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- PDB-4nwq: Computationally Designed Two-Component Self-Assembling Tetrahedra... -

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Basic information

Entry
Database: PDB / ID: 4nwq
TitleComputationally Designed Two-Component Self-Assembling Tetrahedral Cage, T33-21, Crystallized in Space Group F4132
Components
  • Putative uncharacterized protein PH0671
  • Uncharacterized protein
KeywordsPROTEIN BINDING / two-component / self-assembling / tetrahedron / designed protein cage / computational design / protein engineering / multimerization / nanomaterial / nanostructure / transferase / isomerase
Function / homology
Function and homology information


5-carboxymethyl-2-hydroxymuconate delta-isomerase activity / catabolic process / transferase activity / ATP binding / metal ion binding
Similarity search - Function
5-carboxymethyl-2-hydroxymuconate isomerase / 5-carboxymethyl-2-hydroxymuconate isomerase / Hypothetical Protein Ta1238; Chain: A; / Cobalamin adenosyltransferase-like / Cobalamin adenosyltransferase-like / Corrinoid adenosyltransferase, PduO-type / Cobalamin adenosyltransferase / Cobalamin adenosyltransferase-like superfamily / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor ...5-carboxymethyl-2-hydroxymuconate isomerase / 5-carboxymethyl-2-hydroxymuconate isomerase / Hypothetical Protein Ta1238; Chain: A; / Cobalamin adenosyltransferase-like / Cobalamin adenosyltransferase-like / Corrinoid adenosyltransferase, PduO-type / Cobalamin adenosyltransferase / Cobalamin adenosyltransferase-like superfamily / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Cobalamin adenosyltransferase-like domain-containing protein / 5-carboxymethyl-2-hydroxymuconate isomerase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
Pseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsMcNamara, D.E. / King, N.P. / Bale, J.B. / Sheffler, W. / Baker, D. / Yeates, T.O.
CitationJournal: Nature / Year: 2014
Title: Accurate design of co-assembling multi-component protein nanomaterials.
Authors: King, N.P. / Bale, J.B. / Sheffler, W. / McNamara, D.E. / Gonen, S. / Gonen, T. / Yeates, T.O. / Baker, D.
History
DepositionDec 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein PH0671
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,72013
Polymers33,6632
Non-polymers1,05711
Water28816
1
A: Putative uncharacterized protein PH0671
B: Uncharacterized protein
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)416,635156
Polymers403,95424
Non-polymers12,680132
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_545-z+1/2,x-1/2,-y1
crystal symmetry operation11_555y+1/2,-z,-x+1/21
crystal symmetry operation27_555-x+1/2,y,-z+1/21
crystal symmetry operation29_545z,x-1/2,y+1/21
crystal symmetry operation36_555-y,-z,x1
crystal symmetry operation50_545-x+1/2,-y-1/2,z1
crystal symmetry operation54_555z,-x,-y1
crystal symmetry operation58_545-y,z-1/2,-x+1/21
crystal symmetry operation76_545x,-y-1/2,-z+1/21
crystal symmetry operation79_555-z+1/2,-x,y+1/21
crystal symmetry operation81_545y+1/2,z-1/2,x1
Buried area70230 Å2
ΔGint-351 kcal/mol
Surface area111070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)272.180, 272.180, 272.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number210
Space group name H-MF4132
Components on special symmetry positions
IDModelComponents
11A-201-

SO4

21A-201-

SO4

31A-205-

SO4

41B-201-

SO4

51B-201-

SO4

61B-206-

SO4

71B-206-

SO4

DetailsThe biological assembly is a protein cage with tetrahedral point group symmetry. One asymmetric unit contains one heterodimer, with each chain from a different homotrimer in the biological assembly.

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Components

#1: Protein Putative uncharacterized protein PH0671


Mass: 19316.582 Da / Num. of mol.: 1
Mutation: K85A, E88L, G89K, S92L, E95M, E126L, A130L, L133T, K140A, L143A, V144A, N147L, R148A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH0671 / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O58404
#2: Protein Uncharacterized protein


Mass: 14346.274 Da / Num. of mol.: 1 / Mutation: A27K, A74I, Q78T, A79L, E82A, E86A, G90E, A112L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA1966 / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I2D8
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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

Crystal growTemperature: 298 K / pH: 5.5
Details: 100 mM bis-tris pH 5.5, 2.12 M (NH4)2 SO4, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9716
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9716 Å / Relative weight: 1
ReflectionResolution: 2.8→96.23 Å / Num. obs: 21830 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 19.77 % / Biso Wilson estimate: 68.99 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 20.91
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 20.03 % / Rmerge(I) obs: 1.277 / Mean I/σ(I) obs: 2.94 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.21 Å96.23 Å
Translation4.21 Å96.23 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WY1 AND 3E6Q

1wy1

3e6q


Resolution: 2.8→96.23 Å / Occupancy max: 1 / Occupancy min: 0.31 / SU ML: 0.29 / σ(F): 1.35 / Phase error: 20.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.196 2184 10.01 %
Rwork0.181 --
obs0.183 21829 100 %
all-21833 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.13 Å2
Refinement stepCycle: LAST / Resolution: 2.8→96.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2041 0 55 16 2112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0012105
X-RAY DIFFRACTIONf_angle_d0.412846
X-RAY DIFFRACTIONf_dihedral_angle_d10.177765
X-RAY DIFFRACTIONf_chiral_restr0.015335
X-RAY DIFFRACTIONf_plane_restr0.002355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8002-2.86110.37431320.36451190X-RAY DIFFRACTION100
2.8611-2.92760.34081350.26751218X-RAY DIFFRACTION100
2.9276-3.00080.27581320.26581186X-RAY DIFFRACTION100
3.0008-3.0820.26251320.24181193X-RAY DIFFRACTION100
3.082-3.17270.22491340.21411205X-RAY DIFFRACTION100
3.1727-3.27510.21341340.2011204X-RAY DIFFRACTION100
3.2751-3.39220.21561340.19541209X-RAY DIFFRACTION100
3.3922-3.5280.20361350.17551207X-RAY DIFFRACTION100
3.528-3.68850.21340.17241211X-RAY DIFFRACTION100
3.6885-3.8830.16741360.16791223X-RAY DIFFRACTION100
3.883-4.12630.18851360.14861219X-RAY DIFFRACTION100
4.1263-4.44490.15681360.13371227X-RAY DIFFRACTION100
4.4449-4.89220.14661380.14151245X-RAY DIFFRACTION100
4.8922-5.60.18111390.16821248X-RAY DIFFRACTION100
5.6-7.05510.21921420.22241277X-RAY DIFFRACTION100
7.0551-96.2870.18411550.18061383X-RAY DIFFRACTION100
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)
17.0071-1.2380.87914.05630.08925.0776-0.12-0.09370.70140.06510.04470.4566-0.7079-0.40470.07590.53360.09030.05470.3047-0.00270.541542.8789-37.901857.5298
21.98530.70690.23772.43320.03411.18910.03670.27740.2299-0.08270.11260.2188-0.0134-0.2457-0.12220.4012-0.07040.07520.58280.12080.497883.8271-39.529137.3051
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 169 )
2X-RAY DIFFRACTION2chain 'B' and (resid 2 through 122 )

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