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- PDB-5h71: Structure of alginate-binding protein AlgQ2 in complex with an al... -

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Basic information

Entry
Database: PDB / ID: 5h71
TitleStructure of alginate-binding protein AlgQ2 in complex with an alginate trisaccharide
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
DI(HYDROXYETHYL)ETHER / AlgQ2
Similarity search - Component
Biological speciesSphingomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.549 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: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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_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)115,92310
Polymers114,5032
Non-polymers1,4208
Water26,5361473
1
A: AlgQ2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9264
Polymers57,2521
Non-polymers6753
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area21220 Å2
MethodPISA
2
B: AlgQ2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9976
Polymers57,2521
Non-polymers7455
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-8 kcal/mol
Surface area21590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.274, 53.150, 127.451
Angle α, β, γ (deg.)90.00, 93.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein AlgQ2


Mass: 57251.715 Da / Num. of mol.: 2 / Fragment: UNP residues 25-516 / 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 4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D- ...4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid


Type: oligosaccharide / Mass: 528.372 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a1122A-1b_1-5][a11eEA-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-4-deoxy-ManpA]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 1479 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Ca
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1473 / 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: 2.26 Å3/Da / Density % sol: 45.55 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG4000, 0.2 M lithium sulfate, 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: Oct 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.549→30 Å / Num. obs: 143400 / % possible obs: 96.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 25.9
Reflection shellResolution: 1.549→1.58 Å / Redundancy: 2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.2 / % possible all: 89.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J1N

1j1n


Resolution: 1.549→29.852 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.4
RfactorNum. reflection% reflection
Rfree0.1965 7280 5.08 %
Rwork0.1671 --
obs0.1686 143354 96.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.549→29.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8065 0 90 1473 9628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078466
X-RAY DIFFRACTIONf_angle_d1.12611476
X-RAY DIFFRACTIONf_dihedral_angle_d13.2933187
X-RAY DIFFRACTIONf_chiral_restr0.0481153
X-RAY DIFFRACTIONf_plane_restr0.0061490
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5486-1.56620.22822020.21414084X-RAY DIFFRACTION87
1.5662-1.58460.23612100.2024391X-RAY DIFFRACTION94
1.5846-1.60390.2152440.18524444X-RAY DIFFRACTION95
1.6039-1.62420.21662240.18614408X-RAY DIFFRACTION95
1.6242-1.64560.21982550.18574390X-RAY DIFFRACTION95
1.6456-1.66810.24592290.18574429X-RAY DIFFRACTION95
1.6681-1.69190.23762680.1864398X-RAY DIFFRACTION94
1.6919-1.71720.22922440.1864397X-RAY DIFFRACTION94
1.7172-1.7440.21592340.18594426X-RAY DIFFRACTION95
1.744-1.77260.21832450.18314466X-RAY DIFFRACTION95
1.7726-1.80320.25432310.18314402X-RAY DIFFRACTION95
1.8032-1.8360.21622380.17684477X-RAY DIFFRACTION95
1.836-1.87130.21432350.17084460X-RAY DIFFRACTION96
1.8713-1.90950.19352240.16954495X-RAY DIFFRACTION96
1.9095-1.9510.20452320.17314544X-RAY DIFFRACTION96
1.951-1.99630.19982230.17934512X-RAY DIFFRACTION97
1.9963-2.04630.22512430.1714580X-RAY DIFFRACTION97
2.0463-2.10160.19172440.17374543X-RAY DIFFRACTION97
2.1016-2.16340.19952470.17234585X-RAY DIFFRACTION98
2.1634-2.23320.20912380.16724614X-RAY DIFFRACTION98
2.2332-2.3130.20832570.17034649X-RAY DIFFRACTION98
2.313-2.40560.19652760.17014596X-RAY DIFFRACTION99
2.4056-2.5150.20482760.17674611X-RAY DIFFRACTION99
2.515-2.64750.18712230.17434694X-RAY DIFFRACTION99
2.6475-2.81330.19882460.1774676X-RAY DIFFRACTION99
2.8133-3.03030.20792630.1794663X-RAY DIFFRACTION99
3.0303-3.33490.19252390.17084756X-RAY DIFFRACTION100
3.3349-3.81660.17692730.14724729X-RAY DIFFRACTION100
3.8166-4.80520.1562400.12774787X-RAY DIFFRACTION100
4.8052-29.85780.16882770.1534868X-RAY DIFFRACTION100

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