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- PDB-6egc: Single-chain version of 2L4HC2_23 (PDB 5J0K) -

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Basic information

Entry
Database: PDB / ID: 6egc
TitleSingle-chain version of 2L4HC2_23 (PDB 5J0K)
ComponentsSC_2L4HC2_23
KeywordsDE NOVO PROTEIN / Computational Design / helical bundle / coiled-coil
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsBick, M.J. / Chen, Z. / DiMaio, F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM123089 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Self-Assembling 2D Arrays with de Novo Protein Building Blocks.
Authors: Chen, Z. / Johnson, M.C. / Chen, J. / Bick, M.J. / Boyken, S.E. / Lin, B. / De Yoreo, J.J. / Kollman, J.M. / Baker, D. / DiMaio, F.
History
DepositionAug 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: 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_author.identifier_ORCID
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 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 1.4Apr 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: SC_2L4HC2_23


Theoretical massNumber of molelcules
Total (without water)19,0311
Polymers19,0311
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Protein elutes as a monodisperse peak at the expected mass
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.253, 49.360, 41.239
Angle α, β, γ (deg.)90.00, 104.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SC_2L4HC2_23


Mass: 19030.600 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.19 Å3/Da / Density % sol: 43.72 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Molecular Dimensions Morpheus H9 (0.1M Amino acids, 0.1M Buffer System 3 pH 8.5, 50% (v/v) Precipitant Mix 1)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.999978 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 9, 2016
RadiationMonochromator: Double-crystal Si(111) and multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999978 Å / Relative weight: 1
ReflectionResolution: 1.47→50 Å / Num. obs: 20818 / % possible obs: 75.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.034 / Rrim(I) all: 0.064 / Χ2: 0.908 / Net I/av σ(I): 15.2 / Net I/σ(I): 7.3
Reflection shellResolution: 1.47→1.5 Å / Redundancy: 1.1 % / Rmerge(I) obs: 2.723 / Mean I/σ(I) obs: 0.15 / Num. unique obs: 79 / CC1/2: 0.647 / Rrim(I) all: 3.794 / Χ2: 0.119 / % possible all: 5.8

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Processing

Software
NameVersionClassification
PHENIX(dev_3112: ???)refinement
HKL-2000v715data reduction
HKL-2000v715data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Computational design model

Resolution: 1.74→22.52 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 32.84
Details: Iterative rounds of model building in Coot and refinement in Phenix.
RfactorNum. reflection% reflection
Rfree0.2658 1461 9.57 %
Rwork0.2266 --
obs0.2304 15269 92.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 58.9 Å2
Refinement stepCycle: LAST / Resolution: 1.74→22.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1128 0 0 47 1175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191135
X-RAY DIFFRACTIONf_angle_d1.4481522
X-RAY DIFFRACTIONf_dihedral_angle_d14.404735
X-RAY DIFFRACTIONf_chiral_restr0.072185
X-RAY DIFFRACTIONf_plane_restr0.008199
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7401-1.80220.42041210.38691120X-RAY DIFFRACTION76
1.8022-1.87430.36031260.32351204X-RAY DIFFRACTION80
1.8743-1.95960.34141330.27511271X-RAY DIFFRACTION86
1.9596-2.06290.28511530.25351395X-RAY DIFFRACTION94
2.0629-2.1920.31791500.22371448X-RAY DIFFRACTION97
2.192-2.36110.26191490.21861478X-RAY DIFFRACTION99
2.3611-2.59840.261620.21791490X-RAY DIFFRACTION99
2.5984-2.97360.25271620.23211493X-RAY DIFFRACTION100
2.9736-3.74370.27381590.21931506X-RAY DIFFRACTION100
3.7437-22.52190.24351460.21781403X-RAY DIFFRACTION91
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)
14.0929-0.7142-1.88160.81431.31928.23980.33040.78440.2886-0.2647-0.34660.1158-0.5885-0.8759-0.17950.40040.0513-0.06590.4075-0.00460.39997.277226.1111.7753
28.58690.467-2.891.9029-0.5474.7551-0.0177-0.6264-0.49760.163-0.1920.22370.1743-0.27520.4380.3319-0.0432-0.02670.3528-0.05350.36116.753518.76136.6441
33.74491.0898-2.25562.0943-1.67447.11050.6286-1.4834-0.570.5114-0.7572-0.3195-0.20021.040.1760.3925-0.0381-0.07040.44560.05140.347815.722321.784312.5267
45.9563-0.1048-3.90781.82330.1827.720.3056-0.35180.37260.2587-0.19460.0775-0.3192-0.2349-0.20050.3614-0.0407-0.03730.3528-0.05070.312911.568429.349611.0825
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 35 )
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 73 )
3X-RAY DIFFRACTION3chain 'A' and (resid 79 through 112 )
4X-RAY DIFFRACTION4chain 'A' and (resid 113 through 151 )

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