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- PDB-3csb: Crystal Structure of Monobody YSX1/Maltose Binding Protein Fusion... -

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Basic information

Entry
Database: PDB / ID: 3csb
TitleCrystal Structure of Monobody YSX1/Maltose Binding Protein Fusion Complex
ComponentsMaltose-binding protein Monobody YSX1 Fusion
KeywordsDE NOVO PROTEIN / SUGAR BINDING PROTEIN / Engineered Binding Protein / Antibody Mimic / Synthetic Protein Interface / Minimalist Protein Interface
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
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 / Immunoglobulins / Immunoglobulin-like / Sandwich ...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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.999 Å
AuthorsGilbreth, R.N. / Koide, S.
Citation
Journal: J.Mol.Biol. / Year: 2008
Title: A Dominant Conformational Role for Amino Acid Diversity in Minimalist Protein-Protein Interfaces
Authors: Gilbreth, R.N. / Esaki, K. / Koide, A. / Sidhu, S.S. / Koide, S.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: High affinity single-domain binding proteins with a binary code interface
Authors: Koide, A. / Gilbreth, R.N. / Esaki, K. / Tereshko, V. / Koide, S.
History
DepositionApr 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose-binding protein Monobody YSX1 Fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,66119
Polymers50,7791
Non-polymers1,88218
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.818, 98.818, 134.619
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Maltose-binding protein Monobody YSX1 Fusion / MBP / Maltodextrin-binding protein / MMBP


Mass: 50779.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: malE includes residues 5-370, Monobody YSX1 377-467, 371-373 comprise an engineered linker
Source: (gene. exp.) Escherichia coli, synthetic / Gene: malE / Plasmid: pHFT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AEX9

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Non-polymers , 7 types, 226 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 3.24 Å3/Da / Density % sol: 61.99 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 41% polyethelyeneglycol-400, 2% 2-methyl-2,4-pentanediol, 50 mM MnCl2, 0.1 M 2-(N-morpholino)ethanesulfonic acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 21, 2007
RadiationMonochromator: double crystal monochromator and K-B pair of biomorph mirrors for vertical and horizontal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.999→50 Å / Num. all: 45823 / Num. obs: 45823 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.999→2.07 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CNS5.2.0019refinement
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
CNS5.2.0019phasing
REFMAC5.2.0019phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.999→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / SU B: 6.123 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23608 4569 10 %RANDOM
Rwork0.19494 ---
all0.19905 45672 --
obs0.19905 45672 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.551 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2--0.23 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.999→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3607 0 51 271 3929
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223798
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.985128
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9455471
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.87525.355155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.37715600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.389158
X-RAY DIFFRACTIONr_chiral_restr0.1280.2554
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022826
X-RAY DIFFRACTIONr_nbd_refined0.2130.21651
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22595
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2216
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.218
X-RAY DIFFRACTIONr_mcbond_it1.2291.52390
X-RAY DIFFRACTIONr_mcangle_it1.89923741
X-RAY DIFFRACTIONr_scbond_it2.73431651
X-RAY DIFFRACTIONr_scangle_it4.0074.51384
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 329 -
Rwork0.205 2959 -
obs--99.58 %

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