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- PDB-6lce: Crystal Structure of beta-L-arabinobiose binding protein - seleno... -

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Basic information

Entry
Database: PDB / ID: 6lce
TitleCrystal Structure of beta-L-arabinobiose binding protein - selenomethionine derivative
ComponentsABC transporter substrate binding component
KeywordsSUGAR BINDING PROTEIN / substrate-binding protein of ABC transporter
Function / homologyBacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / ABC transporter substrate binding component
Function and homology information
Biological speciesBifidobacterium longum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.78 Å
AuthorsMiyake, M. / Arakawa, T. / Fushinobu, S.
CitationJournal: Febs J. / Year: 2020
Title: Structural analysis of beta-L-arabinobiose-binding protein in the metabolic pathway of hydroxyproline-rich glycoproteins in Bifidobacterium longum.
Authors: Miyake, M. / Terada, T. / Shimokawa, M. / Sugimoto, N. / Arakawa, T. / Shimizu, K. / Igarashi, K. / Fujita, K. / Fushinobu, S.
History
DepositionNov 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 23, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / struct_conn
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ABC transporter substrate binding component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2002
Polymers46,9181
Non-polymers2821
Water7,008389
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.339, 66.277, 92.118
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ABC transporter substrate binding component / Bacterial extracellular solute-binding protein / Sugar ABC transporter substrate-binding protein / ...Bacterial extracellular solute-binding protein / Sugar ABC transporter substrate-binding protein / Sugars ABC transporter substrate-binding protein


Mass: 46918.191 Da / Num. of mol.: 1 / Fragment: ligand binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium longum (bacteria)
Gene: APC1462_0182, APC1476_0195, APC1503_0213, APS65_00860, BBG7_0210, BL105A_0201, DPC6316_0214, DPC6317_0191, DW237_03380, DW792_04665, DWV59_05050, DWV93_04885, DWZ73_01175, EAI75_02995, HMPREF0177_01141
Plasmid: pET-16b / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: A0A0A1GL90
#2: Polysaccharide beta-L-arabinofuranose-(1-2)-alpha-L-arabinofuranose


Type: oligosaccharide / Mass: 282.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LArafb1-2LArafa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a211h-1a_1-4][a211h-1b_1-4]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][a-L-Araf]{[(2+1)][b-L-Araf]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 1.74 Å3/Da / Density % sol: 29.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 18% PEG 1000, 0.1M Na-citrate (pH 3.5), 0.6mM beta-L-arabinobiose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 13, 2013
RadiationMonochromator: Bartels Monochromator with dual channel cut crystals (DCCM) in (+--+) geometry
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.78→46.2 Å / Num. obs: 31327 / % possible obs: 98 % / Redundancy: 17.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.161 / Net I/σ(I): 18.3
Reflection shellResolution: 1.78→1.82 Å / Rmerge(I) obs: 0.947 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1476 / CC1/2: 0.759

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.78→46.2 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.419 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.114
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1822 1568 5 %RANDOM
Rwork0.1394 ---
obs0.1415 29706 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 64.76 Å2 / Biso mean: 13.722 Å2 / Biso min: 6.92 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.78→46.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3049 0 19 389 3457
Biso mean--12.27 26.74 -
Num. residues----407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133149
X-RAY DIFFRACTIONr_bond_other_d0.0030.0172826
X-RAY DIFFRACTIONr_angle_refined_deg1.7491.654283
X-RAY DIFFRACTIONr_angle_other_deg1.541.5896620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1895412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.56426.503143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.33715486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.177154
X-RAY DIFFRACTIONr_chiral_restr0.080.2424
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023588
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02572
LS refinement shellResolution: 1.78→1.826 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 93 -
Rwork0.21 1814 -
all-1907 -
obs--82.41 %

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