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- PDB-6fes: Crystal structure of novel repeat protein BRIC2 fused to DARPin D12 -

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Basic information

Entry
Database: PDB / ID: 6fes
TitleCrystal structure of novel repeat protein BRIC2 fused to DARPin D12
ComponentsD12_BRIC2, a synthetic protein,D12_BRIC2, a synthetic protein
KeywordsDE NOVO PROTEIN / Novel fold / computational design / corrugated repeat
Function / homologyAnkyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsElGamacy, M. / Coles, M. / Ernst, P. / Zhu, H. / Hartmann, M.D. / Plueckthun, A. / Lupas, A.
CitationJournal: ACS Synth Biol / Year: 2018
Title: An Interface-Driven Design Strategy Yields a Novel, Corrugated Protein Architecture.
Authors: ElGamacy, M. / Coles, M. / Ernst, P. / Zhu, H. / Hartmann, M.D. / Pluckthun, A. / Lupas, A.N.
History
DepositionJan 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
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
Revision 1.3Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D12_BRIC2, a synthetic protein,D12_BRIC2, a synthetic protein
B: D12_BRIC2, a synthetic protein,D12_BRIC2, a synthetic protein
C: D12_BRIC2, a synthetic protein,D12_BRIC2, a synthetic protein
D: D12_BRIC2, a synthetic protein,D12_BRIC2, a synthetic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,54520
Polymers164,2464
Non-polymers1,29916
Water91951
1
A: D12_BRIC2, a synthetic protein,D12_BRIC2, a synthetic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4746
Polymers41,0621
Non-polymers4125
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: D12_BRIC2, a synthetic protein,D12_BRIC2, a synthetic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3164
Polymers41,0621
Non-polymers2543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: D12_BRIC2, a synthetic protein,D12_BRIC2, a synthetic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2824
Polymers41,0621
Non-polymers2203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: D12_BRIC2, a synthetic protein,D12_BRIC2, a synthetic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4746
Polymers41,0621
Non-polymers4125
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.990, 63.000, 133.540
Angle α, β, γ (deg.)97.99, 91.92, 110.81
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
D12_BRIC2, a synthetic protein,D12_BRIC2, a synthetic protein


Mass: 41061.582 Da / Num. of mol.: 4
Fragment: D12 residues 11-157, linker residues 158-172,Residues 173-375,D12 residues 11-157, linker residues 158-172,Residues 173-375
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.5 Å3/Da / Density % sol: 50.85 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion
Details: 0.2 M Ammonium sulfate, 0.1M Bis-Tris pH 5.5, 25 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→49.33 Å / Num. obs: 31567 / % possible obs: 99 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.177 / Net I/σ(I): 7.6
Reflection shellResolution: 3→3.08 Å / Rmerge(I) obs: 1.308 / Mean I/σ(I) obs: 2.15 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: one DARPin chain from structure 4ydw

4ydw


Resolution: 3→44.895 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 34.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2919 1573 4.99 %
Rwork0.2509 --
obs0.2529 31544 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→44.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11402 0 73 51 11526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311625
X-RAY DIFFRACTIONf_angle_d0.65915702
X-RAY DIFFRACTIONf_dihedral_angle_d7.1547875
X-RAY DIFFRACTIONf_chiral_restr0.041883
X-RAY DIFFRACTIONf_plane_restr0.0041983
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.09690.35971440.35562757X-RAY DIFFRACTION100
3.0969-3.20750.37621410.34462680X-RAY DIFFRACTION99
3.2075-3.33590.38091460.3382785X-RAY DIFFRACTION99
3.3359-3.48770.39411420.33932733X-RAY DIFFRACTION99
3.4877-3.67150.39131410.31492701X-RAY DIFFRACTION98
3.6715-3.90140.33591380.27912678X-RAY DIFFRACTION97
3.9014-4.20240.30681440.24292737X-RAY DIFFRACTION100
4.2024-4.62490.24751440.21762707X-RAY DIFFRACTION99
4.6249-5.29320.29671470.22532784X-RAY DIFFRACTION100
5.2932-6.66540.30961440.27372728X-RAY DIFFRACTION99
6.6654-44.90030.2081420.18272681X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -13.3111 Å / Origin y: 2.9493 Å / Origin z: 19.6649 Å
111213212223313233
T0.4603 Å2-0.0384 Å20.0566 Å2-0.4467 Å20.0046 Å2--0.6163 Å2
L0.5622 °2-0.0298 °2-0.1339 °2-0.3586 °20.0044 °2--0.4233 °2
S-0.0153 Å °-0.0611 Å °0.0204 Å °0.0528 Å °-0.0036 Å °-0.0545 Å °-0.0231 Å °-0.0034 Å °0.0159 Å °
Refinement TLS groupSelection details: all

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