0.034247
0.000000
0.007215
0.000000
0.205339
0.000000
0.000000
0.000000
0.031503
0.000000
0.000000
0.000000
0000-0003-0874-9043
Sawaya, M.R.
0000-0002-9612-0511
Warmack, R.A.
0000-0002-4487-0230
Boyer, D.R.
0000-0002-6630-706X
Zee, C.T.
0000-0002-1694-1652
Richards, L.S.
0000-0002-3877-6803
Cascio, D.
0000-0002-9254-4069
Gonen, T.
0000-0002-7303-6632
Clarke, S.G.
0000-0003-2432-5419
Eisenberg, D.S.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
2
90.000
101.900
90.000
29.200
4.870
32.440
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
H2 O
18.015
WATER
non-polymer
C4 H7 N O4
133.103
BETA-L-ASPARTIC ACID
L-aspartic acid
L-beta-peptide, C-gamma linking
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
UK
Nat Commun
2041-1723
10
3357
3357
10.1038/s41467-019-11183-z
31350392
Structure of amyloid-beta (20-34) with Alzheimer's-associated isomerization at Asp23 reveals a distinct protofilament interface.
2019
0000-0002-9612-0511
0000-0003-0874-9043
0000-0001-8285-754X
0000-0002-9254-4069
0000-0003-2432-5419
10.2210/pdb6nb9/pdb
pdb_00006nb9
100
1
CMOS CAMERA
2018-04-13
CETA 16M
0.0251
1.0
0.0251
ELECTRON MICROSCOPE
TALOS ARCTICA
90.000
101.897
90.000
29.20
4.87
32.44
P 21
4
10.135
OTHER
RECIPROCAL
maximum liklihood
6NB9
DIFFRACTION PATTERN/LAYERLINES
3D CRYSTAL
7.6
water
1
1
NONE
1050
1
1
41.2
1.00
1.05
3.09
315
0.1
82.7
1.05
1
16529
3946
28.4
0.1
0.1
0.197
0.197
1
crystal of amyloid-beta residues 20-34 with L-isoaspartate at position 23
0
MULTIPLE SOURCES
COMPLEX
NO
KILODALTONS/NANOMETER
6.21
3D ARRAY
1
1
CRYSTALLOGRAPHY
3
0.01
FEI CETA (4k x 4k)
159
2
2048
2048
6NB9
200
BASIC
NITROGEN
FIELD EMISSION GUN
FLOOD BEAM
FEI TALOS ARCTICA
DIFFRACTION
100
100
FEI TITAN KRIOS AUTOGRID HOLDER
1
COPPER
300
Quantifoil R1.2/1.3
IMAGE ACQUISITION
1
MASKING
CTF CORRECTION
1
LAYERLINE INDEXING
DIFFRACTION INDEXING
MODEL FITTING
1
Coot
0.8.9.1
OTHER
MOLECULAR REPLACEMENT
1
LATTICE DISTORTION CORRECTION
1
SYMMETRY DETERMINATION
1
CRYSTALLOGRAPHY MERGING
1
RECONSTRUCTION
1
MODEL REFINEMENT
1
PHENIX
1.14-3260
2.5
This sample is a crystal.
NO
NO
NO
YES
100
ETHANE
6NB9
FEI VITROBOT MARK IV
1491.666
Amyloid-beta A4 protein
residues 20-34
L-isoaspartate 23
1
syn
polymer
18.015
water
4
nat
water
ABPP,APPI,APP,Alzheimer disease amyloid protein,Amyloid precursor protein,Amyloid-beta precursor protein,Cerebral vascular amyloid peptide,CVAP,PreA4,Protease nexin-II,PN-II
no
yes
FAE(IAS)VGSNKGAIIGL
FAEDVGSNKGAIIGL
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
1.51
18.76
BATCH
7.6
0.05M Tris-HCl, 0.15M NaCl, 1% DMSO
310
pdbx_audit_support
database_2
em_diffraction_shell
refine_hist
repository
Initial release
Author supporting evidence
Data collection
Database references
Refinement description
1
0
2019-08-07
1
1
2019-11-20
1
2
2022-09-07
_pdbx_audit_support.funding_organization
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_em_diffraction_shell.em_diffraction_stats_id
_em_diffraction_shell.id
_refine_hist.pdbx_refine_id
United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)
5T32GM008496
United States
National Science Foundation (NSF, United States)
MCB-1714569
United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)
GM-007185
United States
Howard Hughes Medical Institute (HHMI)
Amyloid-Beta (20-34) with L-isoaspartate 23
N
RCSB
Y
RCSB
2018-12-06
REL
REL
HOH
water
human
9606
Human
Homo sapiens
sample
1
15
HOH
3
2
HOH
HOH
101
A
HOH
4
2
HOH
HOH
102
A
HOH
1
2
HOH
HOH
103
A
HOH
2
2
HOH
HOH
104
A
PHE
20
n
1
PHE
20
A
ALA
21
n
2
ALA
21
A
GLU
22
n
3
GLU
22
A
ASI
23
n
4
IAS
23
A
VAL
24
n
5
VAL
24
A
GLY
25
n
6
GLY
25
A
SER
26
n
7
SER
26
A
ASN
27
n
8
ASN
27
A
LYS
28
n
9
LYS
28
A
GLY
29
n
10
GLY
29
A
ALA
30
n
11
ALA
30
A
ILE
31
n
12
ILE
31
A
ILE
32
n
13
ILE
32
A
GLY
33
n
14
GLY
33
A
LEU
34
n
15
LEU
34
A
author_defined_assembly
10
decameric
microscopy
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_545
x,y-1,z
crystal symmetry operation
0.0000000000
-4.8700000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_535
x,y-2,z
crystal symmetry operation
0.0000000000
-9.7400000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_565
x,y+1,z
crystal symmetry operation
0.0000000000
4.8700000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_575
x,y+2,z
crystal symmetry operation
0.0000000000
9.7400000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
2_555
-x,y+1/2,-z
crystal symmetry operation
0.0000000000
2.4350000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
2_545
-x,y-1/2,-z
crystal symmetry operation
0.0000000000
-2.4350000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
2_535
-x,y-3/2,-z
crystal symmetry operation
0.0000000000
-7.3050000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
2_565
-x,y+3/2,-z
crystal symmetry operation
0.0000000000
7.3050000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
2_575
-x,y+5/2,-z
crystal symmetry operation
0.0000000000
12.1750000000
0.0000000000
34.450
10.1351
3.360
0.2458
0.1976
0.2022
1.0500
5.9550
394
3943
9.9900
83.4500
0.1000
Random
1
THROUGHOUT
1.360
AB INITIO PHASING
28.4000
0.9000
1.1100
1.0500
5.9550
4
109
27.22
0
0
105
15
0.3257
0.0000
0.2697
1.2010
116
1051
1167
3
75.0000
0.2482
0.0000
0.2373
1.5090
134
1206
1340
3
89.0000
0.2233
0.0000
0.1676
5.9546
144
1292
1436
3
86.0000
9.691
1.050
5.955
6NB9
3946
0.984
0.197
0.224
0.888
1
3.760
16529
4.189
16
82.700
0.494
1.050
1.100
1.400
974
594
315
0.779
0.589
1
3.092
53.000
0.603
1.100
1.150
1.690
1794
511
452
0.661
0.690
1
3.969
88.500
0.509
1.150
1.200
2.210
2024
443
392
0.661
0.570
1
5.163
88.500
0.413
1.200
1.300
2.430
2436
645
567
0.832
0.471
1
4.296
87.900
0.347
1.300
1.400
2.800
1630
469
424
0.876
0.403
1
3.844
90.400
0.330
1.400
1.500
3.380
1432
376
333
0.851
0.378
1
4.300
88.600
0.219
1.500
2.000
5.410
3712
943
832
0.952
0.246
1
4.462
88.200
0.159
2.000
3.000
7.320
1853
529
450
0.975
0.182
1
4.118
85.100
0.129
3.000
5.000
7.660
650
201
171
0.980
0.145
1
3.801
85.100
0.076
5.000
5.955
5.920
22
58
10
0.989
0.105
1
2.200
17.200
data reduction
Wolfgang Kabsch
Wolfgang.Kabsch@mpimf-heidelberg.mpg.de
http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/
XDS
package
data scaling
Wolfgang Kabsch
http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html
XSCALE
package
refinement
Paul D. Adams
PDAdams@lbl.gov
C++
http://www.phenix-online.org/
PHENIX
package
data extraction
PDB
deposit@deposit.rcsb.org
Sep. 1, 2017
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.24
phasing
SHELXDE
N
Protofilament structure of Amyloid-beta 20-34 with the age-associated post-translational modification of aspartate isomerization at position 23
Amyloid-Beta (20-34) with L-isoaspartate 23
1
N
N
2
N
N
covale
1.344
both
A
GLU
22
A
C
GLU
3
1_555
A
IAS
23
A
N
IAS
4
1_555
covale
1.328
both
A
IAS
23
A
CG
IAS
4
1_555
A
VAL
24
A
N
VAL
5
1_555
PROTEIN FIBRIL
protofilament, 2 sub 1 screw symmetry, post-translational modification, isoaspartate, PROTEIN FIBRIL
A4_HUMAN
UNP
1
691
P05067
FAEDVGSNKGAIIGL
691
705
6NB9
20
34
P05067
A
1
1
15
1
ASP
engineered mutation
IAS
23
6NB9
A
P05067
UNP
694
4
4
P 1 21 1