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- PDB-4tqu: Crystal structure of a bacterial ABC transporter involved in the ... -

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Basic information

Entry
Database: PDB / ID: 4tqu
TitleCrystal structure of a bacterial ABC transporter involved in the import of the acidic polysaccharide alginate
Components
  • AlgM1
  • AlgM2
  • AlgQ2
  • AlgS
KeywordsTRANSPORT PROTEIN / ABC / sphingomonas / alginate / transporter
Function / homology
Function and homology information


carbohydrate transport / ABC-type transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / 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. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.204 Å
AuthorsMaruyama, Y. / Itoh, T. / Kaneko, A. / Nishitani, Y. / Mikami, B. / Hashimoto, W. / Murata, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Grants-in-Aid for Scientific Research from Japan Society for the Promotion of Science Japan
Targeted Proteins Research Program from Ministry of Education, Culture, Sports, Science, and Technology Japan
CitationJournal: Structure / Year: 2015
Title: Structure of a Bacterial ABC Transporter Involved in the Import of an Acidic Polysaccharide Alginate
Authors: Maruyama, Y. / Itoh, T. / Kaneko, A. / Nishitani, Y. / Mikami, B. / Hashimoto, W. / Murata, K.
History
DepositionJun 12, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Sep 16, 2015Group: Database references
Revision 1.3Jan 29, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / 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 / _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_comp_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.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / 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)208,3667
Polymers207,6215
Non-polymers7452
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19580 Å2
ΔGint-116 kcal/mol
Surface area74910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.367, 134.177, 273.798
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 4 types, 5 molecules MNSTQ

#1: Protein AlgM1


Mass: 34286.555 Da / Num. of mol.: 1 / Fragment: UNP residues 25-324
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas sp. (bacteria) / 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. (bacteria) / Gene: algM2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KWT7
#3: Protein AlgS


Mass: 39574.508 Da / Num. of mol.: 2 / Mutation: E160Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas sp. (bacteria) / 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. (bacteria) / Gene: algQ2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KWT5

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Sugars / Non-polymers , 2 types, 2 molecules

#5: 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-(1-4)-beta-D-mannopyranuronic acid


Type: oligosaccharide / Mass: 704.495 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,4,3/[a1122A-1b_1-5][a11eEA-1a_1-5]/1-1-1-2/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-4-deoxy-ManpA]{}}}}LINUCSPDB-CARE
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG3000, N-(2-acetamido)iminodiacetic acid NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 43105 / % possible obs: 97.6 % / Redundancy: 3.7 % / Net I/σ(I): 23.9

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementResolution: 3.204→29.638 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2816 2164 5.03 %
Rwork0.2369 --
obs0.2393 43033 97.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.204→29.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14149 0 49 0 14198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00514531
X-RAY DIFFRACTIONf_angle_d1.05719732
X-RAY DIFFRACTIONf_dihedral_angle_d14.6165344
X-RAY DIFFRACTIONf_chiral_restr0.0792231
X-RAY DIFFRACTIONf_plane_restr0.0052514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2038-3.27820.3821400.31892580X-RAY DIFFRACTION94
3.2782-3.36010.3541380.30952627X-RAY DIFFRACTION96
3.3601-3.45080.3711480.3132682X-RAY DIFFRACTION98
3.4508-3.55220.31661300.29262722X-RAY DIFFRACTION98
3.5522-3.66670.35051450.27272666X-RAY DIFFRACTION98
3.6667-3.79750.32611380.27132738X-RAY DIFFRACTION99
3.7975-3.94920.30081380.25512754X-RAY DIFFRACTION99
3.9492-4.12850.28271510.24532711X-RAY DIFFRACTION99
4.1285-4.34550.25691500.21792765X-RAY DIFFRACTION99
4.3455-4.61680.27291560.20612721X-RAY DIFFRACTION99
4.6168-4.97170.25961390.19372788X-RAY DIFFRACTION99
4.9717-5.46920.29421410.22182795X-RAY DIFFRACTION99
5.4692-6.25420.24681370.25252793X-RAY DIFFRACTION99
6.2542-7.85520.28181670.24092842X-RAY DIFFRACTION99
7.8552-29.63930.2361460.20272685X-RAY DIFFRACTION90
Refinement TLS params.Method: refined / Origin x: -32.5299 Å / Origin y: 7.3295 Å / Origin z: -31.0518 Å
111213212223313233
T0.6636 Å2-0.1227 Å20.0741 Å2-0.614 Å2-0.0139 Å2--0.7124 Å2
L0.8278 °20.168 °2-0.6813 °2-0.4317 °2-0.4001 °2--2.2615 °2
S0.0952 Å °0.1607 Å °-0.1211 Å °-0.2175 Å °-0.0145 Å °0.2435 Å °-0.0149 Å °0.163 Å °-0.1044 Å °
Refinement TLS groupSelection details: ALL

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