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- PDB-6ft5: Structure of A3_A3, an artificial bi-domain protein based on two ... -

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Basic information

Entry
Database: PDB / ID: 6ft5
TitleStructure of A3_A3, an artificial bi-domain protein based on two identical alphaRep A3 domains
ComponentsalphaRep A3_A3
KeywordsBIOSYNTHETIC PROTEIN / alphaRep / artificial protein / chimera / bidomain
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsLi de la Sierra-Gallay, I. / Leger, C. / Di Meo, T.
Citation
#1: Journal: To Be Published
Title: Bi-domain artificial protein alphaRep display inducible cooperativity
Authors: Leger, C. / Gallay, I.
History
DepositionFeb 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: alphaRep A3_A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3669
Polymers44,6051
Non-polymers7618
Water99155
1
A: alphaRep A3_A3
hetero molecules

A: alphaRep A3_A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,73218
Polymers89,2102
Non-polymers1,52116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area6210 Å2
ΔGint-176 kcal/mol
Surface area16660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.870, 46.678, 63.337
Angle α, β, γ (deg.)90.00, 128.91, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein alphaRep A3_A3


Mass: 44605.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: Sodium-citrate (0.1M) Ammonium Sulfate (2.4M)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.94→44.691 Å / Num. obs: 15038 / % possible obs: 97.6 % / Redundancy: 4.549 % / Biso Wilson estimate: 35.369 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.099 / Χ2: 0.895 / Net I/σ(I): 10.71
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.94-2.064.3350.7011.9423400.8750.79694.7
2.06-2.24.750.493.0122670.9490.55197.6
2.2-2.374.6350.2895.0421150.9680.32698.1
2.37-2.64.3320.1867.119530.9820.21298.2
2.6-2.914.770.1419.9217800.9910.15898.3
2.91-3.354.6710.08315.0715750.9950.09498.6
3.35-4.14.3430.04624.6813340.9970.05298.8
4.1-5.774.6620.03729.6310620.9980.04198.1
5.77-44.6914.3220.03331.686120.9990.03797.1

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHASER2.5.6phasing
REFMAC5.8.0158refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LTJ

3ltj


Resolution: 1.94→44.69 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.86 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.144 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22214 752 5 %RANDOM
Rwork0.17478 ---
obs0.1772 14285 98.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.059 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å21.5 Å2
2---0.81 Å20 Å2
3----0.55 Å2
Refinement stepCycle: 1 / Resolution: 1.94→44.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1432 0 42 55 1529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191487
X-RAY DIFFRACTIONr_bond_other_d0.0020.021424
X-RAY DIFFRACTIONr_angle_refined_deg1.8551.9912005
X-RAY DIFFRACTIONr_angle_other_deg1.04533280
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7315184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.86424.14370
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.65915259
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.871514
X-RAY DIFFRACTIONr_chiral_restr0.0960.2222
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021641
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02297
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2113.931739
X-RAY DIFFRACTIONr_mcbond_other3.2113.925738
X-RAY DIFFRACTIONr_mcangle_it4.1985.876922
X-RAY DIFFRACTIONr_mcangle_other4.1965.884923
X-RAY DIFFRACTIONr_scbond_it5.9034.982748
X-RAY DIFFRACTIONr_scbond_other5.6584.858724
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.56.9591048
X-RAY DIFFRACTIONr_long_range_B_refined10.06549.0571734
X-RAY DIFFRACTIONr_long_range_B_other10.06949.1051735
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.939→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 50 -
Rwork0.334 963 -
obs--91.43 %

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