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- PDB-6ff6: Crystal structure of novel repeat protein BRIC1 -

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Basic information

Entry
Database: PDB / ID: 6ff6
TitleCrystal structure of novel repeat protein BRIC1
ComponentsBRIC1
KeywordsDE NOVO PROTEIN / Novel fold / computational design / corrugated repeat
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsElGamacy, M. / Coles, M. / Ernst, P. / Zhu, H. / Hartmann, M.D. / Plueckthun, A. / Lupas, A.N.
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 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: BRIC1


Theoretical massNumber of molelcules
Total (without water)28,4911
Polymers28,4911
Non-polymers00
Water00
1
A: BRIC1

A: BRIC1


Theoretical massNumber of molelcules
Total (without water)56,9832
Polymers56,9832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area3420 Å2
ΔGint-38 kcal/mol
Surface area21340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.661, 41.953, 58.263
Angle α, β, γ (deg.)90.00, 90.46, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein BRIC1


Mass: 28491.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 1-99: N-terminal designed bundle. 100-104: designed loop 105-203: C-terminal designed bundle 204-228: Natural capping helix from the CheA HPT domain.
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)

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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: 49.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% v/v PEG 500 MME, 10 % w/v PEG 20,000, 30 mM MgCl2, 30 mM CaCl2 and 100 mM Tris-BICINE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→40.84 Å / Num. obs: 9739 / % possible obs: 99.7 % / Redundancy: 6.55 % / Biso Wilson estimate: 88.12 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 12.1
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 6.16 % / Rmerge(I) obs: 0.787 / Mean I/σ(I) obs: 1.67 / % possible all: 98.8

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Processing

Software
NameClassification
BUSTERrefinement
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementResolution: 2.5→40.84 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.91 / SU R Cruickshank DPI: 0.476 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.454 / SU Rfree Blow DPI: 0.291 / SU Rfree Cruickshank DPI: 0.298
RfactorNum. reflection% reflectionSelection details
Rfree0.279 780 8.01 %RANDOM
Rwork0.229 ---
obs0.233 9739 99.7 %-
Displacement parametersBiso mean: 116.65 Å2
Baniso -1Baniso -2Baniso -3
1-4.2563 Å20 Å2-12.9121 Å2
2---22.8791 Å20 Å2
3---18.6228 Å2
Refine analyzeLuzzati coordinate error obs: 0.47 Å
Refinement stepCycle: 1 / Resolution: 2.5→40.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1791 0 0 0 1791
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011821HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.992450HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d660SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes319HARMONIC5
X-RAY DIFFRACTIONt_it1821HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.39
X-RAY DIFFRACTIONt_other_torsion21.2
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion234SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2153SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.79 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3023 218 8.01 %
Rwork0.2492 2503 -
all0.2532 2721 -
obs--99.05 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.30691.33070.47887.01630.02946.0806-0.17330.24870.4994-0.3049-0.0392-0.5086-0.0091-0.43990.2125-0.3049-0.07080.06-0.0683-0.0622-0.179221.91922.850360.7388
26.0039-0.9495-2.90542.4257-1.02365.3314-0.0763-0.11670.2746-0.0524-0.24010.034-0.5474-0.54520.3164-0.22140.149-0.06460.304-0.1303-0.305-12.05180.010435.0153
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|1 - 101}
2X-RAY DIFFRACTION2{A|102 - 228}

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