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- PDB-5lem: Crystal structure of DARPin-DARPin rigid fusion, variant DD_Off7_... -

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Basic information

Entry
Database: PDB / ID: 5lem
TitleCrystal structure of DARPin-DARPin rigid fusion, variant DD_Off7_11_3G124 in complex with Maltose-binding Protein and Green Fluorescent Protein
Components
  • DD_Off7_11_3G124
  • Green fluorescent protein
  • Maltose-binding periplasmic protein
KeywordsFLUORESCENT PROTEIN / X-ray crystallography / designed ankyrin repeat proteins / protein design / protein engineering / rigid domain fusions
Function / homology
Function and homology information


carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / bioluminescence / generation of precursor metabolites and energy / outer membrane-bounded periplasmic space
Similarity search - Function
Ankyrin repeat-containing domain / Green Fluorescent Protein / Green fluorescent protein / 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 / Green fluorescent protein, GFP / Green fluorescent protein-related ...Ankyrin repeat-containing domain / Green Fluorescent Protein / Green fluorescent protein / 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 / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Beta Barrel / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / Green fluorescent protein
Similarity search - Component
Biological speciessynthetic construct (others)
Escherichia coli K-12 (bacteria)
Aequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsBatyuk, A. / Wu, Y. / Mittl, P.R. / Plueckthun, A.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_166676 Switzerland
European Research CouncilNEXTBINDERS
CitationJournal: Sci Rep / Year: 2017
Title: Rigidly connected multispecific artificial binders with adjustable geometries.
Authors: Wu, Y. / Batyuk, A. / Honegger, A. / Brandl, F. / Mittl, P.R.E. / Pluckthun, A.
History
DepositionJun 30, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
Revision 1.2Mar 20, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.4Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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
A: DD_Off7_11_3G124
B: Maltose-binding periplasmic protein
C: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)106,6813
Polymers106,6813
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-16 kcal/mol
Surface area39370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.430, 169.950, 95.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein DD_Off7_11_3G124


Mass: 35288.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 / Variant (production host): XL1-Blue
#2: Protein Maltose-binding periplasmic protein / MBP / MMBP / Maltodextrin-binding protein


Mass: 43172.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: malE, Z5632, ECs5017 / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 / Variant (production host): XL1-Blue / References: UniProt: P0AEY0
#3: Protein Green fluorescent protein


Mass: 28219.721 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 / Variant (production host): XL1-Blue / References: UniProt: P42212
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.65 Å3/Da / Density % sol: 53.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: PEG6000 20% w/v, TAPS 0.02 M, pH 9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.98→48.785 Å / Num. obs: 23885 / % possible obs: 98.71 % / Redundancy: 6.5 % / CC1/2: 0.997 / Net I/σ(I): 9.4

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX(dev_2400)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.98→48.785 Å / SU ML: 0.8 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 41.7
RfactorNum. reflection% reflection
Rfree0.2947 1185 5.02 %
Rwork0.2447 --
obs0.2472 23623 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.98→48.785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7085 0 0 1 7086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027245
X-RAY DIFFRACTIONf_angle_d0.4349824
X-RAY DIFFRACTIONf_dihedral_angle_d8.1954287
X-RAY DIFFRACTIONf_chiral_restr0.0391082
X-RAY DIFFRACTIONf_plane_restr0.0021282
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9799-3.11550.45941360.46382551X-RAY DIFFRACTION92
3.1155-3.27980.51711480.46662792X-RAY DIFFRACTION99
3.2798-3.48520.39791470.36292787X-RAY DIFFRACTION100
3.4852-3.75420.3631470.31332788X-RAY DIFFRACTION100
3.7542-4.13180.30161480.26362819X-RAY DIFFRACTION100
4.1318-4.72930.30131490.22392830X-RAY DIFFRACTION100
4.7293-5.95670.29881510.23942870X-RAY DIFFRACTION100
5.9567-48.79130.23961590.19573001X-RAY DIFFRACTION99
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)
11.854-2.4899-0.39061.81990.5611.9133-0.12370.5068-0.27310.42430.45230.26710.11990.4400.7802-0.006-0.05760.9103-0.05560.8514-0.7789-15.3555-8.8268
21.625-0.6335-1.48960.04610.59511.13810.18510.9529-0.9749-0.0950.08210.29-0.1262-0.552300.9343-0.0062-0.05280.88870.16161.0938-20.0413-6.5911-4.4207
3-0.0663-0.6602-0.80983.94210.59180.6647-0.02310.1949-0.53610.4535-0.2109-0.41360.00440.0966-0.0050.9024-0.012-0.13650.87910.20420.7902-17.117815.651614.5699
40.78151.8062-0.25151.8413-1.3381.78430.2895-0.98360.1712-1.50490.4039-1.8526-1.03860.14760.0212.11820.25480.16952.22690.31741.6998-7.5973-15.9286-64.6331
52.23240.5394-0.09954.1825-0.50264.70490.0870.2426-0.0482-0.07010.09160.34550.1284-0.9683-00.71110.1189-0.09560.86790.04520.7898-16.8329-14.413-38.6646
60.23820.0525-0.1491-0.0292-0.17280.1287-0.1031.4354-1.30290.2423-0.93490.6060.2206-0.246-0.00122.99250.1383-0.7052.0034-0.221.8064-18.6604-23.6484-65.8859
71.4273-1.70380.13661.31890.7861.26690.32970.23190.37860.0126-0.55710.1439-0.8506-0.813301.4366-0.08020.0181.17420.13970.7096-15.4505-10.0154-41.7219
82.2596-2.02070.19540.4987-0.26451.2784-0.4976-0.4261-0.41660.32970.17670.22390.1397-0.69810.0070.8647-0.01340.00910.86760.1660.8631-31.875925.9088-1.1246
9-0.4053-1.08170.51431.05430.10883.7054-0.38520.3655-0.13870.12850.3640.3634-0.31760.18450.01630.8120.02680.05950.95110.40081.114-30.276135.6195-0.8245
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 101 )
2X-RAY DIFFRACTION2chain 'A' and (resid 102 through 158 )
3X-RAY DIFFRACTION3chain 'A' and (resid 159 through 325 )
4X-RAY DIFFRACTION4chain 'B' and (resid 5 through 82 )
5X-RAY DIFFRACTION5chain 'B' and (resid 83 through 273 )
6X-RAY DIFFRACTION6chain 'B' and (resid 274 through 296 )
7X-RAY DIFFRACTION7chain 'B' and (resid 297 through 368 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 68 )
9X-RAY DIFFRACTION9chain 'C' and (resid 69 through 230 )

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