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- PDB-6w6x: Crystal Structure of ABLE Apo-protein -

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Basic information

Entry
Database: PDB / ID: 6w6x
TitleCrystal Structure of ABLE Apo-protein
ComponentsDe novo designed ABLE protein
KeywordsDE NOVO PROTEIN / 4-helix bundle / de novo / ligand-binding
Function / homologyACETATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.297 Å
AuthorsPolizzi, N.F.
Funding support1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
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
DepositionMar 18, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0417
Polymers27,6352
Non-polymers4065
Water5,693316
1
A: De novo designed ABLE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9733
Polymers13,8171
Non-polymers1552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: De novo designed ABLE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0694
Polymers13,8171
Non-polymers2513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: De novo designed ABLE protein
hetero molecules

A: De novo designed ABLE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9456
Polymers27,6352
Non-polymers3104
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2280 Å2
ΔGint-27 kcal/mol
Surface area12420 Å2
MethodPISA
4
B: De novo designed ABLE protein
hetero molecules

B: De novo designed ABLE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1378
Polymers27,6352
Non-polymers5026
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area2810 Å2
ΔGint-54 kcal/mol
Surface area12060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.426, 43.648, 91.835
Angle α, β, γ (deg.)90.000, 91.360, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-436-

HOH

21A-460-

HOH

31B-437-

HOH

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Components

#1: Protein De novo designed ABLE protein


Mass: 13817.490 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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 316 / 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

CrystalDensity Matthews: 1.86 Å3/Da / Density % sol: 34.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 2.6 M AmSO4, 0.1 M Na acetate

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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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.267→45.905 Å / Num. all: 53412 / Num. obs: 53412 / % possible obs: 98.5 % / Redundancy: 6.2 % / Rpim(I) all: 0.028 / Rrim(I) all: 0.073 / Rsym value: 0.061 / Net I/av σ(I): 4.9 / Net I/σ(I): 12.4 / Num. measured all: 330471
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.27-1.345.20.5071.33932675010.2660.6410.5071.695.2
1.34-1.426.20.3851.74560373780.190.4820.3852.698.9
1.42-1.516.10.2162.64154568240.1070.2720.2164.897.4
1.51-1.646.40.1613.64152964860.0780.20.1618.199.6
1.64-1.796.50.124.93897059930.0580.1470.1211.799.6
1.79-26.10.0836.93298153920.0410.1020.08316.698.7
2-2.316.70.0649.13213248040.0290.0780.0642499.9
2.31-2.836.60.05710.12676440860.0260.0670.0572899.8
2.83-4.016.10.04910.91932331510.0230.0590.04930.299.2
4.01-45.9056.80.0459.61229817970.0190.0510.04532.899.9

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Designed model

Resolution: 1.297→45.905 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 23.78
RfactorNum. reflection% reflection
Rfree0.2135 2472 4.95 %
Rwork0.1664 --
obs0.1688 49894 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 111.51 Å2 / Biso mean: 23.238 Å2 / Biso min: 9.76 Å2
Refinement stepCycle: final / Resolution: 1.297→45.905 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1914 0 29 316 2259
Biso mean--60.75 31.79 -
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 (%)
1.2973-1.32230.29871250.2663255098
1.3223-1.34930.32051180.2599270299
1.3493-1.37860.28461300.2439254899
1.3786-1.41070.29291600.2288263999
1.4107-1.4460.29121550.2289250097
1.446-1.48510.26911490.2123254896
1.4851-1.52880.19871660.1787260798
1.5288-1.57810.2241150.1704262899
1.5781-1.63450.24621340.16172656100
1.6345-1.70.19451400.1509266399
1.7-1.77730.20591290.15662675100
1.7773-1.8710.20331400.1611262399
1.871-1.98830.23251260.1591265598
1.9883-2.14180.2021410.14852626100
2.1418-2.35730.17851160.14922701100
2.3573-2.69840.19881310.15532685100
2.6984-3.39950.21631360.1632711100
3.3995-45.9050.2041610.1669270599

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