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- PDB-4ddf: Computationally Designed Self-assembling Octahedral Cage protein,... -

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Basic information

Entry
Database: PDB / ID: 4ddf
TitleComputationally Designed Self-assembling Octahedral Cage protein, O333, Crystallized in space group P4
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: 3.15 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 18, 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
I: Propanediol utilization polyhedral body protein PduT
J: Propanediol utilization polyhedral body protein PduT
K: Propanediol utilization polyhedral body protein PduT
L: Propanediol utilization polyhedral body protein PduT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,14736
Polymers239,56912
Non-polymers1,57824
Water1086
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
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
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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)482,29472
Polymers479,13824
Non-polymers3,15648
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area64640 Å2
ΔGint-1023 kcal/mol
Surface area150070 Å2
MethodPISA
2
G: Propanediol utilization polyhedral body protein PduT
H: Propanediol utilization polyhedral body protein PduT
I: Propanediol utilization polyhedral body protein PduT
J: Propanediol utilization polyhedral body protein PduT
K: Propanediol utilization polyhedral body protein PduT
L: Propanediol utilization polyhedral body protein PduT
hetero molecules

G: Propanediol utilization polyhedral body protein PduT
H: Propanediol utilization polyhedral body protein PduT
I: Propanediol utilization polyhedral body protein PduT
J: Propanediol utilization polyhedral body protein PduT
K: Propanediol utilization polyhedral body protein PduT
L: Propanediol utilization polyhedral body protein PduT
hetero molecules

G: Propanediol utilization polyhedral body protein PduT
H: Propanediol utilization polyhedral body protein PduT
I: Propanediol utilization polyhedral body protein PduT
J: Propanediol utilization polyhedral body protein PduT
K: Propanediol utilization polyhedral body protein PduT
L: Propanediol utilization polyhedral body protein PduT
hetero molecules

G: Propanediol utilization polyhedral body protein PduT
H: Propanediol utilization polyhedral body protein PduT
I: Propanediol utilization polyhedral body protein PduT
J: Propanediol utilization polyhedral body protein PduT
K: Propanediol utilization polyhedral body protein PduT
L: Propanediol utilization polyhedral body protein PduT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)482,29472
Polymers479,13824
Non-polymers3,15648
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area63990 Å2
ΔGint-998 kcal/mol
Surface area151420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.460, 169.460, 119.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number75
Space group name H-MP4

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Components

#1: Protein
Propanediol utilization polyhedral body protein PduT


Mass: 19964.084 Da / Num. of mol.: 12
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


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.59 Å3/Da / Density % sol: 65.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 1.0M sodium chloride, 0.35M lithium sulfate, 0.1 M sodium acetate, pH 4.5, 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: 0.9201 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 22, 2011
RadiationMonochromator: Cryo-Cooled Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 3.15→19.8 Å / Num. all: 57838 / Num. obs: 57838 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 52.5 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 8.74
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3.15-3.230.5761.55192.1
3.23-3.320.4592.11193.1
3.32-3.420.4482.8199.8
3.42-3.520.3723.42199.8
3.52-3.650.2644.69199.6
3.64-3.770.2175.62199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å75.97 Å
Translation3.5 Å75.97 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
BUSTER-TNTrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
XSCALEdata scaling
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→19.84 Å / Cor.coef. Fo:Fc: 0.9416 / Cor.coef. Fo:Fc free: 0.91 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2212 2704 5.11 %RANDOM
Rwork0.1832 ---
obs0.1851 52871 90.26 %-
Displacement parametersBiso max: 196.88 Å2 / Biso mean: 75.8543 Å2 / Biso min: 5.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.5801 Å20 Å20 Å2
2---0.5801 Å20 Å2
3---1.1602 Å2
Refine analyzeLuzzati coordinate error obs: 0.578 Å
Refinement stepCycle: LAST / Resolution: 3.15→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15720 0 72 6 15798
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5388SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes312HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2364HARMONIC5
X-RAY DIFFRACTIONt_it15972HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2208SEMIHARMONIC5
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_contact19636SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d15972HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg21708HARMONIC21.28
X-RAY DIFFRACTIONt_omega_torsion2.57
X-RAY DIFFRACTIONt_other_torsion20.75
LS refinement shellResolution: 3.15→3.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3298 218 5.82 %
Rwork0.2808 3528 -
all0.2837 3746 -
obs--90.26 %
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)
13.266-2.6043-1.07289.33961.2531.3886-0.0887-0.33910.09250.47230.3413-0.3035-0.08840.3073-0.25260.1185-0.03-0.0687-0.0837-0.0592-0.195731.42184.223943.0799
25.822-0.1399-3.56542.8345-0.29084.45860.1642-0.01820.03910.0025-0.0213-0.1634-0.379-0.0155-0.1429-0.1258-0.1343-0.0317-0.0318-0.0738-0.018130.204433.909527.888
31.36991.1965-1.48816.5696-4.51595.5393-0.262-0.1081-0.3362-0.27150.0588-0.80210.15370.52580.2032-0.1052-0.07540.15440.0734-0.1432-0.045950.08769.763915.9882
45.088-1.38664.00321.9219-2.14095.0031-0.07670.45260.6162-0.4644-0.1405-0.2314-0.42250.47680.21720.2202-0.26240.17890.1651-0.1434-0.342341.929.5089-15.206
53.5614-2.8555-0.89674.83291.53773.11880.21540.60070.1278-0.19580.062-0.0880.06970.4758-0.27730.0966-0.06690.2330.42870.0361-0.401924.614920.1059-42.2749
63.59483.17462.14614.61863.73878.90770.01660.530.20660.19330.1616-0.45480.35840.547-0.1782-0.09050.05880.07940.0977-0.2824-0.253145.8274-1.3504-27.2354
72.4786-2.50970.91766.5669-2.63342.439-0.0367-0.31730.07520.01430.00960.28880.2254-0.31020.027-0.1152-0.09370.1826-0.0398-0.15520.045653.22780.770491.173
84.5870.2024.25951.3778-1.78566.57580.1535-0.2882-0.2787-0.0824-0.04390.30890.4362-0.2906-0.1096-0.0978-0.03920.1578-0.2228-0.06090.254254.27250.736576.1296
91.7731.42120.94184.31723.67255.4971-0.2553-0.5916-0.0778-0.0624-0.110.1298-0.1531-0.38670.3653-0.2805-0.02830.13160.0432-0.22770.128834.655874.747164.063
104.5888-2.52-3.15944.34992.45195.32220.0056-0.24340.1847-0.06560.13320.1735-0.0810.0732-0.1389-0.1631-0.2253-0.0328-0.1058-0.06530.091743.514455.044832.8799
113.4721-2.40641.37699.8361-3.27122.09060.00590.15920.0921-0.4766-0.0793-0.2052-0.0391-0.42650.0734-0.2129-0.01650.1742-0.1515-0.06320.140560.446264.60285.5835
121.82831.9998-2.32145.1725-3.80555.15060.06750.0929-0.03090.22260.10640.4163-0.008-0.6346-0.1739-0.29230.0536-0.0104-0.294-0.11820.398139.037685.62220.5881
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|2 - A|184 }A2 - 184
2X-RAY DIFFRACTION2{ B|2 - B|184 }B2 - 184
3X-RAY DIFFRACTION3{ C|2 - C|184 }C2 - 184
4X-RAY DIFFRACTION4{ D|2 - D|184 }D2 - 184
5X-RAY DIFFRACTION5{ E|2 - E|184 }E2 - 184
6X-RAY DIFFRACTION6{ F|2 - F|184 }F2 - 184
7X-RAY DIFFRACTION7{ G|2 - G|184 }G2 - 184
8X-RAY DIFFRACTION8{ H|2 - H|184 }H2 - 184
9X-RAY DIFFRACTION9{ I|2 - I|184 }I2 - 184
10X-RAY DIFFRACTION10{ J|2 - J|184 }J2 - 184
11X-RAY DIFFRACTION11{ K|2 - K|184 }K2 - 184
12X-RAY DIFFRACTION12{ L|2 - L|184 }L2 - 184

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