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- PDB-5hpn: A circularly permuted PduA forming an icosahedral cage -

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Basic information

Entry
Database: PDB / ID: 5hpn
TitleA circularly permuted PduA forming an icosahedral cage
ComponentsPermuted PduA
KeywordsDE NOVO PROTEIN / PduA / protein design / icosahedron / cage / BMC / MCP / microcompartment / design
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.509 Å
AuthorsLeibly, D.J. / Jorda, J. / Yeates, T.O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1332907 United States
CitationJournal: Chem.Commun.(Camb.) / Year: 2016
Title: Structure of a novel 13 nm dodecahedral nanocage assembled from a redesigned bacterial microcompartment shell protein.
Authors: Jorda, J. / Leibly, D.J. / Thompson, M.C. / Yeates, T.O.
History
DepositionJan 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2Apr 20, 2016Group: Derived calculations
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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: Permuted PduA
B: Permuted PduA
C: Permuted PduA
D: Permuted PduA
E: Permuted PduA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9866
Polymers43,8905
Non-polymers961
Water30617
1
A: Permuted PduA
B: Permuted PduA
C: Permuted PduA
D: Permuted PduA
E: Permuted PduA
hetero molecules

A: Permuted PduA
B: Permuted PduA
C: Permuted PduA
D: Permuted PduA
E: Permuted PduA
hetero molecules

A: Permuted PduA
B: Permuted PduA
C: Permuted PduA
D: Permuted PduA
E: Permuted PduA
hetero molecules

A: Permuted PduA
B: Permuted PduA
C: Permuted PduA
D: Permuted PduA
E: Permuted PduA
hetero molecules

A: Permuted PduA
B: Permuted PduA
C: Permuted PduA
D: Permuted PduA
E: Permuted PduA
hetero molecules

A: Permuted PduA
B: Permuted PduA
C: Permuted PduA
D: Permuted PduA
E: Permuted PduA
hetero molecules

A: Permuted PduA
B: Permuted PduA
C: Permuted PduA
D: Permuted PduA
E: Permuted PduA
hetero molecules

A: Permuted PduA
B: Permuted PduA
C: Permuted PduA
D: Permuted PduA
E: Permuted PduA
hetero molecules

A: Permuted PduA
B: Permuted PduA
C: Permuted PduA
D: Permuted PduA
E: Permuted PduA
hetero molecules

A: Permuted PduA
B: Permuted PduA
C: Permuted PduA
D: Permuted PduA
E: Permuted PduA
hetero molecules

A: Permuted PduA
B: Permuted PduA
C: Permuted PduA
D: Permuted PduA
E: Permuted PduA
hetero molecules

A: Permuted PduA
B: Permuted PduA
C: Permuted PduA
D: Permuted PduA
E: Permuted PduA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)527,83672
Polymers526,68460
Non-polymers1,15312
Water1,08160
TypeNameSymmetry operationNumber
crystal symmetry operation13_456y-1/2,x+1/2,-z+3/21
crystal symmetry operation14_656-y+3/2,-x+1/2,-z+3/21
crystal symmetry operation15_454y-1/2,-x+1/2,z-1/21
crystal symmetry operation16_654-y+3/2,x+1/2,z-1/21
crystal symmetry operation17_546x+1/2,z-1/2,-y+3/21
crystal symmetry operation18_544-x+1/2,z-1/2,y-1/21
crystal symmetry operation19_566-x+1/2,-z+3/2,-y+3/21
crystal symmetry operation20_564x+1/2,-z+3/2,y-1/21
crystal symmetry operation21_445z-1/2,y-1/2,-x+1/21
crystal symmetry operation22_465z-1/2,-y+3/2,x+1/21
crystal symmetry operation23_645-z+3/2,y-1/2,x+1/21
crystal symmetry operation24_665-z+3/2,-y+3/2,-x+1/21
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7890 Å2
ΔGint-87 kcal/mol
Surface area16630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.500, 144.500, 144.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number208
Space group name H-MP4232

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Components

#1: Protein
Permuted PduA


Mass: 8778.060 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.86 Å3/Da / Density % sol: 57.06 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 1.8M Ammonium Sulfate 0.1M Tris pH8.5 1.25% w/v Peg 10000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9717 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9717 Å / Relative weight: 1
ReflectionResolution: 2.509→83.43 Å / Num. obs: 18264 / % possible obs: 99.95 % / Redundancy: 10.6 % / Rsym value: 0.1335 / Net I/σ(I): 14.71
Reflection shellResolution: 2.509→2.598 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PPD

4ppd


Resolution: 2.509→83.427 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2556 1827 10 %
Rwork0.212 --
obs0.2164 18262 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.509→83.427 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2858 0 5 17 2880
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012891
X-RAY DIFFRACTIONf_angle_d1.3523934
X-RAY DIFFRACTIONf_dihedral_angle_d13.447970
X-RAY DIFFRACTIONf_chiral_restr0.06509
X-RAY DIFFRACTIONf_plane_restr0.009508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5086-2.57640.32761390.28841244X-RAY DIFFRACTION100
2.5764-2.65220.33051350.3081220X-RAY DIFFRACTION100
2.6522-2.73780.36351380.28881242X-RAY DIFFRACTION100
2.7378-2.83570.35881370.29291240X-RAY DIFFRACTION100
2.8357-2.94920.2881380.26711239X-RAY DIFFRACTION100
2.9492-3.08350.27791360.27481226X-RAY DIFFRACTION100
3.0835-3.24610.29061390.25011249X-RAY DIFFRACTION100
3.2461-3.44940.31411400.22491251X-RAY DIFFRACTION100
3.4494-3.71580.28161400.21451267X-RAY DIFFRACTION100
3.7158-4.08970.23091420.17871270X-RAY DIFFRACTION100
4.0897-4.68140.19511420.1631275X-RAY DIFFRACTION100
4.6814-5.89790.22961440.18331302X-RAY DIFFRACTION100
5.8979-83.47320.23371570.20491410X-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)
14.99431.7068-0.71125.2028-0.68124.065-0.17340.4953-0.2125-0.55310.0649-0.62640.09130.08880.09430.41860.01820.03540.3738-0.01580.372641.437112.9459149.4993
25.45882.56271.6875.72390.65443.84420.1645-0.1528-0.4035-0.3011-0.0406-0.16110.0903-0.1101-0.07640.5554-0.0538-0.07290.69240.00450.451614.889196.7967129.7432
34.7641.4761-0.91864.3499-1.38382.8438-0.0766-0.2387-0.4772-0.05930.0133-0.10690.33770.15330.02390.4770.0451-0.08290.6370.05020.382410.528793.7761151.2873
45.06651.5183-2.10894.75530.08964.3974-0.39040.5129-0.424-0.85980.1628-0.47710.3991-0.16370.25950.763-0.04140.09690.53870.00840.430233.686108.7679128.1747
53.47440.49580.261.6016-0.70095.814-0.0246-0.0601-0.1735-0.02890.0667-0.04620.4683-0.1266-0.09450.41840.0602-0.0540.40840.03650.394826.6694103.915163.1697
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 1:89)
2X-RAY DIFFRACTION2(chain B and resseq 1:89)
3X-RAY DIFFRACTION3(chain C and resseq 1:89)
4X-RAY DIFFRACTION4(chain D and resseq 1:89)
5X-RAY DIFFRACTION5(chain E and resseq 1:89)

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