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- PDB-6dkm: DHD131 -

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Basic information

Entry
Database: PDB / ID: 6dkm
TitleDHD131
Components
  • DHD131_A
  • DHD131_B
KeywordsDE NOVO PROTEIN / Computational Design / Heterodimer / Coiled-coil
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 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 29, 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

Downloads & links

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Assembly

Deposited unit
A: DHD131_A
B: DHD131_B
C: DHD131_A
D: DHD131_B
E: DHD131_A
F: DHD131_B
G: DHD131_A
H: DHD131_B


Theoretical massNumber of molelcules
Total (without water)77,8998
Polymers77,8998
Non-polymers00
Water1,13563
1
A: DHD131_A
B: DHD131_B


Theoretical massNumber of molelcules
Total (without water)19,4752
Polymers19,4752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-25 kcal/mol
Surface area9030 Å2
MethodPISA
2
C: DHD131_A
D: DHD131_B


Theoretical massNumber of molelcules
Total (without water)19,4752
Polymers19,4752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-22 kcal/mol
Surface area9310 Å2
MethodPISA
3
E: DHD131_A
F: DHD131_B


Theoretical massNumber of molelcules
Total (without water)19,4752
Polymers19,4752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-22 kcal/mol
Surface area8050 Å2
MethodPISA
4
G: DHD131_A
H: DHD131_B


Theoretical massNumber of molelcules
Total (without water)19,4752
Polymers19,4752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-24 kcal/mol
Surface area9060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.199, 74.709, 105.257
Angle α, β, γ (deg.)90.00, 92.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DHD131_A


Mass: 9540.786 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein
DHD131_B


Mass: 9933.978 Da / Num. of mol.: 4
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 / Water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.17 Å3/Da / Density % sol: 37.76 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M Ammonium acetate, 0.1M HEPES pH 7.5, 25% (w/v) Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.977017 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 2, 2018
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977017 Å / Relative weight: 1
ReflectionResolution: 2.38→42.99 Å / Num. obs: 24465 / % possible obs: 99.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 31.51 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.18 / Rpim(I) all: 0.102 / Rrim(I) all: 0.207 / Net I/σ(I): 6.6
Reflection shellResolution: 2.38→2.47 Å / Redundancy: 4.2 % / Rmerge(I) obs: 1.56 / Mean I/σ(I) obs: 1 / Num. unique obs: 2584 / CC1/2: 0.344 / Rpim(I) all: 0.878 / Rrim(I) all: 1.794 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(dev_3112: ???)refinement
XDSJune 17, 2015data reduction
XDSJune 17, 2015data scaling
PHASER2.8.0.phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Computational design model

Resolution: 2.38→42.99 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 31.78
Details: Iterative rounds of model building in Coot and refinement with Phenix.
RfactorNum. reflection% reflection
Rfree0.2832 1738 8.14 %
Rwork0.2408 --
obs0.2443 21356 87.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.38→42.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4622 0 0 63 4685
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024650
X-RAY DIFFRACTIONf_angle_d0.4466258
X-RAY DIFFRACTIONf_dihedral_angle_d14.742933
X-RAY DIFFRACTIONf_chiral_restr0.024741
X-RAY DIFFRACTIONf_plane_restr0.001803
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3801-2.45010.44561210.3441379X-RAY DIFFRACTION73
2.4501-2.52920.40131220.3251384X-RAY DIFFRACTION75
2.5292-2.61960.3611220.33141462X-RAY DIFFRACTION77
2.6196-2.72440.38511260.31411450X-RAY DIFFRACTION79
2.7244-2.84840.35361410.28461541X-RAY DIFFRACTION82
2.8484-2.99850.31211470.27121578X-RAY DIFFRACTION85
2.9985-3.18630.2981540.25921659X-RAY DIFFRACTION90
3.1863-3.43230.29751630.24421790X-RAY DIFFRACTION95
3.4323-3.77750.27511510.20351815X-RAY DIFFRACTION96
3.7775-4.32370.231610.19181836X-RAY DIFFRACTION97
4.3237-5.44560.21961620.19941831X-RAY DIFFRACTION98
5.4456-42.99880.24661680.23391893X-RAY DIFFRACTION98

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