HEADER DE NOVO PROTEIN 16-AUG-21 7RTZ TITLE X-RAY CRYSTALLOGRAPHIC STRUCTURE OF A BETA-HAIRPIN PEPTIDE DERIVED TITLE 2 FROM AMYLOID BETA 14-40 COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOID-BETA PROTEIN 40; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ABETA40,BETA-APP40; 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, OLIGOMER, HAIRPIN, BARREL, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.D.SAMDIN,A.G.KREUTZER,J.S.NOWICK REVDAT 3 13-DEC-23 7RTZ 1 JRNL REVDAT 2 18-OCT-23 7RTZ 1 REMARK REVDAT 1 31-AUG-22 7RTZ 0 JRNL AUTH T.D.SAMDIN,C.R.JONES,G.GUAGLIANONE,A.G.KREUTZER,J.A.FREITES, JRNL AUTH 2 M.WIERZBICKI,J.S.NOWICK JRNL TITL A BETA-BARREL-LIKE TETRAMER FORMED BY A BETA-HAIRPIN DERIVED JRNL TITL 2 FROM A BETA JRNL REF CHEM SCI 2023 JRNL REFN ESSN 2041-6539 JRNL DOI 10.1039/D3SC05185D REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19_4092 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.52 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 7150 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.266 REMARK 3 R VALUE (WORKING SET) : 0.263 REMARK 3 FREE R VALUE : 0.293 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.040 REMARK 3 FREE R VALUE TEST SET COUNT : 718 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 36.5200 - 3.5900 1.00 1286 144 0.2371 0.2916 REMARK 3 2 3.5900 - 2.8500 1.00 1289 145 0.2636 0.2504 REMARK 3 3 2.8500 - 2.4900 1.00 1281 143 0.3211 0.3251 REMARK 3 4 2.4900 - 2.2600 1.00 1291 145 0.2997 0.3390 REMARK 3 5 2.2600 - 2.1000 1.00 1285 141 0.3250 0.3258 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) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 41.120 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 60.81 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 7RTZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-AUG-21. REMARK 100 THE DEPOSITION ID IS D_1000258985. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAR-21 REMARK 200 TEMPERATURE (KELVIN) : 123 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7150 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 36.520 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 48.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.8300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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 REMARK 200 STARTING MODEL: 6WXM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM ACETATE TETRAHYDRATE, REMARK 280 0.1 M SODIUM CACODYLATE TRIHYDRATE PH 6.5, AND 30% (V/V) 2- REMARK 280 METHYL-2,4-PENTANEDIOL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 296.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 32.21350 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 22.16350 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 22.16350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 16.10675 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 22.16350 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 22.16350 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 48.32025 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 22.16350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 22.16350 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 16.10675 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 22.16350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 22.16350 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 48.32025 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 32.21350 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL 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 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 B 104 O HOH B 106 2.04 REMARK 500 O HOH B 103 O HOH B 104 2.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 H ORN A 13 O VAL B 23 7556 1.52 REMARK 500 REMARK 500 REMARK: NULL DBREF 7RTZ A 1 24 UNP P05067 A4_HUMAN 682 711 DBREF 7RTZ B 1 24 UNP P05067 A4_HUMAN 682 711 SEQADV 7RTZ ORN A 1 UNP P05067 GLU 682 CONFLICT SEQADV 7RTZ CYS A 5 UNP P05067 GLN 686 CONFLICT SEQADV 7RTZ A UNP P05067 ASP 694 DELETION SEQADV 7RTZ A UNP P05067 VAL 695 DELETION SEQADV 7RTZ A UNP P05067 GLY 696 DELETION SEQADV 7RTZ A UNP P05067 SER 697 DELETION SEQADV 7RTZ A UNP P05067 ASN 698 DELETION SEQADV 7RTZ A UNP P05067 LYS 699 DELETION SEQADV 7RTZ ORN A 13 UNP P05067 GLY 700 CONFLICT SEQADV 7RTZ CYS A 21 UNP P05067 GLY 708 CONFLICT SEQADV 7RTZ ORN B 1 UNP P05067 GLU 682 CONFLICT SEQADV 7RTZ CYS B 5 UNP P05067 GLN 686 CONFLICT SEQADV 7RTZ B UNP P05067 ASP 694 DELETION SEQADV 7RTZ B UNP P05067 VAL 695 DELETION SEQADV 7RTZ B UNP P05067 GLY 696 DELETION SEQADV 7RTZ B UNP P05067 SER 697 DELETION SEQADV 7RTZ B UNP P05067 ASN 698 DELETION SEQADV 7RTZ B UNP P05067 LYS 699 DELETION SEQADV 7RTZ ORN B 13 UNP P05067 GLY 700 CONFLICT SEQADV 7RTZ CYS B 21 UNP P05067 GLY 708 CONFLICT SEQRES 1 A 24 ORN VAL HIS HIS CYS LYS LEU VAL PHE PHE ALA GLU ORN SEQRES 2 A 24 ALA ILE ILE SAR LEU MET VAL CYS GLY VAL VAL SEQRES 1 B 24 ORN VAL HIS HIS CYS LYS LEU VAL PHE PHE ALA GLU ORN SEQRES 2 B 24 ALA ILE ILE SAR LEU MET VAL CYS GLY VAL VAL MODRES 7RTZ SAR A 17 GLY MODIFIED RESIDUE MODRES 7RTZ SAR B 17 GLY MODIFIED RESIDUE HET ORN A 1 19 HET ORN A 13 18 HET SAR A 17 10 HET ORN B 1 19 HET ORN B 13 18 HET SAR B 17 10 HET CL A 101 1 HETNAM ORN L-ORNITHINE HETNAM SAR SARCOSINE HETNAM CL CHLORIDE ION FORMUL 1 ORN 4(C5 H12 N2 O2) FORMUL 1 SAR 2(C3 H7 N O2) FORMUL 3 CL CL 1- FORMUL 4 HOH *11(H2 O) SHEET 1 AA1 4 VAL A 2 ALA A 11 0 SHEET 2 AA1 4 ILE A 15 VAL A 24 -1 O GLY A 22 N HIS A 4 SHEET 3 AA1 4 ILE B 15 VAL B 24 -1 O MET B 19 N CYS A 21 SHEET 4 AA1 4 VAL B 2 ALA B 11 -1 N PHE B 10 O ILE B 16 SSBOND 1 CYS A 5 CYS A 21 1555 1555 2.03 SSBOND 2 CYS B 5 CYS B 21 1555 1555 2.04 LINK C ORN A 1 N VAL A 2 1555 1555 1.37 LINK NE ORN A 1 C VAL A 24 1555 1555 1.38 LINK C GLU A 12 NE ORN A 13 1555 1555 1.38 LINK C ORN A 13 N ALA A 14 1555 1555 1.37 LINK C ILE A 16 N SAR A 17 1555 1555 1.33 LINK C SAR A 17 N LEU A 18 1555 1555 1.33 LINK C ORN B 1 N VAL B 2 1555 1555 1.38 LINK NE ORN B 1 C VAL B 24 1555 1555 1.38 LINK C GLU B 12 NE ORN B 13 1555 1555 1.38 LINK C ORN B 13 N ALA B 14 1555 1555 1.37 LINK C ILE B 16 N SAR B 17 1555 1555 1.34 LINK C SAR B 17 N LEU B 18 1555 1555 1.33 CRYST1 44.327 44.327 64.427 90.00 90.00 90.00 P 41 21 2 16 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 0.022560 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022560 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015522 0.00000 HETATM 1 N ORN A 1 -0.501 36.196 18.371 1.00 80.79 N HETATM 2 CA ORN A 1 0.339 36.136 19.605 1.00 58.45 C HETATM 3 CB ORN A 1 -0.547 35.949 20.850 1.00 64.24 C HETATM 4 CG ORN A 1 -1.027 37.274 21.453 1.00 69.49 C HETATM 5 CD ORN A 1 0.020 37.862 22.412 1.00 74.91 C HETATM 6 NE ORN A 1 0.147 37.047 23.610 1.00 77.18 N HETATM 7 C ORN A 1 1.411 35.005 19.512 1.00 62.46 C HETATM 8 O ORN A 1 1.593 34.370 18.471 1.00 50.19 O HETATM 9 H1 ORN A 1 0.036 36.302 17.506 1.00 97.02 H HETATM 10 H2 ORN A 1 -1.074 35.362 18.217 1.00 97.02 H HETATM 11 H3 ORN A 1 -1.167 36.972 18.358 1.00 97.02 H HETATM 12 HA ORN A 1 0.885 37.083 19.636 1.00 70.20 H HETATM 13 HB2 ORN A 1 -1.435 35.366 20.568 1.00 77.15 H HETATM 14 HB3 ORN A 1 0.032 35.419 21.619 1.00 77.15 H HETATM 15 HG2 ORN A 1 -1.224 37.990 20.646 1.00 83.46 H HETATM 16 HG3 ORN A 1 -1.965 37.108 21.995 1.00 83.46 H HETATM 17 HD2 ORN A 1 -0.289 38.871 22.700 1.00 89.96 H HETATM 18 HD3 ORN A 1 0.988 37.898 21.902 1.00 89.96 H HETATM 19 HE1 ORN A 1 -0.694 36.955 24.177 1.00 92.68 H