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- PDB-1svx: Crystal structure of a designed selected Ankyrin Repeat protein i... -

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Basic information

Entry
Database: PDB / ID: 1svx
TitleCrystal structure of a designed selected Ankyrin Repeat protein in complex with the Maltose Binding Protein
Components
  • Ankyrin Repeat Protein off7
  • Maltose-binding periplasmic protein
Keywordsde novo protein/sugar binding protein / Ankyrin Repeat Protein / selected binder / Protein design / artificial complex / de novo protein-sugar binding protein COMPLEX
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 / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe ...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 / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / 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: 2.24 Å
AuthorsBinz, H.K. / Amstutz, P. / Kohl, A. / Stumpp, M.T. / Briand, C. / Forrer, P. / Gruetter, M.G. / Plueckthun, A.
CitationJournal: NAT.BIOTECHNOL. / Year: 2004
Title: High-affinity binders selected from designed ankyrin repeat protein libraries
Authors: Binz, H.K. / Amstutz, P. / Kohl, A. / Stumpp, M.T. / Briand, C. / Forrer, P. / Gruetter, M.G. / Plueckthun, A.
History
DepositionMar 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Ankyrin Repeat Protein off7
B: Maltose-binding periplasmic protein


Theoretical massNumber of molelcules
Total (without water)61,4962
Polymers61,4962
Non-polymers00
Water3,873215
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.680, 45.150, 79.570
Angle α, β, γ (deg.)90.00, 107.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ankyrin Repeat Protein off7


Mass: 18308.467 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Gene: designed synthetic gene / Plasmid: QE30 / Production host: Escherichia coli (E. coli) / Strain (production host): XL-1 blue / References: GenBank: 37576201
#2: Protein Maltose-binding periplasmic protein / Maltodextrin-binding protein / MMBP


Mass: 43187.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: MALE, B4034, Z5632, ECS5017 / Plasmid: QE30 / Production host: Escherichia coli (E. coli) / Strain (production host): XL-1 blue / References: UniProt: P02928, UniProt: P0AEX9*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.08 Å3/Da / Density % sol: 40.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30% PEG 6000, 0.1M Tris, 0.1M NaCl, pH 8-9, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.24→25 Å / Num. obs: 22902

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→25 Å /
RfactorNum. reflection
Rfree0.249 -
Rwork0.195 -
obs-22902
Refinement stepCycle: LAST / Resolution: 2.24→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4030 0 0 215 4245

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