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- PDB-6dlc: Designed protein DHD1:234_A, Designed protein DHD1:234_B -

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Basic information

Entry
Database: PDB / ID: 6dlc
TitleDesigned protein DHD1:234_A, Designed protein DHD1:234_B
Components
  • Designed protein DHD1:234_A
  • Designed protein DHD1:234_B
KeywordsDE NOVO PROTEIN / Computational Design / Heterodimer / Coiled-coil
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.261 Å
AuthorsBick, M.J. / Chen, Z. / Baker, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2019
Title: Programmable design of orthogonal protein heterodimers.
Authors: Chen, Z. / Boyken, S.E. / Jia, M. / Busch, F. / Flores-Solis, D. / Bick, M.J. / Lu, P. / VanAernum, Z.L. / Sahasrabuddhe, A. / Langan, R.A. / Bermeo, S. / Brunette, T.J. / Mulligan, V.K. / ...Authors: Chen, Z. / Boyken, S.E. / Jia, M. / Busch, F. / Flores-Solis, D. / Bick, M.J. / Lu, P. / VanAernum, Z.L. / Sahasrabuddhe, A. / Langan, R.A. / Bermeo, S. / Brunette, T.J. / Mulligan, V.K. / Carter, L.P. / DiMaio, F. / Sgourakis, N.G. / Wysocki, V.H. / Baker, D.
History
DepositionMay 31, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2019Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 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 1.5Apr 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: Designed protein DHD1:234_A
B: Designed protein DHD1:234_B


Theoretical massNumber of molelcules
Total (without water)18,0752
Polymers18,0752
Non-polymers00
Water00
1
A: Designed protein DHD1:234_A
B: Designed protein DHD1:234_B

A: Designed protein DHD1:234_A
B: Designed protein DHD1:234_B


Theoretical massNumber of molelcules
Total (without water)36,1504
Polymers36,1504
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
Buried area5670 Å2
ΔGint-68 kcal/mol
Surface area15030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.885, 96.885, 27.846
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein Designed protein DHD1:234_A


Mass: 13897.054 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: Protein/peptide Designed protein DHD1:234_B


Mass: 4177.902 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)

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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: 2.22 Å3/Da / Density % sol: 44.7 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.15M Potassium bromide, 30% (w/v) PEG 2,000 MME, plus 20% glycerol as cryoprotectant

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.999954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 14, 2017
RadiationMonochromator: Double-crystal Si(111) and multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999954 Å / Relative weight: 1
ReflectionResolution: 3.26→48.44 Å / Num. obs: 2485 / % possible obs: 99.8 % / Redundancy: 7.6 % / Biso Wilson estimate: 109.04 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.049 / Rrim(I) all: 0.135 / Net I/σ(I): 9.7
Reflection shellResolution: 3.26→3.52 Å / Redundancy: 7.8 % / Rmerge(I) obs: 1.343 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 512 / CC1/2: 0.472 / Rpim(I) all: 0.708 / Rrim(I) all: 1.44 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIXdev_3112refinement
XDSJune 17, 2015data reduction
XDSJune 17, 2015data scaling
PHASER2.5.6.phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Computational Design Model

Resolution: 3.261→48.44 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.34
RfactorNum. reflection% reflection
Rfree0.2855 252 10.15 %
Rwork0.2583 --
obs0.2614 2482 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 117.01 Å2
Refinement stepCycle: LAST / Resolution: 3.261→48.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms932 0 0 0 932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003941
X-RAY DIFFRACTIONf_angle_d0.6381286
X-RAY DIFFRACTIONf_dihedral_angle_d8.952575
X-RAY DIFFRACTIONf_chiral_restr0.034169
X-RAY DIFFRACTIONf_plane_restr0.005164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2609-4.1080.34221180.29961105X-RAY DIFFRACTION100
4.108-48.44780.26991340.24431125X-RAY DIFFRACTION100

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