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- PDB-3sew: Zn-mediated Polymer of Maltose-binding Protein A216H/K220H by Syn... -

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Basic information

Entry
Database: PDB / ID: 3sew
TitleZn-mediated Polymer of Maltose-binding Protein A216H/K220H by Synthetic Symmetrization (Form I)
ComponentsMaltose-binding periplasmic protein
KeywordsSUGAR BINDING PROTEIN / metal-mediated synthetic symmetrization / synthetic symmetrization
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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsZhao, M. / Soriaga, A.B. / Laganowsky, A. / Sawaya, M.R. / Cascio, D. / Yeates, T.O.
CitationJournal: Protein Sci. / Year: 2011
Title: An approach to crystallizing proteins by metal-mediated synthetic symmetrization.
Authors: Laganowsky, A. / Zhao, M. / Soriaga, A.B. / Sawaya, M.R. / Cascio, D. / Yeates, T.O.
History
DepositionJun 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2011Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / struct_conn / struct_conn_type / struct_ref_seq_dif / 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_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,70812
Polymers40,6981
Non-polymers1,01011
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.580, 63.440, 66.390
Angle α, β, γ (deg.)90.000, 90.750, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Maltose-binding periplasmic protein / MMBP / Maltodextrin-binding protein


Mass: 40698.020 Da / Num. of mol.: 1 / Mutation: A216H, K220H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b4034, JW3994, malE / Plasmid: pMal-a1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P0AEX9
#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

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Non-polymers , 4 types, 278 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.21 Å3/Da / Density % sol: 44.44 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M TRIS, 0.2M SODIUM CHLORIDE, 30% (W/V) PEG 3000, pH 8.0, vapor diffusion, hanging drop, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.55→66.384 Å / Num. obs: 51444 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.915 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 16.22
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.55-1.590.5672.3914017378699.4
1.59-1.630.4852.7213611367699.5
1.63-1.680.3683.6113325359799.6
1.68-1.730.2854.6212985350299.7
1.73-1.790.2265.8112518337999.7
1.79-1.850.187.3412138326499.5
1.85-1.920.1399.4511702314899.8
1.92-20.10212.4211377305799.7
2-2.090.08215.410875292499.9
2.09-2.190.06219.0410387279699.8
2.19-2.310.05721.099904266599.7
2.31-2.450.04923.989296250099.4
2.45-2.620.04426.138713235399.6
2.62-2.830.0429.158142221599.7
2.83-3.10.03631.967365202099.6
3.1-3.470.03136.736723185199.7
3.47-40.02540.935882164399.6
4-4.90.02244.285160137799.7
4.9-6.930.02343.224020108199.9
6.930.02144.06215761099

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.7 Å66.38 Å
Translation1.7 Å66.38 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→66.384 Å / Occupancy max: 1 / Occupancy min: 0.43 / FOM work R set: 0.8966 / SU ML: 0.37 / σ(F): 2 / Phase error: 17.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1876 2572 5 %
Rwork0.1608 --
obs0.1622 51437 99.63 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.879 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 51.37 Å2 / Biso mean: 15.1354 Å2 / Biso min: 4.24 Å2
Baniso -1Baniso -2Baniso -3
1-4.485 Å20 Å21.9786 Å2
2---1.9084 Å2-0 Å2
3----2.5766 Å2
Refinement stepCycle: LAST / Resolution: 1.55→66.384 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2841 0 58 268 3167
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053041
X-RAY DIFFRACTIONf_angle_d14145
X-RAY DIFFRACTIONf_chiral_restr0.066462
X-RAY DIFFRACTIONf_plane_restr0.004529
X-RAY DIFFRACTIONf_dihedral_angle_d10.9981123
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.57980.28371440.23427232867100
1.5798-1.61210.2991420.22142701284399
1.6121-1.64710.24261400.216526662806100
1.6471-1.68540.23391420.198126842826100
1.6854-1.72760.21211420.184727162858100
1.7276-1.77430.19871440.177727242868100
1.7743-1.82650.23331410.173626912832100
1.8265-1.88550.18361430.158927072850100
1.8855-1.95290.1981420.14827062848100
1.9529-2.03110.17931430.141427072850100
2.0311-2.12350.16111430.150727252868100
2.1235-2.23550.19751420.146626872829100
2.2355-2.37550.17021440.148627382882100
2.3755-2.5590.161430.153727132856100
2.559-2.81650.17141430.151727262869100
2.8165-3.2240.19421420.157627062848100
3.224-4.06180.16621450.146327552900100
4.0618-66.44530.17381470.16232790293799
Refinement TLS params.Method: refined / Origin x: 19.3492 Å / Origin y: -9.4048 Å / Origin z: -16.2592 Å
111213212223313233
T0.0454 Å20.0026 Å20.0082 Å2-0.0664 Å2-0.0086 Å2--0.0432 Å2
L0.234 °2-0.099 °20.0465 °2-0.8264 °2-0.1374 °2--0.2996 °2
S0.0064 Å °-0.0013 Å °-0.0059 Å °-0.0345 Å °-0.0092 Å °0.0037 Å °0.0184 Å °0.0125 Å °0.0038 Å °
Refinement TLS groupSelection details: ALL

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