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- PDB-6x1i: Two-Component D3 Assembly Constructed by Fusing Symmetric Oligome... -

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Basic information

Entry
Database: PDB / ID: 6x1i
TitleTwo-Component D3 Assembly Constructed by Fusing Symmetric Oligomers to Coiled Coils
Components
  • Cob_adeno_trans domain-containing protein PH0671 fused to a coiled coil
  • SnoaL-like Protein fused to a coiled coil
KeywordsBIOSYNTHETIC PROTEIN / Two-Component / Self-Assembling / Symmetric / D3 / Coiled Coil / Helical Fusion / Design
Function / homology
Function and homology information


corrinoid adenosyltransferase activity / ATP binding / metal ion binding
Similarity search - Function
Cobalamin adenosyltransferase-like / Corrinoid adenosyltransferase, PduO-type / Cobalamin adenosyltransferase / Cobalamin adenosyltransferase-like superfamily / SnoaL-like domain / SnoaL-like domain / NTF2-like domain superfamily
Similarity search - Domain/homology
Cobalamin adenosyltransferase-like domain-containing protein / SnoaL-like domain-containing protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
Pyrococcus horikoshii OT3 (archaea)
Agrobacterium fabrum str. C58 (bacteria)
Agrobacterium fabrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.32 Å
AuthorsLaniado, J. / Yeates, T.O. / Sawaya, M.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1629214 United States
CitationJournal: Acs Nano / Year: 2021
Title: Geometric Lessons and Design Strategies for Nanoscale Protein Cages.
Authors: Laniado, J. / Cannon, K.A. / Miller, J.E. / Sawaya, M.R. / McNamara, D.E. / Yeates, T.O.
History
DepositionMay 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Apr 7, 2021Group: 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 1.3Oct 18, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cob_adeno_trans domain-containing protein PH0671 fused to a coiled coil
B: SnoaL-like Protein fused to a coiled coil


Theoretical massNumber of molelcules
Total (without water)37,0752
Polymers37,0752
Non-polymers00
Water00
1
A: Cob_adeno_trans domain-containing protein PH0671 fused to a coiled coil
B: SnoaL-like Protein fused to a coiled coil

A: Cob_adeno_trans domain-containing protein PH0671 fused to a coiled coil
B: SnoaL-like Protein fused to a coiled coil

A: Cob_adeno_trans domain-containing protein PH0671 fused to a coiled coil
B: SnoaL-like Protein fused to a coiled coil

A: Cob_adeno_trans domain-containing protein PH0671 fused to a coiled coil
B: SnoaL-like Protein fused to a coiled coil

A: Cob_adeno_trans domain-containing protein PH0671 fused to a coiled coil
B: SnoaL-like Protein fused to a coiled coil

A: Cob_adeno_trans domain-containing protein PH0671 fused to a coiled coil
B: SnoaL-like Protein fused to a coiled coil


Theoretical massNumber of molelcules
Total (without water)222,45212
Polymers222,45212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation14_555-y+1/4,-x+1/4,-z+1/41
crystal symmetry operation19_555-x+1/4,-z+1/4,-y+1/41
crystal symmetry operation24_555-z+1/4,-y+1/4,-x+1/41
Unit cell
Length a, b, c (Å)146.340, 146.340, 146.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number212
Space group name H-MP4332
Space group name HallP4acd2ab3
Symmetry operation#1: x,y,z
#2: x+3/4,-z+3/4,y+1/4
#3: x+1/4,z+3/4,-y+3/4
#4: z+1/4,y+3/4,-x+3/4
#5: -z+3/4,y+1/4,x+3/4
#6: -y+3/4,x+1/4,z+3/4
#7: y+3/4,-x+3/4,z+1/4
#8: z,x,y
#9: y,z,x
#10: -y+1/2,-z,x+1/2
#11: z+1/2,-x+1/2,-y
#12: -y,z+1/2,-x+1/2
#13: -z+1/2,-x,y+1/2
#14: -z,x+1/2,-y+1/2
#15: y+1/2,-z+1/2,-x
#16: x+1/2,-y+1/2,-z
#17: -x,y+1/2,-z+1/2
#18: -x+1/2,-y,z+1/2
#19: y+1/4,x+3/4,-z+3/4
#20: -y+1/4,-x+1/4,-z+1/4
#21: z+3/4,-y+3/4,x+1/4
#22: -z+1/4,-y+1/4,-x+1/4
#23: -x+3/4,z+1/4,y+3/4
#24: -x+1/4,-z+1/4,-y+1/4

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Components

#1: Protein Cob_adeno_trans domain-containing protein PH0671 fused to a coiled coil


Mass: 19430.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (archaea), (gene. exp.) Pyrococcus horikoshii OT3 (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: PH0671 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O58404
#2: Protein SnoaL-like Protein fused to a coiled coil


Mass: 17644.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum str. C58 (bacteria), (gene. exp.) Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria)
Strain: C58 / ATCC 33970 / Gene: Atu0744 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7D0S4

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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: 3.52 Å3/Da / Density % sol: 65.08 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: Reagent Well: - 10ul of Silver Bullets additive screen reagent B9: 0.25% w/v Hexamminecobalt(III) chloride, 0.25% w/v Salicylamide, 0.25% w/v Sulfanilamide, 0.25% w/v Vanillic acid, 0.02 M ...Details: Reagent Well: - 10ul of Silver Bullets additive screen reagent B9: 0.25% w/v Hexamminecobalt(III) chloride, 0.25% w/v Salicylamide, 0.25% w/v Sulfanilamide, 0.25% w/v Vanillic acid, 0.02 M HEPES sodium pH 6.8 - 90ul of crystallization reagent: 0.10 M Sodium Acetate pH 5.4, 66% MPD Drop: - 2:1 protein sample to well reagent ratio - Protein sample: 2.8mg/ml of purified protein in 0.5M NaCl, 5% Glycerol, 2.8mM beta-mercaptoethanol, 50 mM Tris pH 7.5, 5mM MgCl2 sample buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 4.32→84.5 Å / Num. obs: 3945 / % possible obs: 99.7 % / Redundancy: 17.657 % / Biso Wilson estimate: 237.211 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.095 / Rrim(I) all: 0.099 / Χ2: 0.998 / Net I/σ(I): 14.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
4.32-4.4416.7652.3741.32810.4112.44996.9
4.44-4.5618.8561.8871.952640.7461.939100
4.56-4.6917.951.5772.282580.791.62399.6
4.69-4.8316.8680.9983.242650.8791.029100
4.83-4.9919.3360.6075.172470.9880.624100
4.99-5.1719.5590.5585.672470.9830.573100
5.17-5.36190.49862420.9930.512100
5.36-5.5819.0220.5365.872260.9860.551100
5.58-5.8318.3710.6165.362130.970.634100
5.83-6.1117.7290.5336.132180.9740.548100
6.11-6.4416.6230.4287.452040.9660.442100
6.44-6.8319.120.20415.211910.9930.209100
6.83-7.3118.5680.13122.441850.9980.135100
7.31-7.8917.9650.09231.21720.9980.094100
7.89-8.6516.5150.07236.031650.9980.074100
8.65-9.6714.8840.05942.661460.9980.061100
9.67-11.1616.3560.05449.341350.9990.056100
11.16-13.6715.210.04949.61190.9990.051100
13.67-19.3313.1730.04347.32980.9990.044100
19.33-84.511.7390.04546.86910.04897.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSVERSION Oct 15, 2015data reduction
XSCALEVERSION Oct 15, 2015data scaling
PHASER2.8.3phasing
PHENIXdev 3724refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WY1, 3DXO

1wy1

3dxo


Resolution: 4.32→84.49 Å / SU ML: 0.6069 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 43.638
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2926 391 10 %
Rwork0.2778 3519 -
obs0.2796 3910 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 267.69 Å2
Refinement stepCycle: LAST / Resolution: 4.32→84.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2507 0 0 0 2507
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00422543
X-RAY DIFFRACTIONf_angle_d0.92023421
X-RAY DIFFRACTIONf_chiral_restr0.0522380
X-RAY DIFFRACTIONf_plane_restr0.0039443
X-RAY DIFFRACTIONf_dihedral_angle_d14.7134966
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.32-4.950.42511240.40391122X-RAY DIFFRACTION98.97
4.95-6.230.45571270.45191145X-RAY DIFFRACTION99.45
6.24-84.490.24681400.22681252X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -21.6837214664 Å / Origin y: -3.49920025763 Å / Origin z: 4.27013204244 Å
111213212223313233
T1.75171890574 Å2-0.43226750827 Å2-0.0701406520304 Å2-2.06183065063 Å20.313834654617 Å2--1.44975340898 Å2
L2.89094022973 °22.48600199681 °20.932657103822 °2-8.82866925215 °24.03708450741 °2--2.90858788207 °2
S0.835757290141 Å °-0.462621168491 Å °-0.045012249451 Å °0.551176001079 Å °-1.55494478699 Å °0.479707903664 Å °-0.124552175224 Å °-0.755072867776 Å °0.570331786576 Å °
Refinement TLS groupSelection details: all

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