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- PDB-5h6u: Structure of alginate-binding protein AlgQ2 in complex with an al... -

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Basic information

Entry
Database: PDB / ID: 5h6u
TitleStructure of alginate-binding protein AlgQ2 in complex with an alginate pentasaccharide
ComponentsAlgQ2
KeywordsSUGAR BINDING PROTEIN / Alginate oligosaccharide / closed conformation / Solute-binding protein / Sphingomonas
Function / homology
Function and homology information


periplasmic space / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSphingomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.006 Å
AuthorsUenishi, K. / Kaneko, A. / Maruyama, Y. / Mikami, B. / Murata, K. / Hashimoto, W.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science Japan
CitationJournal: J. Biol. Chem. / Year: 2017
Title: A solute-binding protein in the closed conformation induces ATP hydrolysis in a bacterial ATP-binding cassette transporter involved in the import of alginate
Authors: Kaneko, A. / Uenishi, K. / Maruyama, Y. / Mizuno, N. / Baba, S. / Kumasaka, T. / Mikami, B. / Murata, K. / Hashimoto, W.
History
DepositionNov 15, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / 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 / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AlgQ2
B: AlgQ2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,54110
Polymers114,5032
Non-polymers2,0388
Water9,944552
1
A: AlgQ2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2715
Polymers57,2521
Non-polymers1,0194
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint16 kcal/mol
Surface area20190 Å2
MethodPISA
2
B: AlgQ2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2715
Polymers57,2521
Non-polymers1,0194
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint2 kcal/mol
Surface area20130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.107, 59.179, 82.724
Angle α, β, γ (deg.)84.62, 90.16, 87.99
Int Tables number1
Space group name H-MP1

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Components

#1: Protein AlgQ2


Mass: 57251.715 Da / Num. of mol.: 2 / Fragment: UNP residues 28-514 / Mutation: R253K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas sp. (bacteria) / Gene: algQ2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KWT5
#2: Polysaccharide beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid- ...beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid


Type: oligosaccharide / Mass: 898.634 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpAb1-4DManpAb1-4DManpAb1-4DManpAb1-4DManpAb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a1122A-1b_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{}}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 552 / 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: 1.99 Å3/Da / Density % sol: 38.07 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% PEG4000, 0.2 M calcium chloride, 0.1 M tris(hydroxymethyl)aminomethan-hydrochloride acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 56452 / % possible obs: 97.4 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 31.4
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 5.6 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J1N

1j1n


Resolution: 2.006→35.68 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 29.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2607 2814 4.99 %
Rwork0.2013 --
obs0.2043 56430 96.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.006→35.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7989 0 128 552 8669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018383
X-RAY DIFFRACTIONf_angle_d1.04111374
X-RAY DIFFRACTIONf_dihedral_angle_d16.344948
X-RAY DIFFRACTIONf_chiral_restr0.0551160
X-RAY DIFFRACTIONf_plane_restr0.0071462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0061-2.04070.32511260.26382371X-RAY DIFFRACTION87
2.0407-2.07780.33611310.28152614X-RAY DIFFRACTION95
2.0778-2.11780.31931460.26572701X-RAY DIFFRACTION96
2.1178-2.1610.34981380.26152639X-RAY DIFFRACTION96
2.161-2.2080.35261380.2482695X-RAY DIFFRACTION96
2.208-2.25930.31131540.25852616X-RAY DIFFRACTION96
2.2593-2.31580.32641360.24572660X-RAY DIFFRACTION95
2.3158-2.37840.30071520.23112662X-RAY DIFFRACTION97
2.3784-2.44840.33011420.23362705X-RAY DIFFRACTION97
2.4484-2.52740.30691340.22872691X-RAY DIFFRACTION97
2.5274-2.61770.26171360.22172683X-RAY DIFFRACTION98
2.6177-2.72250.30841400.22372748X-RAY DIFFRACTION97
2.7225-2.84630.28561620.22252680X-RAY DIFFRACTION98
2.8463-2.99630.33211200.22032726X-RAY DIFFRACTION98
2.9963-3.18390.28431330.21462729X-RAY DIFFRACTION98
3.1839-3.42960.24771380.20462734X-RAY DIFFRACTION98
3.4296-3.77440.21981560.18242739X-RAY DIFFRACTION99
3.7744-4.31970.21861740.16482705X-RAY DIFFRACTION99
4.3197-5.43930.20431300.15722748X-RAY DIFFRACTION99
5.4393-35.68520.18961280.15172770X-RAY DIFFRACTION99

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