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- PDB-6ob5: Computationally-designed, modular sense/response system (S3-2D) -

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Basic information

Entry
Database: PDB / ID: 6ob5
TitleComputationally-designed, modular sense/response system (S3-2D)
Components
  • Ankyrin Repeat Domain (AR), S3-2D variant
  • Maltodextrin-binding protein
KeywordsSUGAR BINDING PROTEIN / computational protein design / chemically-induced dimerization / biosensor / Rosetta
Function / homology
Function and homology information


detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane
Similarity search - Function
Ankyrin repeat-containing domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
alpha-maltose / FARNESYL DIPHOSPHATE / Maltodextrin-binding protein / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.208 Å
AuthorsThompson, M.C. / Glasgow, A.A. / Huang, Y.M. / Fraser, J.S. / Kortemme, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM110089 United States
CitationJournal: Science / Year: 2019
Title: Computational design of a modular protein sense-response system.
Authors: Glasgow, A.A. / Huang, Y.M. / Mandell, D.J. / Thompson, M. / Ritterson, R. / Loshbaugh, A.L. / Pellegrino, J. / Krivacic, C. / Pache, R.A. / Barlow, K.A. / Ollikainen, N. / Jeon, D. / Kelly, ...Authors: Glasgow, A.A. / Huang, Y.M. / Mandell, D.J. / Thompson, M. / Ritterson, R. / Loshbaugh, A.L. / Pellegrino, J. / Krivacic, C. / Pache, R.A. / Barlow, K.A. / Ollikainen, N. / Jeon, D. / Kelly, M.J.S. / Fraser, J.S. / Kortemme, T.
History
DepositionMar 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_2
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
B: Maltodextrin-binding protein
A: Maltodextrin-binding protein
C: Ankyrin Repeat Domain (AR), S3-2D variant
D: Ankyrin Repeat Domain (AR), S3-2D variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,2757
Polymers117,2084
Non-polymers1,0673
Water2,540141
1
B: Maltodextrin-binding protein
D: Ankyrin Repeat Domain (AR), S3-2D variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3294
Polymers58,6042
Non-polymers7252
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Maltodextrin-binding protein
C: Ankyrin Repeat Domain (AR), S3-2D variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9463
Polymers58,6042
Non-polymers3421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.570, 190.920, 55.480
Angle α, β, γ (deg.)90.00, 90.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Maltodextrin-binding protein


Mass: 40825.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: malE, SAMEA3485101_02947 / Variant: S3-2D / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2Y0TBT9, UniProt: P0AEX9*PLUS
#2: Protein Ankyrin Repeat Domain (AR), S3-2D variant


Mass: 17778.896 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: computationally-designed sequence / Source: (gene. exp.) unidentified (others) / Variant: S3-2D / Production host: Escherichia coli (E. coli)
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Chemical ChemComp-FPP / FARNESYL DIPHOSPHATE


Mass: 382.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C15H28O7P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.12 Å3/Da / Density % sol: 41.86 % / Description: Thin, flat plates. Commonly stacked.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 0.1M Tris Buffer, 0.1M sodium chloride, and 32% PEG-6000
PH range: 8.5-8.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.12 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 22, 2016
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 2.2→95.47 Å / Num. obs: 45972 / % possible obs: 98.5 % / Redundancy: 3.7 % / CC1/2: 0.997 / Rpim(I) all: 0.033 / Net I/σ(I): 17.5
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 8.3 / Num. unique obs: 7746 / CC1/2: 0.966 / Rpim(I) all: 0.09 / % possible all: 91.5

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Processing

Software
NameVersionClassification
PHENIX(dev_3120: ???)refinement
xia2data reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SVX, 1FQD

1svx

1fqd


Resolution: 2.208→95.46 Å / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 32.71
RfactorNum. reflection% reflection
Rfree0.2534 2789 6.12 %
Rwork0.202 --
obs0.2384 45553 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.208→95.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7875 0 70 141 8086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038149
X-RAY DIFFRACTIONf_angle_d0.56211068
X-RAY DIFFRACTIONf_dihedral_angle_d14.7224806
X-RAY DIFFRACTIONf_chiral_restr0.0381232
X-RAY DIFFRACTIONf_plane_restr0.0031430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2098-2.24790.4661270.33832057X-RAY DIFFRACTION90
2.2479-2.28880.4121320.34282163X-RAY DIFFRACTION93
2.2888-2.33280.41861510.32532117X-RAY DIFFRACTION92
2.3328-2.38050.39431310.31782139X-RAY DIFFRACTION93
2.3805-2.43220.36411360.33012119X-RAY DIFFRACTION92
2.4322-2.48880.35721560.30832164X-RAY DIFFRACTION92
2.4888-2.5510.35221260.31412124X-RAY DIFFRACTION93
2.551-2.620.28921550.2962168X-RAY DIFFRACTION92
2.62-2.69710.30261270.28392072X-RAY DIFFRACTION93
2.6971-2.78410.3151320.29142174X-RAY DIFFRACTION92
2.7841-2.88360.30921360.27712095X-RAY DIFFRACTION93
2.8836-2.9990.30551480.27232172X-RAY DIFFRACTION92
2.999-3.13550.2711390.2382116X-RAY DIFFRACTION92
3.1355-3.30070.32371340.22992148X-RAY DIFFRACTION93
3.3007-3.50740.32151500.21932145X-RAY DIFFRACTION92
3.5074-3.77810.25381360.19772150X-RAY DIFFRACTION93
3.7781-4.1580.25841290.16712143X-RAY DIFFRACTION93
4.158-4.75910.20661410.15532149X-RAY DIFFRACTION92
4.7591-5.99340.23231390.1692156X-RAY DIFFRACTION93
5.9934-43.41120.24761460.18122191X-RAY DIFFRACTION93

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