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Basic information

Entry
Database: PDB / ID: 4xtc
TitleCrystal structure of bacterial alginate ABC transporter in complex with alginate pentasaccharide-bound periplasmic protein
Components
  • AlgM1
  • AlgM2
  • AlgQ2
  • AlgSApex Legends Global Series
KeywordsTRANSPORT PROTEIN / ABC / alginate / sphingomonas / transporter
Function / homology
Function and homology information


carbohydrate transport / ABC-type transporter activity / ATP-binding cassette (ABC) transporter complex / transmembrane transport / periplasmic space / ATP hydrolysis activity / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
Transport-associated OB, type 1 / TOBE domain / MetI-like fold / MetI-like / MalK, OB fold domain / MalK OB fold domain / ABC transporter, maltose/maltodextrin import, MalK-like / : / Molybdate/tungstate binding, C-terminal / ABC transporter type 1, transmembrane domain MetI-like ...Transport-associated OB, type 1 / TOBE domain / MetI-like fold / MetI-like / MalK, OB fold domain / MalK OB fold domain / ABC transporter, maltose/maltodextrin import, MalK-like / : / Molybdate/tungstate binding, C-terminal / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily / Binding-protein-dependent transport system inner membrane component / ABC transporter integral membrane type-1 domain profile. / Bacterial extracellular solute-binding protein / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Nucleic acid-binding proteins / ABC transporter-like, conserved site / ABC transporters family signature. / Periplasmic binding protein-like II / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / D-Maltodextrin-Binding Protein; domain 2 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
AlgQ2 / AlgM2 / AlgM1 / AlgS
Similarity search - Component
Biological speciesSphingomonas sp. A1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsKaneko, A. / Maruyama, Y. / Mizuno, N. / Baba, S. / Kumasaka, T. / Mikami, B. / Murata, K. / Hashimoto, W.
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
DepositionJan 23, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 1, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_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
M: AlgM1
N: AlgM2
S: AlgS
Q: AlgQ2
T: AlgS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,5206
Polymers207,6215
Non-polymers8991
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20690 Å2
ΔGint-118 kcal/mol
Surface area74080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.608, 132.963, 272.973
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AlgM1


Mass: 34286.555 Da / Num. of mol.: 1 / Mutation: 2-24 deletion mutant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas sp. A1 (bacteria) / Strain: A1 / Gene: algM1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KWT8
#2: Protein AlgM2


Mass: 34496.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas sp. A1 (bacteria) / Strain: A1 / Gene: algM2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KWT7
#3: Protein AlgS / Apex Legends Global Series


Mass: 39574.508 Da / Num. of mol.: 2 / Mutation: E160Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas sp. A1 (bacteria) / Strain: A1 / Gene: algS / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KWT9
#4: Protein AlgQ2


Mass: 59688.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas sp. A1 (bacteria) / Strain: A1 / Gene: algQ2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KWT5
#5: 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.: 1
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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PEG3000, N-(2-acetamido)iminodiacetic acid, sodium formate, 3-[(3-cholamidopropyl)dimethylammonio]-2-hydroxypropanesulfonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 30118 / % possible obs: 95.6 % / Redundancy: 4.9 % / Net I/σ(I): 9.2
Reflection shellResolution: 3.6→3.66 Å / Redundancy: 5 % / Rmerge(I) obs: 0.461 / % possible all: 98

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XIG

4xig


Resolution: 3.6→37.42 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2885 1487 5.03 %
Rwork0.2384 --
obs0.241 29557 95.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.6→37.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14203 0 61 0 14264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314598
X-RAY DIFFRACTIONf_angle_d0.78119825
X-RAY DIFFRACTIONf_dihedral_angle_d12.1975374
X-RAY DIFFRACTIONf_chiral_restr0.032249
X-RAY DIFFRACTIONf_plane_restr0.0032519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6001-3.71620.33811230.28642555X-RAY DIFFRACTION97
3.7162-3.84890.32361390.26992556X-RAY DIFFRACTION97
3.8489-4.00280.32311460.26582558X-RAY DIFFRACTION97
4.0028-4.18470.28711430.2442538X-RAY DIFFRACTION97
4.1847-4.4050.30161480.22542541X-RAY DIFFRACTION96
4.405-4.68060.25411340.21542537X-RAY DIFFRACTION96
4.6806-5.04120.27261280.22652577X-RAY DIFFRACTION96
5.0412-5.5470.32561260.25572549X-RAY DIFFRACTION95
5.547-6.34630.28521220.25872582X-RAY DIFFRACTION95
6.3463-7.98290.35241470.25722587X-RAY DIFFRACTION95
7.9829-37.4220.23321310.21082490X-RAY DIFFRACTION87
Refinement TLS params.Method: refined / Origin x: -32.1378 Å / Origin y: 7.1878 Å / Origin z: -31.1622 Å
111213212223313233
T0.5913 Å2-0.1555 Å20.1181 Å2-0.5402 Å2-0.01 Å2--0.7925 Å2
L0.9943 °20.3204 °2-0.9247 °2-0.7377 °2-0.5975 °2--3.2904 °2
S0.1725 Å °-0.2718 Å °0.0068 Å °0.2057 Å °-0.0368 Å °0.3281 Å °-0.2857 Å °0.3847 Å °-0.1234 Å °
Refinement TLS groupSelection details: all

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