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- PDB-6hwp: Structure of A3_bGFPD, an artificial bi-domain protein based on t... -

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Basic information

Entry
Database: PDB / ID: 6hwp
TitleStructure of A3_bGFPD, an artificial bi-domain protein based on two different alphaRep domains : A3 and a GFP binding domain (bGFPD)
ComponentsA3_bGFPD
KeywordsBIOSYNTHETIC PROTEIN / alphaRep / artificial protein / chimera / bidomain
Function / homologyMALONATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.547 Å
AuthorsLi de la Sierra-Gallay, I. / Leger, C.
Funding support France, 1items
OrganizationGrant numberCountry
France
Citation
#1: Journal: To Be Published
Title: Bi-domain artificial protein alphaRep display inducible cooperativity
Authors: Leger, C. / Li de la Sierra-Gallay, I.
History
DepositionOct 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 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 1.2Oct 16, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_CC_half
Revision 1.3Jan 24, 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: A3_bGFPD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5853
Polymers44,4601
Non-polymers1252
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint-10 kcal/mol
Surface area17880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.910, 89.000, 143.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein A3_bGFPD


Mass: 44460.203 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-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na

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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: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.6M Tri-sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.547→44.5 Å / Num. obs: 14334 / % possible obs: 98.94 % / Redundancy: 6.61 % / Biso Wilson estimate: 61.69 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.155 / Rrim(I) all: 0.169 / Net I/σ(I): 9.24
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.55-2.76.751.7391.0922300.8221.88398.6
2.7-2.896.411.0511.8121390.8521.14499.9
2.89-3.126.910.6223.1720090.9420.672100
3.12-3.416.70.02666.3918520.990.028899.9
3.41-3.816.550.13911.4116820.9940.151100
3.81-4.46.730.09216.6315090.9970.1100
4.4-5.376.520.0818.8812760.9960.087100
5.37-7.546.360.07219.9210180.9980.07999.7
7.54-506.070.04831.276160.9970.05399.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIXphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LTJ

3ltj


Resolution: 2.547→44.5 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35
RfactorNum. reflection% reflection
Rfree0.2624 1324 4.95 %
Rwork0.2359 --
obs0.2372 14334 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 118.95 Å2 / Biso mean: 68.7056 Å2 / Biso min: 40.89 Å2
Refinement stepCycle: final / Resolution: 2.547→44.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2829 0 8 0 2837
Biso mean--65.91 --
Num. residues----368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022872
X-RAY DIFFRACTIONf_angle_d0.4933868
X-RAY DIFFRACTIONf_chiral_restr0.036427
X-RAY DIFFRACTIONf_plane_restr0.004511
X-RAY DIFFRACTIONf_dihedral_angle_d6.7651768
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5473-2.64930.52421390.49912754289396
2.6493-2.76980.42441430.41622777292098
2.7698-2.91580.35831460.36562833297999
2.9158-3.09850.3321450.32542852299799
3.0985-3.33760.32981520.28582823297599
3.3376-3.67340.2521480.218828533001100
3.6734-4.20460.2131540.201628422996100
4.2046-5.29590.21831490.189828563005100
5.2959-44.50680.22441480.18328593007100

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