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- PDB-5ysb: Crystal structure of beta-1,2-glucooligosaccharide binding protei... -

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Basic information

Entry
Database: PDB / ID: 5ysb
TitleCrystal structure of beta-1,2-glucooligosaccharide binding protein in ligand-free form
ComponentsLin1841 protein
KeywordsSUGAR BINDING PROTEIN / solute-binding protein / protein-carbohydrate complex / beta-1 / 2-glucooligosaccharide / sophorooligosaccharide / alpha/beta domain
Function / homology
Function and homology information


maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / metal ion binding
Similarity search - Function
Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Lin1841 protein
Similarity search - Component
Biological speciesListeria innocua serovar 6a
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsAbe, K. / Nakajima, M. / Taguchi, H. / Arakawa, T. / Fushinobu, S.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural and thermodynamic insights into beta-1,2-glucooligosaccharide capture by a solute-binding protein inListeria innocua.
Authors: Abe, K. / Sunagawa, N. / Terada, T. / Takahashi, Y. / Arakawa, T. / Igarashi, K. / Samejima, M. / Nakai, H. / Taguchi, H. / Nakajima, M. / Fushinobu, S.
History
DepositionNov 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lin1841 protein
B: Lin1841 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,94628
Polymers89,1642
Non-polymers1,78226
Water3,693205
1
A: Lin1841 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,66917
Polymers44,5821
Non-polymers1,08716
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lin1841 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,27711
Polymers44,5821
Non-polymers69510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.925, 74.925, 120.844
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: _ / Auth seq-ID: 36 - 419 / Label seq-ID: 11 - 394

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Lin1841 protein / beta-1 / 2-glucooligosaccharide binding protein


Mass: 44582.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262) (bacteria)
Strain: ATCC BAA-680 / CLIP 11262 / Gene: lin1841 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q92AS8
#2: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.15M zinc acetate, 15% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 28, 2015
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: 2.2→50 Å / Num. obs: 38141 / % possible obs: 98.8 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.047 / Net I/σ(I): 21
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.571 / Num. unique obs: 1912 / CC1/2: 0.906 / Rpim(I) all: 0.263 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
HKL-2000data processing
MOLREPphasing
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UOR

3uor


Resolution: 2.2→19.24 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.922 / SU B: 10.858 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.32 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24679 1856 4.8 %RANDOM
Rwork0.18975 ---
obs0.19246 36488 99.57 %-
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 mean: 49.947 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20.12 Å20 Å2
2--0.23 Å20 Å2
3----0.76 Å2
Refinement stepCycle: 1 / Resolution: 2.2→19.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6093 0 38 205 6336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0156259
X-RAY DIFFRACTIONr_bond_other_d0.0060.0175648
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.758469
X-RAY DIFFRACTIONr_angle_other_deg0.5671.71813257
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25769
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.72922.283184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.02515938
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8081512
X-RAY DIFFRACTIONr_chiral_restr0.0880.2789
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216953
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021176
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7832.8583082
X-RAY DIFFRACTIONr_mcbond_other2.7822.8593083
X-RAY DIFFRACTIONr_mcangle_it3.9854.2733849
X-RAY DIFFRACTIONr_mcangle_other3.9864.2743850
X-RAY DIFFRACTIONr_scbond_it3.4353.2283177
X-RAY DIFFRACTIONr_scbond_other3.4343.2283177
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2034.6694621
X-RAY DIFFRACTIONr_long_range_B_refined7.67754.56126912
X-RAY DIFFRACTIONr_long_range_B_other7.67754.5626912
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 12594 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 138 -
Rwork0.147 2702 -
obs--99.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1644-0.15770.1460.7344-0.1320.3007-0.03520.03090.04390.1110.0069-0.01480.03150.04550.02830.05310.00980.02110.0131-0.00360.589935.1597.5780.168
20.1193-0.1766-0.08660.6545-0.00580.4161-0.03790.0011-0.02750.03870.04770.05090.01-0.0649-0.00980.02230.0036-0.00760.01480.01520.5756-0.20412.3052.515
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 420
2X-RAY DIFFRACTION2B36 - 420

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