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- PDB-1y4c: Designed Helical Protein fusion MBP -

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Basic information

Entry
Database: PDB / ID: 1y4c
TitleDesigned Helical Protein fusion MBP
ComponentsMaltose binding protein fused with designed helical protein
KeywordsDE NOVO PROTEIN / De Novo Designed Helical Protein / Maltose binding protein fusion
Function / homology
Function and homology information


detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane
Similarity search - Function
IL-4 antagonist (De novo design) like 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Up-down Bundle ...IL-4 antagonist (De novo design) like 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLaPorte, S.L. / Forsyth, C.M. / Cunningham, B.C. / Miercke, L.J. / Akhavan, D. / Stroud, R.M.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: De novo design of an IL-4 antagonist and its structure at 1.9 A.
Authors: LaPorte, S.L. / Forsyth, C.M. / Cunningham, B.C. / Miercke, L.J. / Akhavan, D. / Stroud, R.M.
History
DepositionNov 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2013Group: Other
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / 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_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 14, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE THE PROTEIN WAS EXPRESSED AS A SINGLE POLYPEPTIDE CHAIN. THE N-TERM IS MISSING 3 RESIDUES ...SEQUENCE THE PROTEIN WAS EXPRESSED AS A SINGLE POLYPEPTIDE CHAIN. THE N-TERM IS MISSING 3 RESIDUES KIE. 10 N RESIDUES ARE MISSING IN THE FLEXIBLE LINKER BETWEEN MBP AND THE DESIGNED HELICAL BUNDLE PROTEIN. THE C-TERM OF THE HELICAL BUNDLE, K, IS MISSING. THERE IS NO SEQUENCE DATABASE REFERENCE FOR THE LINKER OR THE DESIGNED HELICAL BUNDLE PROTEIN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose binding protein fused with designed helical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6312
Polymers54,2891
Non-polymers3421
Water5,116284
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.557, 74.690, 103.686
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Maltose binding protein fused with designed helical protein


Mass: 54289.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: a flexible linker links the MBP with the designed protein
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: malE / Production host: Escherichia coli (E. coli) / References: UniProt: P02928, UniProt: P0AEX9*PLUS
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.48 Å3/Da / Density % sol: 50.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 6, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT1.501data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.225 2161 5 %
Rwork0.202 --
all-43208 -
obs-43208 99.9 %
Displacement parametersBiso mean: 56.229 Å2
Baniso -1Baniso -2Baniso -3
1--8.704 Å20 Å20 Å2
2--3.961 Å20 Å2
3---4.743 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3672 0 23 284 3979

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