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- PDB-7n8r: FGTGFG segment from the Nucleoporin p54, residues 63-68 -

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Basic information

Entry
Database: PDB / ID: 7n8r
TitleFGTGFG segment from the Nucleoporin p54, residues 63-68
ComponentsFGTGFG segment from the Nucleoporin p54, residues 63-68
KeywordsPROTEIN FIBRIL / amyloid-like fibril
Function / homologytrifluoroacetic acid
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å
Model detailsAmyloid Fibril
AuthorsHughes, M.P. / Sawaya, M.R. / Eisenberg, D.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM08042 United States
CitationJournal: Acs Nano / Year: 2022
Title: Extended beta-Strands Contribute to Reversible Amyloid Formation.
Authors: Murray, K.A. / Evans, D. / Hughes, M.P. / Sawaya, M.R. / Hu, C.J. / Houk, K.N. / Eisenberg, D.
History
DepositionJun 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FGTGFG segment from the Nucleoporin p54, residues 63-68
B: FGTGFG segment from the Nucleoporin p54, residues 63-68
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,2833
Polymers1,1692
Non-polymers1141
Water362
1
A: FGTGFG segment from the Nucleoporin p54, residues 63-68
B: FGTGFG segment from the Nucleoporin p54, residues 63-68
hetero molecules

A: FGTGFG segment from the Nucleoporin p54, residues 63-68
B: FGTGFG segment from the Nucleoporin p54, residues 63-68
hetero molecules

A: FGTGFG segment from the Nucleoporin p54, residues 63-68
B: FGTGFG segment from the Nucleoporin p54, residues 63-68
hetero molecules

A: FGTGFG segment from the Nucleoporin p54, residues 63-68
B: FGTGFG segment from the Nucleoporin p54, residues 63-68
hetero molecules

A: FGTGFG segment from the Nucleoporin p54, residues 63-68
B: FGTGFG segment from the Nucleoporin p54, residues 63-68
hetero molecules

A: FGTGFG segment from the Nucleoporin p54, residues 63-68

A: FGTGFG segment from the Nucleoporin p54, residues 63-68

A: FGTGFG segment from the Nucleoporin p54, residues 63-68

A: FGTGFG segment from the Nucleoporin p54, residues 63-68

A: FGTGFG segment from the Nucleoporin p54, residues 63-68

B: FGTGFG segment from the Nucleoporin p54, residues 63-68
hetero molecules

B: FGTGFG segment from the Nucleoporin p54, residues 63-68
hetero molecules

B: FGTGFG segment from the Nucleoporin p54, residues 63-68
hetero molecules

B: FGTGFG segment from the Nucleoporin p54, residues 63-68
hetero molecules

B: FGTGFG segment from the Nucleoporin p54, residues 63-68
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,83330
Polymers11,69220
Non-polymers1,14010
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_535x,y-2,z1
crystal symmetry operation1_575x,y+2,z1
crystal symmetry operation2_545-x,y-1/2,-z1
crystal symmetry operation2_555-x,y+1/2,-z1
crystal symmetry operation2_535-x,y-3/2,-z1
crystal symmetry operation2_565-x,y+3/2,-z1
crystal symmetry operation2_525-x,y-5/2,-z1
crystal symmetry operation2_6461-x,y-1/2,-z+11
crystal symmetry operation2_6561-x,y+1/2,-z+11
crystal symmetry operation2_6361-x,y-3/2,-z+11
crystal symmetry operation2_6661-x,y+3/2,-z+11
crystal symmetry operation2_6261-x,y-5/2,-z+11
Unit cell
Length a, b, c (Å)15.710, 9.400, 23.260
Angle α, β, γ (deg.)90.000, 108.520, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide FGTGFG segment from the Nucleoporin p54, residues 63-68


Mass: 584.622 Da / Num. of mol.: 2 / Fragment: FGTGFG / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-TFA / trifluoroacetic acid / Trifluoroacetic acid


Mass: 114.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2HF3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 22, 2017
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.2→22.06 Å / Num. obs: 2137 / % possible obs: 98.8 % / Redundancy: 3.969 % / Biso Wilson estimate: 11.597 Å2 / CC1/2: 0.972 / Rmerge(I) obs: 0.186 / Rrim(I) all: 0.215 / Χ2: 0.819 / Net I/σ(I): 5.43 / Num. measured all: 8482 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.2-1.233.1330.3862.631430.9150.45492.3
1.23-1.263.4430.3993.031490.8650.475100
1.26-1.33.9540.3633.631520.9140.42695
1.3-1.343.8520.2684.331420.9370.31100
1.34-1.384.2020.2873.831290.9490.328100
1.38-1.434.2390.2494.61340.9480.28598.5
1.43-1.493.9090.2514.691320.8830.292100
1.49-1.554.2670.2555.21350.9080.29298.5
1.55-1.624.0850.2185.51170.8460.261100
1.62-1.74.2230.1886.141210.9720.21399.2
1.7-1.794.1740.196.231090.9750.21799.1
1.79-1.94.20.1626.991050.9850.18499.1
1.9-2.034.3010.1597.371030.9850.1898.1
2.03-2.194.1260.1787.2870.9740.203100
2.19-2.43.9660.1877.68890.9710.21498.9
2.4-2.684.1130.1497.64800.9880.173100
2.68-3.140.1538.26750.9310.18100
3.1-3.793.9820.1678.2560.9710.196100
3.79-5.363.660.1728.06500.9720.292.6
5.36-22.063.310.1847.72290.9840.21396.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.2 Å22.06 Å
Translation1.2 Å22.06 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASER2.8.3phasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→22.06 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.697 / SU ML: 0.033 / SU R Cruickshank DPI: 0.0521 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1745 214 10 %RANDOM
Rwork0.1429 ---
obs0.146 1923 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 23.79 Å2 / Biso mean: 5.347 Å2 / Biso min: 3.06 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å2-0 Å2-0.33 Å2
2---0.37 Å2-0 Å2
3---0.77 Å2
Refinement stepCycle: final / Resolution: 1.2→22.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms84 0 7 2 93
Biso mean--15.58 8.74 -
Num. residues----12
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01392
X-RAY DIFFRACTIONr_bond_other_d0.0010.01870
X-RAY DIFFRACTIONr_angle_refined_deg1.9681.713121
X-RAY DIFFRACTIONr_angle_other_deg1.8681.673158
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.914510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.35204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.763156
X-RAY DIFFRACTIONr_chiral_restr0.0870.28
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02118
X-RAY DIFFRACTIONr_gen_planes_other00.0230
X-RAY DIFFRACTIONr_rigid_bond_restr1.553162
LS refinement shellResolution: 1.2→1.23 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.292 14 -
Rwork0.213 129 -
obs--94.08 %

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