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- PDB-6dlm: DHD127 -

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Basic information

Entry
Database: PDB / ID: 6dlm
TitleDHD127
Components
  • DHD127_A
  • DHD127_B
KeywordsDE NOVO PROTEIN / Computational design / heterodimer / coiled-coil
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.753 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
DepositionJun 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
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: DHD127_A
B: DHD127_B


Theoretical massNumber of molelcules
Total (without water)18,3332
Polymers18,3332
Non-polymers00
Water2,684149
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: SAXS, Theoretical and experimental curves match, and Radius of gyration agrees with the design model., mass spectrometry, Native mass spectrometry confirmed the presence of the heterodimer ...Evidence: SAXS, Theoretical and experimental curves match, and Radius of gyration agrees with the design model., mass spectrometry, Native mass spectrometry confirmed the presence of the heterodimer in solution., gel filtration, Protein eluted as a monodisperse peak at the expected volume.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-18 kcal/mol
Surface area8560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.918, 48.755, 64.152
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DHD127_A


Mass: 9119.329 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 DHD127_B


Mass: 9213.521 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)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 35.8 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Molecular Dimensions Morpheus condition E9 - 0.12M Ethylene glycols (0.3M Diethylene glycol; 0.3M Triethylene glycol; 0.3M Tetraethylene glycol; 0.3M Pentaethylene glycol), 0.1M Buffer ...Details: Molecular Dimensions Morpheus condition E9 - 0.12M Ethylene glycols (0.3M Diethylene glycol; 0.3M Triethylene glycol; 0.3M Tetraethylene glycol; 0.3M Pentaethylene glycol), 0.1M Buffer System 3 (1.0M Tris (base); BICINE, pH 8.5 at 20C), pH 8.5, 50% (v/v) Precipitant Mix 1 (40% v/v PEG 500* MME; 20% w/v PEG 20000)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.999995 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 28, 2018
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999995 Å / Relative weight: 1
ReflectionResolution: 1.75→40 Å / Num. obs: 14674 / % possible obs: 100 % / Redundancy: 7.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.048 / Rrim(I) all: 0.132 / Χ2: 1.219 / Net I/σ(I): 18.1
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.734 / Mean I/σ(I) obs: 2.16 / Num. unique obs: 1189 / CC1/2: 0.848 / Rpim(I) all: 0.282 / Rrim(I) all: 0.787 / Χ2: 0.599 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(dev_3084: ???)refinement
HKL-2000715data reduction
HKL-2000715data scaling
PHASER2.8.0.phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Computational design model

Resolution: 1.753→38.817 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.77
Details: Iterative rounds of manual model building in Coot and refinement with Phenix.
RfactorNum. reflection% reflection
Rfree0.2085 687 4.73 %
Rwork0.1968 --
obs0.1974 14512 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.1 Å2
Refinement stepCycle: LAST / Resolution: 1.753→38.817 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1241 0 0 149 1390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111293
X-RAY DIFFRACTIONf_angle_d1.1571734
X-RAY DIFFRACTIONf_dihedral_angle_d24.268846
X-RAY DIFFRACTIONf_chiral_restr0.073197
X-RAY DIFFRACTIONf_plane_restr0.008232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7534-1.88880.32811340.26132708X-RAY DIFFRACTION99
1.8888-2.07890.31921150.27342667X-RAY DIFFRACTION97
2.0789-2.37970.2311190.19872772X-RAY DIFFRACTION99
2.3797-2.9980.20091610.18292774X-RAY DIFFRACTION100
2.998-38.82650.17131580.17522904X-RAY DIFFRACTION100

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