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- PDB-4dcl: Computationally Designed Self-assembling tetrahedron protein, T30... -

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Basic information

Entry
Database: PDB / ID: 4dcl
TitleComputationally Designed Self-assembling tetrahedron protein, T308, Crystallized in space group F23
ComponentsPutative acetyltransferase SACOL2570
KeywordsTRANSFERASE / self assembling tetrahedron design
Function / homology
Function and homology information


acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Similarity search - Function
Galactoside O-acetyltransferase LacA-like / Maltose/galactoside acetyltransferase / Maltose acetyltransferase / Maltose acetyltransferase / Hexapeptide repeat of succinyl-transferase / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily ...Galactoside O-acetyltransferase LacA-like / Maltose/galactoside acetyltransferase / Maltose acetyltransferase / Maltose acetyltransferase / Hexapeptide repeat of succinyl-transferase / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
Putative acetyltransferase SACOL2570
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.35 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 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative acetyltransferase SACOL2570


Theoretical massNumber of molelcules
Total (without water)22,9911
Polymers22,9911
Non-polymers00
Water181
1
A: Putative acetyltransferase SACOL2570
x 12


Theoretical massNumber of molelcules
Total (without water)275,89212
Polymers275,89212
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
Buried area35990 Å2
ΔGint-163 kcal/mol
Surface area81420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.690, 153.690, 153.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number196
Space group name H-MF23

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Components

#1: Protein Putative acetyltransferase SACOL2570


Mass: 22990.973 Da / Num. of mol.: 1 / Mutation: Y20T, A26L, D30V, E34A, R39N, N44L, E48V, Q52A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Gene: SACOL2570 / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5HCZ5, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.29 Å3/Da / Density % sol: 62.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 2.0 M sodium chloride, 0.1 M sodium acetate, pH 4.6, 35% GLYCEROL AS CRYOPROTECTANT, vapor diffusion, hanging drop, temperature 298K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2011
RadiationMonochromator: Cryo-Cooled Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.35→18.8 Å / Num. all: 4298 / Num. obs: 4298 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 81.567 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 24.14
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
3.35-3.440.5314.391982325198.8
3.44-3.530.5394.272153306197.5
3.53-3.630.3556.111865281192.1
3.63-3.750.17311.531522272189.8
3.75-3.870.18110.711570272193.8
3.87-40.12515.31592259189.9
4-4.160.07819.3119052601100
4.16-4.330.05726.211800249199.6
4.33-4.520.05128.1919092631100
4.52-4.740.04530.7217202351100
4.74-4.990.04134.9216702311100
4.99-5.30.04631.0315302141100
5.3-5.660.04930.4614922091100
5.66-6.120.0463313581921100
6.12-6.70.03936.111166172199.4
6.7-7.490.0348.111071561100
7.49-8.650.0352.9310231471100
8.65-10.60.02957.119031281100
10.6-14.980.02855.3855994197.9
14.98-18.80.0352.8816131149.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.8 Å19.24 Å
Translation3.8 Å19.24 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
BUSTER-TNTrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
XDSdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3V4E
Resolution: 3.35→18.78 Å / Cor.coef. Fo:Fc: 0.9388 / Cor.coef. Fo:Fc free: 0.9093 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2398 215 5 %RANDOM
Rwork0.2311 ---
all0.2316 ---
obs0.2316 4298 97.26 %-
Displacement parametersBiso max: 221.56 Å2 / Biso mean: 135.4875 Å2 / Biso min: 38.54 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 1.44 Å
Refinement stepCycle: LAST / Resolution: 3.35→18.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1456 0 0 1 1457
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d497SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes38HARMONIC2
X-RAY DIFFRACTIONt_gen_planes217HARMONIC5
X-RAY DIFFRACTIONt_it1493HARMONIC50
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion199SEMIHARMONIC5
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_contact1708SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1493HARMONIC20.011
X-RAY DIFFRACTIONt_angle_deg2031HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion3.96
X-RAY DIFFRACTIONt_other_torsion18.78
LS refinement shellResolution: 3.35→3.75 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3619 59 5 %
Rwork0.3453 1121 -
all0.3461 1180 -
obs--97.26 %
Refinement TLS params.Method: refined / Origin x: 13.7287 Å / Origin y: 30.6017 Å / Origin z: -11.4101 Å
111213212223313233
T0.6079 Å20.1392 Å20.1537 Å2--0.452 Å20.304 Å2---0.2215 Å2
L6.5215 °21.5491 °2-1.774 °2-9.3878 °2-1.2781 °2--2.3466 °2
S0.1031 Å °0.7629 Å °1.0885 Å °0.447 Å °-0.0239 Å °-0.8558 Å °-1.0885 Å °-0.6952 Å °-0.0792 Å °
Refinement TLS groupSelection details: { A|* }

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