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- PDB-6dm9: DHD15_extended -

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Basic information

Entry
Database: PDB / ID: 6dm9
TitleDHD15_extended
Components
  • DHD15_extended_A
  • DHD15_extended_B
KeywordsDE NOVO PROTEIN / Computational design / heterodimer / coiled-coil
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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 4, 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 1.4Apr 3, 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 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DHD15_extended_A
B: DHD15_extended_B
C: DHD15_extended_A
D: DHD15_extended_B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3215
Polymers38,2254
Non-polymers961
Water54030
1
A: DHD15_extended_A
B: DHD15_extended_B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2083
Polymers19,1122
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-39 kcal/mol
Surface area11690 Å2
MethodPISA
2
C: DHD15_extended_A
D: DHD15_extended_B


Theoretical massNumber of molelcules
Total (without water)19,1122
Polymers19,1122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-29 kcal/mol
Surface area11460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.854, 92.739, 115.333
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 DHD15_extended_A


Mass: 9529.052 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein DHD15_extended_B


Mass: 9583.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.95 Å3/Da / Density % sol: 37.01 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Ammonium sulfate, 0.1M Bis-Tris pH 6.5, 18% (v/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.00004 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 28, 2017
RadiationMonochromator: Double-crystal Si(111) and multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.83→46.37 Å / Num. obs: 27334 / % possible obs: 99.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 31.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.032 / Rrim(I) all: 0.084 / Net I/σ(I): 12.4
Reflection shellResolution: 1.83→1.87 Å / Redundancy: 6.3 % / Rmerge(I) obs: 2.747 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1646 / CC1/2: 0.259 / Rpim(I) all: 1.173 / Rrim(I) all: 2.992 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(dev_3084: ???)refinement
XDSJune 17, 2015data reduction
XDSJune 17, 2015data scaling
PHASER2.8.2.phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Computational Design Model

Resolution: 2.25→43.023 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 33.46
Details: Iterative rounds of manual model building in Coot and refinement with Phenix Refine. Ultimately, resolution was trimmed to 2.25 from the high of the 1.83 diffraction data, as the high ...Details: Iterative rounds of manual model building in Coot and refinement with Phenix Refine. Ultimately, resolution was trimmed to 2.25 from the high of the 1.83 diffraction data, as the high resolution data, as evidenced by the refinement R-factors, was deemed too weak to be useful.
RfactorNum. reflection% reflection
Rfree0.3097 1033 7.3 %
Rwork0.2609 --
obs0.2645 14150 94.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 39.03 Å2
Refinement stepCycle: LAST / Resolution: 2.25→43.023 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2446 0 5 30 2481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022454
X-RAY DIFFRACTIONf_angle_d0.4113267
X-RAY DIFFRACTIONf_dihedral_angle_d16.0341601
X-RAY DIFFRACTIONf_chiral_restr0.025385
X-RAY DIFFRACTIONf_plane_restr0.001422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2501-2.36870.35551310.31711587X-RAY DIFFRACTION82
2.3687-2.51710.35521340.30771821X-RAY DIFFRACTION93
2.5171-2.71140.35521440.31251818X-RAY DIFFRACTION95
2.7114-2.98420.35911480.29971887X-RAY DIFFRACTION96
2.9842-3.41590.31821550.27891947X-RAY DIFFRACTION99
3.4159-4.3030.27061570.21941975X-RAY DIFFRACTION99
4.303-43.03040.29961640.24622082X-RAY DIFFRACTION98
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)
10.04340.288-0.22420.18760.16740.6199-0.08680.07350.07720.0172-0.22820.06-0.245-0.141-0.03710.43580.0569-0.00720.4365-0.01540.383112.928339.685361.239
20.19430.11460.40520.33210.48222.3622-0.1008-0.0713-0.07760.0512-0.2789-0.0260.86480.3402-0.03950.4147-0.0010.00960.28840.04110.358316.801230.731162.1054
3-0.10060.0125-0.4110.57060.14262.1778-0.0907-0.0255-0.03870.1214-0.2135-0.0858-0.53480.91710.01190.3365-0.02-0.00490.49250.06230.370319.95336.298765.9131
40.1548-0.07390.1670.51150.02211.65620.0538-0.0592-0.0235-0.1098-0.1850.00020.3064-0.56640.0030.3368-0.0879-0.00010.4689-0.03550.384310.221433.82865.1559
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'D' and resid 78 through 151)
2X-RAY DIFFRACTION2(chain 'A' and resid 0 through 77)
3X-RAY DIFFRACTION3(chain 'B' and resid 78 through 152)
4X-RAY DIFFRACTION4(chain 'C' and resid 0 through 77)

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