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- PDB-7bvt: Crystal structure of cyclic alpha-maltosyl-1,6-maltose binding pr... -

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Basic information

Entry
Database: PDB / ID: 7bvt
TitleCrystal structure of cyclic alpha-maltosyl-1,6-maltose binding protein from Arthrobacter globiformis
ComponentsHypothetical sugar ABC-transporter sugar binding protein
KeywordsSUGAR BINDING PROTEIN / substrate-binding protein / ABC transporter
Function / homologyBacterial extracellular solute-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / transmembrane transport / Hypothetical sugar ABC-transporter sugar binding protein
Function and homology information
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsKohno, M. / Arakawa, T. / Mori, T. / Nishimoto, T. / Fushinobu, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)15H02443 Japan
Citation
Journal: Plos One / Year: 2020
Title: Molecular analysis of cyclic alpha-maltosyl-(1→6)-maltose binding protein in the bacterial metabolic pathway.
Authors: Kohno, M. / Arakawa, T. / Sunagawa, N. / Mori, T. / Igarashi, K. / Nishimoto, T. / Fushinobu, S.
#1: Journal: Journal of Applied Glycoscience / Year: 2011
Title: Cloning, Sequencing and Expression of the Genes Encoding Cyclic alpha-Maltosyl-(1->6)-maltose Hydrolase and alpha-Glucosidase from an Arthrobacter globiformis Strain
Authors: Mori, T. / Nishimoto, T. / Okura, T. / Chaen, H. / Fukuda, S.
History
DepositionApr 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Hypothetical sugar ABC-transporter sugar binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0002
Polymers44,4951
Non-polymers5041
Water6,864381
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint13 kcal/mol
Surface area15240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.077, 92.077, 161.584
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Hypothetical sugar ABC-transporter sugar binding protein


Mass: 44495.172 Da / Num. of mol.: 1 / Fragment: substrate binding protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter globiformis (bacteria) / Gene: cmmC / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: UniProt: D2YYD8
#2: Polysaccharide alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b6-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 381 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.11 Å3/Da / Density % sol: 41.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris-HCl (pH 8.5), 2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Nov 18, 2017
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.47→46.04 Å / Num. obs: 68976 / % possible obs: 99.5 % / Redundancy: 19.6 % / CC1/2: 0.981 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.021 / Net I/σ(I): 15.7
Reflection shellResolution: 1.47→1.5 Å / Redundancy: 10 % / Rmerge(I) obs: 1.794 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 32216 / CC1/2: 0.93 / Rpim(I) all: 0.595 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CI5

5ci5


Resolution: 1.47→44.67 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.748 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2066 3434 5 %RANDOM
Rwork0.1848 ---
obs0.1859 65458 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 75.34 Å2 / Biso mean: 22.716 Å2 / Biso min: 8.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.47→44.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2955 0 34 381 3370
Biso mean--30.86 34.49 -
Num. residues----391
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0133067
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172617
X-RAY DIFFRACTIONr_angle_refined_deg1.7951.6514212
X-RAY DIFFRACTIONr_angle_other_deg1.6181.5856118
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2965390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.37925.933150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00715422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.133155
X-RAY DIFFRACTIONr_chiral_restr0.0870.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023515
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02592
LS refinement shellResolution: 1.47→1.508 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 266 -
Rwork0.365 4564 -
all-4830 -
obs--95.61 %

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