HEADER DE NOVO PROTEIN 11-AUG-20 7JQT TITLE ABETA 16-36 BETA-HAIRPIN MIMIC WITH E22K ITALIAN MUTATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: ABETA 16-36 BETA-HAIRPIN MIMIC VAL-ORT-LYS-LEU-VAL-MEA-PHE- COMPND 3 ALA-LYS-ORT-ALA-ILE-ILE-GLY-LEU-MET; COMPND 4 CHAIN: A; 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 ALZHEIMER'S DISEASE, AMYLOID, ABETA, OLIGOMER, FAMILIAL MUTANT, DE KEYWDS 2 NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.G.KREUTZER,K.J.MCKNELLY,J.S.NOWICK REVDAT 4 18-OCT-23 7JQT 1 REMARK REVDAT 3 30-MAR-22 7JQT 1 JRNL REVDAT 2 16-MAR-22 7JQT 1 JRNL REVDAT 1 08-SEP-21 7JQT 0 JRNL AUTH K.J.MCKNELLY,A.G.KREUTZER,W.J.HOWITZ,K.HADUONG,S.YOO,C.HART, JRNL AUTH 2 J.S.NOWICK JRNL TITL EFFECTS OF FAMILIAL ALZHEIMER'S DISEASE MUTATIONS ON THE JRNL TITL 2 ASSEMBLY OF A BETA-HAIRPIN PEPTIDE DERIVED FROM A BETA 16-36 JRNL TITL 3 . JRNL REF BIOCHEMISTRY V. 61 446 2022 JRNL REFN ISSN 0006-2960 JRNL PMID 35213141 JRNL DOI 10.1021/ACS.BIOCHEM.1C00664 REMARK 2 REMARK 2 RESOLUTION. 2.08 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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) : 2.08 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 2159 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.960 REMARK 3 FREE R VALUE TEST SET COUNT : 215 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 17.0810 - 2.6194 0.97 954 105 0.2060 0.2569 REMARK 3 2 2.6194 - 2.0803 1.00 990 110 0.1950 0.2579 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.340 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.44 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 : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 16 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.0503 58.5613 4.0722 REMARK 3 T TENSOR REMARK 3 T11: 0.1767 T22: 0.1420 REMARK 3 T33: 0.1746 T12: -0.0102 REMARK 3 T13: -0.0011 T23: -0.0175 REMARK 3 L TENSOR REMARK 3 L11: 4.8862 L22: 2.2425 REMARK 3 L33: 3.0239 L12: -0.9618 REMARK 3 L13: -1.3034 L23: 2.1993 REMARK 3 S TENSOR REMARK 3 S11: 0.1341 S12: 0.1831 S13: 0.4768 REMARK 3 S21: -0.1294 S22: 0.0457 S23: -0.1931 REMARK 3 S31: -0.3784 S32: 0.0902 S33: -0.2105 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 7JQT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-AUG-20. REMARK 100 THE DEPOSITION ID IS D_1000251239. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-SEP-17 REMARK 200 TEMPERATURE (KELVIN) : 123.15 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2159 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.080 REMARK 200 RESOLUTION RANGE LOW (A) : 17.081 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 40.70 REMARK 200 R MERGE (I) : 0.00879 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 112.7100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.08 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.15 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.00885 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: PHENIX REMARK 200 STARTING MODEL: 7JQR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM THIOCYANATE, PEG 3350, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 297.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 20.68050 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 11.93989 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 18.93200 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 20.68050 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 11.93989 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 18.93200 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 20.68050 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 11.93989 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 18.93200 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 20.68050 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 11.93989 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 18.93200 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 20.68050 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 11.93989 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 18.93200 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 20.68050 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 11.93989 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 18.93200 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 23.87978 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 37.86400 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 23.87978 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 37.86400 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 23.87978 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 37.86400 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 23.87978 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 37.86400 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 23.87978 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 37.86400 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 23.87978 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 37.86400 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 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 REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 82.72200 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 71.63935 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -20.68050 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 107.45903 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -0.500000 0.866025 0.000000 -20.68050 REMARK 350 BIOMT2 4 0.866025 0.500000 0.000000 11.93989 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 18.93200 REMARK 350 BIOMT1 5 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 5 0.000000 -1.000000 0.000000 119.39892 REMARK 350 BIOMT3 5 0.000000 0.000000 -1.000000 18.93200 REMARK 350 BIOMT1 6 -0.500000 -0.866025 0.000000 82.72200 REMARK 350 BIOMT2 6 -0.866025 0.500000 0.000000 47.75957 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 18.93200 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 111 O HOH A 112 2.01 REMARK 500 O HOH A 106 O HOH A 113 2.09 REMARK 500 REMARK 500 REMARK: NULL DBREF 7JQT A 1 16 PDB 7JQT 7JQT 1 16 SEQRES 1 A 16 VAL ORN LYS LEU VAL MEA PHE ALA LYS ORN ALA ILE ILE SEQRES 2 A 16 GLY LEU MET HET ORN A 2 18 HET MEA A 6 23 HET ORN A 10 18 HETNAM ORN L-ORNITHINE HETNAM MEA N-METHYLPHENYLALANINE FORMUL 1 ORN 2(C5 H12 N2 O2) FORMUL 1 MEA C10 H13 N O2 FORMUL 2 HOH *13(H2 O) SHEET 1 AA1 2 VAL A 5 PHE A 7 0 SHEET 2 AA1 2 ILE A 13 LEU A 15 -1 O LEU A 15 N VAL A 5 LINK C VAL A 1 NE ORN A 2 1555 1555 1.38 LINK N VAL A 1 C MET A 16 1555 1555 1.33 LINK C ORN A 2 N LYS A 3 1555 1555 1.37 LINK C VAL A 5 N MEA A 6 1555 1555 1.34 LINK C MEA A 6 N PHE A 7 1555 1555 1.33 LINK C LYS A 9 NE ORN A 10 1555 1555 1.38 LINK C ORN A 10 N ALA A 11 1555 1555 1.37 CRYST1 41.361 41.361 56.796 90.00 90.00 120.00 H 3 2 18 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 0.024177 0.013959 0.000000 0.00000 SCALE2 0.000000 0.027917 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017607 0.00000