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

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Basic information

Entry
Database: PDB / ID: 4nwo
TitleComputationally Designed Two-Component Self-Assembling Tetrahedral Cage T33-15
Components
  • Chorismate mutase AroH
  • Molybdenum cofactor biosynthesis protein MogA
KeywordsPROTEIN BINDING / two-component / self-assembling / tetrahedron / designed protein cage / computational design / protein engineering / multimerization / nanomaterial / nanostructure / molybdenum cofactor biosynthesis protein / mog / chorismate mutase / isomerase
Function / homology
Function and homology information


chorismate metabolic process / chorismate mutase / chorismate mutase activity / Mo-molybdopterin cofactor biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / metal ion binding / cytoplasm
Similarity search - Function
Chorismate mutase, AroH class / Chorismate mutase type I / Chorismate mutase domain profile. / Molybdenum cofactor biosynthesis proteins signature 1. / RutC-like / Molybdenum cofactor biosynthesis, conserved site / RutC-like superfamily / MoaB/Mog-like domain / Molybdenum Cofactor Biosythetic Enzyme; Chain A / MoaB/Mog domain ...Chorismate mutase, AroH class / Chorismate mutase type I / Chorismate mutase domain profile. / Molybdenum cofactor biosynthesis proteins signature 1. / RutC-like / Molybdenum cofactor biosynthesis, conserved site / RutC-like superfamily / MoaB/Mog-like domain / Molybdenum Cofactor Biosythetic Enzyme; Chain A / MoaB/Mog domain / MoaB/Mog-like domain superfamily / Probable molybdopterin binding domain / Probable molybdopterin binding domain / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chorismate mutase AroH / Chorismate mutase AroH / Molybdenum cofactor biosynthesis protein MogA
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
Thermus thermophilus (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_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: Molybdenum cofactor biosynthesis protein MogA
B: Chorismate mutase AroH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6043
Polymers33,5642
Non-polymers401
Water362
1
A: Molybdenum cofactor biosynthesis protein MogA
B: Chorismate mutase AroH
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)403,24636
Polymers402,76524
Non-polymers48112
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_564z,x+1,y-11
crystal symmetry operation9_465y-1,z+1,x1
crystal symmetry operation28_597x,-y+9/2,-z+5/21
crystal symmetry operation30_588z,-x+7/2,-y+7/21
crystal symmetry operation35_487y-1,-z+7/2,-x+5/21
crystal symmetry operation51_757-x+5/2,y,-z+5/21
crystal symmetry operation56_768-z+5/2,x+1,-y+7/21
crystal symmetry operation58_867-y+7/2,z+1,-x+5/21
crystal symmetry operation74_795-x+5/2,-y+9/2,z1
crystal symmetry operation79_784-z+5/2,-x+7/2,y-11
crystal symmetry operation84_885-y+7/2,-z+7/2,x1
Buried area52360 Å2
ΔGint-532 kcal/mol
Surface area112540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)213.520, 213.520, 213.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432

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Components

#1: Protein Molybdenum cofactor biosynthesis protein MogA


Mass: 19049.074 Da / Num. of mol.: 1
Mutation: Y20T, E21A, D30L, T31A, D34L, F110E, K135D, K137A, R140S, E141D, D144L, V168M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Gene: mogA, SO_0065 / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8EKM7
#2: Protein Chorismate mutase AroH


Mass: 14514.650 Da / Num. of mol.: 1
Mutation: E12N, E13S, E17T, A18S, H20I, Q21I, R24I, E25L, L28E, R109S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: aroG, aroH / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q84FH6, UniProt: Q5SJY4*PLUS, chorismate mutase
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.02 Å3/Da / Density % sol: 59.29 %
Crystal growTemperature: 298 K / pH: 6.5
Details: 100 mM sodium cacodylate pH 6.5, 200 mM calcium acetate, 28% (v/v) PEG 300, 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: 0.9792
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.8→75.491 Å / Num. obs: 10783 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 13.59 % / Biso Wilson estimate: 79.22 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 19.43
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 14.34 % / Rmerge(I) obs: 1.863 / Mean I/σ(I) obs: 2.25 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.81 Å75.49 Å
Translation6.81 Å75.49 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: 3K6A AND 1UFY

3k6a

1ufy


Resolution: 2.8→75.49 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.38 / σ(F): 1.34 / Phase error: 25.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.252 1079 10.01 %
Rwork0.202 --
obs0.207 10782 99.9 %
all-10796 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.65 Å2
Refinement stepCycle: LAST / Resolution: 2.8→75.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2008 0 1 2 2011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032041
X-RAY DIFFRACTIONf_angle_d0.772805
X-RAY DIFFRACTIONf_dihedral_angle_d10.277705
X-RAY DIFFRACTIONf_chiral_restr0.028364
X-RAY DIFFRACTIONf_plane_restr0.005357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8008-2.92820.37471300.29671167X-RAY DIFFRACTION100
2.9282-3.08260.33931320.28161183X-RAY DIFFRACTION100
3.0826-3.27580.30361310.24721183X-RAY DIFFRACTION100
3.2758-3.52870.28391310.20771179X-RAY DIFFRACTION100
3.5287-3.88380.25071340.18211206X-RAY DIFFRACTION100
3.8838-4.44570.22551350.17851217X-RAY DIFFRACTION100
4.4457-5.60080.23811360.17611225X-RAY DIFFRACTION100
5.6008-75.51810.2281500.21141343X-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)
13.9602-1.756-1.39864.33820.41564.6552-0.0492-0.13420.01630.1836-0.13960.1034-0.1954-0.19350.17820.546-0.0721-0.03910.5929-0.03110.547229.3791451.4425254.2646
22.84611.9792-1.8934.8858-3.18138.49520.09480.0219-0.3252-0.08720.06540.21540.368-0.1152-0.16130.610.0139-0.08880.6411-0.08650.6688238.0269450.3726281.1316
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 173 )
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 114 )

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