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- PDB-7vfr: GltA N83K mutant from Bifidobacterium infantis JCM 1222 complexed... -

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Basic information

Entry
Database: PDB / ID: 7vfr
TitleGltA N83K mutant from Bifidobacterium infantis JCM 1222 complexed with lacto-N-tetraose
ComponentsExtracellular solute-binding protein, family 1
KeywordsTRANSLOCASE / solute-binding protein
Function / homologyBacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Extracellular solute-binding protein, family 1
Function and homology information
Biological speciesBifidobacterium longum subsp. infantis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsSato, M. / Sakanaka, M. / Katayama, T. / Fushinobu, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K14379 Japan
Japan Society for the Promotion of Science (JSPS)17K19231 Japan
Japan Society for the Promotion of Science (JSPS)21H02116 Japan
CitationJournal: To Be Published
Title: Short stretch sequence of a milk oligosaccharide transporter represents the phenotypic selection trajectory in infant gut microbiome
Authors: Sakanaka, M. / Sato, M. / Fushinobu, S. / Katayama, T.
History
DepositionSep 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Extracellular solute-binding protein, family 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8115
Polymers43,8461
Non-polymers9654
Water7,152397
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-27 kcal/mol
Surface area15790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.995, 42.390, 59.605
Angle α, β, γ (deg.)107.050, 102.060, 104.290
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Extracellular solute-binding protein, family 1


Mass: 43845.848 Da / Num. of mol.: 1 / Mutation: N83K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium longum subsp. infantis (strain ATCC 15697 / DSM 20088 / JCM 1222 / NCTC 11817 / S12) (bacteria)
Gene: Blon_2177 / Plasmid: pET23b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): delta-lacZ / References: UniProt: B7GN82
#2: Polysaccharide beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose- ...beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 707.630 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGlcpNAcb1-3DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5][a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-2-3-2/a4-b1_b3-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 2.03 Å3/Da / Density % sol: 39.54 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 30% (w/v) PEG MME 550, 10mM ZnSO4, 0.1M MES-NaOH (pH 5.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 25, 2016
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.56→54.29 Å / Num. obs: 42429 / % possible obs: 86.5 % / Redundancy: 1.6 % / Biso Wilson estimate: 12.63 Å2 / CC1/2: 0.94 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.076 / Rrim(I) all: 0.108 / Net I/σ(I): 10.1
Reflection shellResolution: 1.56→1.59 Å / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1366 / CC1/2: 0.92 / Rpim(I) all: 0.169 / Rrim(I) all: 0.239

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Z8F

2z8f


Resolution: 1.56→38.29 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.766 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1879 2170 5.1 %RANDOM
Rwork0.1498 ---
obs0.1519 40257 86.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 218.7 Å2 / Biso mean: 20.885 Å2 / Biso min: 13.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å21.07 Å21.27 Å2
2---1.05 Å2-0.12 Å2
3----0.48 Å2
Refinement stepCycle: final / Resolution: 1.56→38.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2992 0 59 397 3448
Biso mean--24.13 32.22 -
Num. residues----397
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133114
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172875
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.6624231
X-RAY DIFFRACTIONr_angle_other_deg1.511.6086665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1945396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.37226.308130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.54315503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.067152
X-RAY DIFFRACTIONr_chiral_restr0.0850.2423
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023543
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02654
LS refinement shellResolution: 1.562→1.603 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 115 -
Rwork0.195 2108 -
all-2223 -
obs--61.02 %

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