECTRON CRYSTALLOGRAPHY AUTHOR M.D.FLORES,L.S.RICHARDS,C.T.ZEE,C.GLYNN,M.GALLAGHER-JONES,M.R.SAWAYA REVDAT 3 22-MAY-24 7N2K 1 REMARK REVDAT 2 10-MAY-23 7N2K 1 JRNL REVDAT 1 01-JUN-22 7N2K 0 JRNL AUTH L.S.RICHARDS,M.D.FLORES,C.MILLAN,C.GLYNN,C.T.ZEE,M.R.SAWAYA, JRNL AUTH 2 M.GALLAGHER-JONES,R.J.BORGES,I.USON,J.A.RODRIGUEZ JRNL TITL FRAGMENT-BASED AB INITIO PHASING OF PEPTIDIC NANOCRYSTALS BY JRNL TITL 2 MICROED. JRNL REF ACS BIO MED CHEM AU V. 3 201 2023 JRNL REFN ESSN 2694-2437 JRNL PMID 37096030 JRNL DOI 10.1021/ACSBIOMEDCHEMAU.2C00082 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 13.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.230 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 969 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 97 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 13.6000 - 2.7958 0.99 84 10 0.1228 0.1032 REMARK 3 2 2.7958 - 2.2222 1.00 88 10 0.1488 0.1450 REMARK 3 3 2.2222 - 1.9422 1.00 93 10 0.1499 0.1815 REMARK 3 4 1.9422 - 1.7651 1.00 87 10 0.1338 0.2253 REMARK 3 5 1.7651 - 1.6388 1.00 78 8 0.1554 0.4104 REMARK 3 6 1.6388 - 1.5423 1.00 93 11 0.1965 0.1744 REMARK 3 7 1.5423 - 1.4652 1.00 96 10 0.1766 0.2370 REMARK 3 8 1.4652 - 1.4014 1.00 90 10 0.2742 0.2141 REMARK 3 9 1.4014 - 1.3475 0.92 84 10 0.2561 0.2343 REMARK 3 10 1.3475 - 1.3011 0.88 79 8 0.2274 0.3074 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.830 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.19 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 7.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7N2K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1000254650. 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 : NULL REMARK 240 TEMPERATURE (KELVIN) : NULL REMARK 240 PH : NULL REMARK 240 NUMBER OF CRYSTALS USED : NULL REMARK 240 MICROSCOPE MODEL : FEI TALOS ARCTICA REMARK 240 DETECTOR TYPE : TVIPS TEMCAM-F416 (4K X 4K) REMARK 240 ACCELERATION VOLTAGE (KV) : 200 REMARK 240 NUMBER OF UNIQUE REFLECTIONS : 1357 REMARK 240 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 240 RESOLUTION RANGE LOW (A) : 13.600 REMARK 240 DATA SCALING SOFTWARE : XSCALE REMARK 240 COMPLETENESS FOR RANGE (%) : 83.4 REMARK 240 DATA REDUNDANCY : 5.817 REMARK 240 IN THE HIGHEST RESOLUTION SHELL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :1.10 REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :1.19 REMARK 240 COMPLETENESS FOR SHELL (%) : 53.2 REMARK 240 DATA REDUNDANCY IN SHELL : 2.26 REMARK 240 R MERGE FOR SHELL (I) : 0.48300 REMARK 240 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 240 SOFTWARE USED : NULL REMARK 240 STARTING MODEL : NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 1.61000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 3.22000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 1010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 DBREF 7N2K A 1 6 PDB 7N2K 7N2K 1 6 SEQRES 1 A 6 ASN TYR ASN ASN TYR GLN FORMUL 2 HOH *3(H2 O) CRYST1 27.200 27.200 4.830 90.00 90.00 120.00 P 31 3 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 0.036765 0.021226 0.000000 0.00000 SCALE2 0.000000 0.042452 0.000000 0.00000 SCALE3 0.000000 0.000000 0.207039 0.00000 ATOM 1 N ASN A 1 22.369 5.744 1.094 1.00 7.07 N ATOM 2 CA ASN A 1 21.081 5.597 0.427 1.00 4.81 C ATOM 3 C ASN A 1 19.985 6.337 1.176 1.00 4.87 C ATOM 4 O ASN A 1 19.911 6.283 2.404 1.00 4.58 O ATOM 5 CB ASN A 1 20.705 4.120 0.277 1.00 6.92 C ATOM 6 CG ASN A 1 21.608 3.376 -0.712 1.00 8.52 C ATOM 7 OD1 ASN A 1 22.486 3.968 -1.343 1.00 10.10 O ATOM 8 ND2 ASN A 1 21.385 2.081 -0.848 1.00 8.89 N ATOM 9 N TYR A 2 19.133 7.037 0.431 1.00 3.79 N ATOM 10 CA TYR A 2 18.017 7.774 1.017 1.00 3.44 C ATOM 11 C TYR A 2 18.476 8.796 2.049 1.00 3.55 C ATOM 12 O TYR A 2 17.754 9.081 2.990 1.00 4.02 O ATOM 13 CB TYR A 2 16.946 6.847 1.599 1.00 3.13 C ATOM 14 CG TYR A 2 16.408 5.869 0.583 1.00 3.49 C ATOM 15 CD1 TYR A 2 15.254 6.155 -0.161 1.00 3.72 C ATOM 16 CD2 TYR A 2 17.051 4.653 0.355 1.00 2.94 C ATOM 17 CE1 TYR A 2 14.753 5.251 -1.108 1.00 2.49 C ATOM 18 CE2 TYR A 2 16.556 3.739 -0.586 1.00 3.92 C ATOM 19 CZ TYR A 2 15.404 4.043 -1.309 1.00 3.93 C ATOM 20 OH TYR A 2 14.931 3.146 -2.242 1.00 4.12 O ATOM 21 N ASN A 3 19.679 9.349 1.874 1.00 4.04 N ATOM 22 CA ASN A 3 20.187 10.413 2.731 1.00 5.20 C ATOM 23 C ASN A 3 19.833 11.778 2.150 1.00 4.91 C ATOM 24 O ASN A 3 19.819 11.967 0.928 1.00 5.39 O ATOM 25 CB ASN A 3 21.713 10.320 2.865 1.00 4.09 C ATOM 26 CG ASN A 3 22.161 9.053 3.561 1.00 3.50 C ATOM 27 OD1 ASN A 3 21.661 8.715 4.624 1.00 4.17 O ATOM 28 ND2 ASN A 3 23.110 8.348 2.964 1.00 5.61 N ATOM 29 N ASN A 4 19.582 12.742 3.038 1.00 4.54 N ATOM 30 CA ASN A 4 19.134 14.077 2.660 1.00 4.93 C ATOM 31 C ASN A 4 20.145 15.116 3.117 1.00 4.47 C ATOM 32 O ASN A 4 20.473 15.179 4.303 1.00 6.47 O ATOM 33 CB ASN A 4 17.784 14.384 3.308 1.00 5.35 C ATOM 34 CG ASN A 4 17.239 15.717 2.880 1.00 4.66 C ATOM 35 OD1 ASN A 4 17.170 16.663 3.662 1.00 7.36 O ATOM 36 ND2 ASN A 4 16.865 15.810 1.619 1.00 7.63 N ATOM 37 N TYR A 5 20.624 15.940 2.183 1.00 6.40 N ATOM 38 CA TYR A 5 21.538 17.037 2.489 1.00 6.80 C ATOM 39 C TYR A 5 20.920 18.310 1.936 1.00 6.81 C ATOM 40 O TYR A 5 20.729 18.434 0.725 1.00 9.22 O ATOM 41 CB TYR A 5 22.919 16.804 1.861 1.00 8.60 C ATOM 42 CG TYR A 5 23.506 15.430 2.138 1.00 8.64 C ATOM 43 CD1 TYR A 5 24.432 15.241 3.165 1.00 11.81 C ATOM 44 CD2 TYR A 5 23.132 14.320 1.381 1.00 8.81 C ATOM 45 CE1 TYR A 5 24.969 13.985 3.431 1.00 9.93 C ATOM 46 CE2 TYR A 5 23.667 13.058 1.634 1.00 7.85 C ATOM 47 CZ TYR A 5 24.586 12.900 2.657 1.00 9.06 C ATOM 48 OH TYR A 5 25.114 11.649 2.919 1.00 11.26 O ATOM 49 N GLN A 6 20.579 19.240 2.815 1.00 8.95 N ATOM 50 CA GLN A 6 19.903 20.443 2.364 1.00 9.37 C ATOM 51 C GLN A 6 20.391 21.670 3.111 1.00 10.61 C ATOM 52 O GLN A 6 20.040 22.795 2.751 1.00 10.30 O ATOM 53 CB GLN A 6 18.401 20.291 2.559 1.00 10.35 C ATOM 54 CG GLN A 6 18.006 20.244 4.007 1.00 11.31 C ATOM 55 CD GLN A 6 16.502 20.307 4.219 1.00 12.98 C ATOM 56 OE1 GLN A 6 16.001 21.164 4.947 1.00 14.24 O ATOM 57 NE2 GLN A 6 15.779 19.394 3.589 1.00 11.39 N ATOM 58 OXT GLN A 6 21.133 21.570 4.086 1.00 9.75 O TER 59 GLN A 6 HETATM 60 O HOH A 101 25.112 10.153 1.079 1.00 10.99 O HETATM 61 O HOH A 102 17.806 23.166 1.286 1.00 15.90 O HETATM 62 O HOH A 103 13.103 21.040 5.211 1.00 18.07 O MASTER 169 0 0 0 0 0 0 6 61 1 0 1 END