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- PDB-3vcd: Computationally Designed Self-assembling Octahedral Cage protein,... -

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Basic information

Entry
Database: PDB / ID: 3vcd
TitleComputationally Designed Self-assembling Octahedral Cage protein, O333, Crystallized in space group R32
ComponentsPropanediol utilization polyhedral body protein PduT
KeywordsELECTRON TRANSPORT / self assembling octahedral cage design
Function / homology
Function and homology information


propanediol degradation polyhedral organelle / propanediol catabolic process / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Bacterial microcompartment shell protein PduT / BMC (bacterial microcompartment) domain / CcmK/CsoS1, bacterial microcompartment domain / Bacterial microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain / CcmK-like superfamily / BMC / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Bacterial microcompartment shell protein PduT
Similarity search - Component
Biological speciesSalmonella enterica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsSawaya, M.R. / King, N.P. / Sheffler, W. / Baker, D. / Yeates, T.O.
CitationJournal: Science / Year: 2012
Title: Computational design of self-assembling protein nanomaterials with atomic level accuracy.
Authors: Neil P King / William Sheffler / Michael R Sawaya / Breanna S Vollmar / John P Sumida / Ingemar André / Tamir Gonen / Todd O Yeates / David Baker /
Abstract: We describe a general computational method for designing proteins that self-assemble to a desired symmetric architecture. Protein building blocks are docked together symmetrically to identify ...We describe a general computational method for designing proteins that self-assemble to a desired symmetric architecture. Protein building blocks are docked together symmetrically to identify complementary packing arrangements, and low-energy protein-protein interfaces are then designed between the building blocks in order to drive self-assembly. We used trimeric protein building blocks to design a 24-subunit, 13-nm diameter complex with octahedral symmetry and a 12-subunit, 11-nm diameter complex with tetrahedral symmetry. The designed proteins assembled to the desired oligomeric states in solution, and the crystal structures of the complexes revealed that the resulting materials closely match the design models. The method can be used to design a wide variety of self-assembling protein nanomaterials.
History
DepositionJan 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: Propanediol utilization polyhedral body protein PduT
B: Propanediol utilization polyhedral body protein PduT
C: Propanediol utilization polyhedral body protein PduT
D: Propanediol utilization polyhedral body protein PduT
E: Propanediol utilization polyhedral body protein PduT
F: Propanediol utilization polyhedral body protein PduT
G: Propanediol utilization polyhedral body protein PduT
H: Propanediol utilization polyhedral body protein PduT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,24635
Polymers159,7138
Non-polymers2,53327
Water6,756375
1
A: Propanediol utilization polyhedral body protein PduT
B: Propanediol utilization polyhedral body protein PduT
C: Propanediol utilization polyhedral body protein PduT
D: Propanediol utilization polyhedral body protein PduT
E: Propanediol utilization polyhedral body protein PduT
F: Propanediol utilization polyhedral body protein PduT
G: Propanediol utilization polyhedral body protein PduT
H: Propanediol utilization polyhedral body protein PduT
hetero molecules

A: Propanediol utilization polyhedral body protein PduT
B: Propanediol utilization polyhedral body protein PduT
C: Propanediol utilization polyhedral body protein PduT
D: Propanediol utilization polyhedral body protein PduT
E: Propanediol utilization polyhedral body protein PduT
F: Propanediol utilization polyhedral body protein PduT
G: Propanediol utilization polyhedral body protein PduT
H: Propanediol utilization polyhedral body protein PduT
hetero molecules

A: Propanediol utilization polyhedral body protein PduT
B: Propanediol utilization polyhedral body protein PduT
C: Propanediol utilization polyhedral body protein PduT
D: Propanediol utilization polyhedral body protein PduT
E: Propanediol utilization polyhedral body protein PduT
F: Propanediol utilization polyhedral body protein PduT
G: Propanediol utilization polyhedral body protein PduT
H: Propanediol utilization polyhedral body protein PduT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)486,737105
Polymers479,13824
Non-polymers7,59981
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area72410 Å2
ΔGint-1564 kcal/mol
Surface area147210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.920, 137.920, 560.570
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein
Propanediol utilization polyhedral body protein PduT


Mass: 19964.084 Da / Num. of mol.: 8
Mutation: K15A, C38S, M67L, N148A, N149L, E156S, E160A, K161Y, R167A, V169L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica (bacteria) / Gene: PduT / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E7V033, UniProt: Q9XDM8*PLUS
#2: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 3.21 Å3/Da / Density % sol: 61.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.8M sodium phosphate monobasic, 1.2M potassium phosphate dibasic, 0.1 M sodium acetate, pH 4.5, 10 mM L-proline, crystal soaked in 2M lithium sulfate as cryoprotectant, VAPOR DIFFUSION, ...Details: 0.8M sodium phosphate monobasic, 1.2M potassium phosphate dibasic, 0.1 M sodium acetate, pH 4.5, 10 mM L-proline, crystal soaked in 2M lithium sulfate as cryoprotectant, 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: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2011
RadiationMonochromator: Cryo-Cooled Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.35→100 Å / Num. all: 81734 / Num. obs: 81734 / % possible obs: 95 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 72.1 Å2 / Rmerge(I) obs: 0.066 / Χ2: 1 / Net I/σ(I): 14.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.35-2.433.70.50975161.097188.5
2.43-2.533.80.36375231.079188.3
2.53-2.653.90.2974521.09187.5
2.65-2.793.90.20274321.071187.1
2.79-2.968.40.2184560.894199.2
2.96-3.198.80.13885660.9171100
3.19-3.518.80.185871.0231100
3.51-4.028.80.08486071.0691100
4.02-5.068.60.05886910.9771100
5.06-1008.20.0489041.005199.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 45.8 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.7 Å19.83 Å
Translation3.7 Å19.83 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
BUSTER-TNTrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→81.74 Å / Cor.coef. Fo:Fc: 0.9617 / Cor.coef. Fo:Fc free: 0.9446 / Occupancy max: 1 / Occupancy min: 0.5 / SU R Cruickshank DPI: 0.232 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2129 4055 4.96 %RANDOM
Rwork0.1805 ---
all0.1821 81684 --
obs0.1821 81684 94.97 %-
Displacement parametersBiso max: 179.18 Å2 / Biso mean: 70.1529 Å2 / Biso min: 36.24 Å2
Baniso -1Baniso -2Baniso -3
1--2.0813 Å20 Å20 Å2
2---2.0813 Å20 Å2
3---4.1626 Å2
Refine analyzeLuzzati coordinate error obs: 0.339 Å
Refinement stepCycle: LAST / Resolution: 2.35→81.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10496 0 131 375 11002
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3598SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes200HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1578HARMONIC5
X-RAY DIFFRACTIONt_it10728HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1474SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact12764SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d10728HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg14586HARMONIC21.17
X-RAY DIFFRACTIONt_omega_torsion3.08
X-RAY DIFFRACTIONt_other_torsion17.26
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2497 277 5.01 %
Rwork0.2225 5253 -
all0.2239 5530 -
obs--94.97 %
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)
12.1779-1.1103-2.75011.02591.52114.89060.27270.44310.0779-0.2871-0.2438-0.0072-0.5629-0.3517-0.0289-0.08530.10750.0825-0.0630.0334-0.0971-10.572249.4795122.702
23.12641.39052.12122.46941.3124.16650.0257-0.0693-0.00430.03920.074-0.0921-0.36230.1766-0.0997-0.0316-0.0670.0978-0.148-0.0335-0.180717.857739.3416108.591
37.3858-1.0628-0.46261.60930.14120.847-0.0208-0.47790.2954-0.036-0.02150.2201-0.0889-0.19340.0423-0.0733-0.0368-0.0301-0.1097-0.0405-0.119617.451350.3858140.345
41.1682-0.096-0.6191.01770.99574.6266-0.0904-0.0249-0.07070.16880.0264-0.04130.09060.05880.064-0.08820.0087-0.0182-0.08620.006-0.050749.5548-1.9446158.123
51.10010.46440.06713.0801-2.30884.7196-0.01890.02730.19450.09910.1203-0.1351-0.6784-0.2-0.1014-0.00050.02610.0518-0.10380.0041-0.180634.942524.8803172.211
61.5664-3.41510.08388.41930.45860.09230.12620.01180.1907-0.4952-0.0359-0.7191-0.05020.1036-0.0903-0.0682-0.04110.0361-0.13980.0744-0.060846.371126.1496140.748
72.52342.16990.03213.91-0.39041.40830.03640.0126-0.35990.09550.0278-0.06430.2473-0.0809-0.0642-0.1725-0.0151-0.00820.0295-0.0138-0.11718.8974-3.9727190.634
82.37791.8392-0.08452.327-0.01310.5006-0.06170.14060.2009-0.14690.08720.3354-0.0984-0.1403-0.0255-0.053-0.0175-0.0277-0.08180.01710.0008-7.635817.578691.0437
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 185
2X-RAY DIFFRACTION2{ B|* }B2 - 184
3X-RAY DIFFRACTION3{ C|* }C2 - 184
4X-RAY DIFFRACTION4{ D|* }D2 - 184
5X-RAY DIFFRACTION5{ E|* }E2 - 185
6X-RAY DIFFRACTION6{ F|* }F2 - 184
7X-RAY DIFFRACTION7{ G|* }G2 - 184
8X-RAY DIFFRACTION8{ H|* }H2 - 184

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