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- PDB-7vfq: Wild type GltA from Bifidobacterium infantis JCM 1222 complexed w... -

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Basic information

Entry
Database: PDB / ID: 7vfq
TitleWild type GltA from Bifidobacterium infantis JCM 1222 complexed with lacto-N-tetraose
ComponentsExtracellular solute-binding protein, family 1
KeywordsTRANSLOCASE / solute-binding protein
Function / homology: / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Prokaryotic membrane lipoprotein lipid attachment site profile. / metal ion binding / plasma membrane / Extracellular solute-binding protein, family 1
Function and homology information
Biological speciesBifidobacterium longum subsp. infantis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSato, M. / Sakanaka, M. / Katayama, T. / Fushinobu, S.
Funding support3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K14379
Japan Society for the Promotion of Science (JSPS)17K19231
Japan Society for the Promotion of Science (JSPS)21H02116
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
B: Extracellular solute-binding protein, family 1
C: Extracellular solute-binding protein, family 1
D: Extracellular solute-binding protein, family 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,63413
Polymers175,3234
Non-polymers3,3119
Water27,4731525
1
A: Extracellular solute-binding protein, family 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6343
Polymers43,8311
Non-polymers8042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-15 kcal/mol
Surface area16240 Å2
MethodPISA
2
B: Extracellular solute-binding protein, family 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7314
Polymers43,8311
Non-polymers9003
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16260 Å2
MethodPISA
3
C: Extracellular solute-binding protein, family 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6343
Polymers43,8311
Non-polymers8042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16330 Å2
MethodPISA
4
D: Extracellular solute-binding protein, family 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6343
Polymers43,8311
Non-polymers8042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.138, 84.381, 106.688
Angle α, β, γ (deg.)97.410, 92.250, 89.920
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 43830.773 Da / Num. of mol.: 4
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.: 4
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.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1525 / 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: 1.99 Å3/Da / Density % sol: 38.23 %
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: 1.55→47.59 Å / Num. obs: 187561 / % possible obs: 95.5 % / Redundancy: 1.8 % / Biso Wilson estimate: 4.9 Å2 / CC1/2: 0.97 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.075 / Rrim(I) all: 0.106 / Net I/σ(I): 5.8
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 2 / Num. unique obs: 8372 / CC1/2: 0.725 / Rpim(I) all: 0.311 / Rrim(I) all: 0.502 / % possible all: 85.7

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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: 1.55→47.59 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / SU B: 1.969 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2271 9435 5 %RANDOM
Rwork0.1909 ---
obs0.1927 178122 95.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.27 Å2 / Biso mean: 10.99 Å2 / Biso min: 3.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20.06 Å2-0.03 Å2
2---0.63 Å2-0.15 Å2
3---0.72 Å2
Refinement stepCycle: final / Resolution: 1.55→47.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11940 0 217 1525 13682
Biso mean--11.91 19.58 -
Num. residues----1584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01312414
X-RAY DIFFRACTIONr_bond_other_d0.0030.01711460
X-RAY DIFFRACTIONr_angle_refined_deg1.6941.66216868
X-RAY DIFFRACTIONr_angle_other_deg1.541.60726559
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.30251578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.50426.322522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.458151998
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.154158
X-RAY DIFFRACTIONr_chiral_restr0.0890.21690
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214144
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022616
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 621 -
Rwork0.245 12173 -
all-12794 -
obs--88.33 %

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