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- PDB-6x8n: Crystal Structure of H49A ABLE mutant -

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Basic information

Entry
Database: PDB / ID: 6x8n
TitleCrystal Structure of H49A ABLE mutant
ComponentsDe novo designed ABLE protein
KeywordsDE NOVO PROTEIN / 4-helix bundle / de novo / ligand-binding
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsPolizzi, N.F.
Funding support2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
National Science Foundation (NSF, United States)
CitationJournal: Science / Year: 2020
Title: A defined structural unit enables de novo design of small-molecule-binding proteins.
Authors: Polizzi, N.F. / DeGrado, W.F.
History
DepositionJun 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: De novo designed ABLE protein
B: De novo designed ABLE protein


Theoretical massNumber of molelcules
Total (without water)27,5012
Polymers27,5012
Non-polymers00
Water4,738263
1
A: De novo designed ABLE protein


Theoretical massNumber of molelcules
Total (without water)13,7501
Polymers13,7501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: De novo designed ABLE protein


Theoretical massNumber of molelcules
Total (without water)13,7501
Polymers13,7501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.750, 46.440, 47.000
Angle α, β, γ (deg.)90.130, 117.660, 106.890
Int Tables number1
Space group name H-MP1

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Components

#1: Protein De novo designed ABLE protein


Mass: 13750.420 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET11 / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O

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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

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 0.03 M Citric acid, 0.07 M BIS-TRIS propane / pH 7.6 with 20% w/v Polyethylene glycol 3,350 (Hampton PEG/Ion 2 screen condition 40)

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.04457 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04457 Å / Relative weight: 1
ReflectionResolution: 1.6→43.851 Å / Num. obs: 32545 / % possible obs: 94.73 % / Redundancy: 3.5 % / CC1/2: 0.998 / Net I/σ(I): 7.91
Reflection shellResolution: 1.6→1.657 Å / Num. unique obs: 3202 / CC1/2: 0.612

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo ABLE

Resolution: 1.6→43.851 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 33.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2404 1381 4.25 %
Rwork0.2052 31098 -
obs0.2067 32479 94.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.94 Å2 / Biso mean: 35.8251 Å2 / Biso min: 16.03 Å2
Refinement stepCycle: final / Resolution: 1.6→43.851 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1885 0 0 263 2148
Biso mean---39.56 -
Num. residues----252
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6-1.65720.42891310.3819306893
1.6572-1.72360.41881310.3417307294
1.7236-1.8020.32431420.3019311195
1.802-1.8970.35661460.2759310795
1.897-2.01590.33061340.2577310994
2.0159-2.17150.23921370.2128313096
2.1715-2.390.21681380.1872305393
2.39-2.73580.19181370.1749318296
2.7358-3.44670.20011420.1781313396
3.4467-43.8510.22451430.1782313395

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