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- PDB-4xig: Crystal structure of bacterial alginate ABC transporter determine... -

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Basic information

Entry
Database: PDB / ID: 4xig
TitleCrystal structure of bacterial alginate ABC transporter determined through humid air and glue-coating method
Components
  • AlgM1
  • AlgM2
  • AlgQ2
  • AlgS
KeywordsTRANSPORT PROTEIN / ABC / alginate / sphingomonas / 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 / MalK, OB fold domain / MetI-like fold / MetI-like / MalK OB fold domain / ABC transporter, maltose/maltodextrin import, MalK-like / : / Molybdate/tungstate binding, C-terminal ...: / Transport-associated OB, type 1 / TOBE domain / MalK, OB fold domain / MetI-like fold / MetI-like / 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 / Periplasmic binding protein-like II / ABC transporter-like, conserved site / ABC transporters family signature. / D-Maltodextrin-Binding Protein; domain 2 / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / P-loop containing nucleotide triphosphate hydrolases / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 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)
Sphingomonas sp. A1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.402 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 7, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 13, 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 / 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 / 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_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 / _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.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
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)208,3256
Polymers207,6215
Non-polymers7041
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20370 Å2
ΔGint-124 kcal/mol
Surface area74700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.175, 133.412, 272.687
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. (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. 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 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)][a-L-4-deoxy-AllpA]{}}}}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: 3.16 Å3/Da / Density % sol: 61.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PEG3000, N-(2-acetamido)iminodiacetic acid, sodium chrolide, 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: ADSC QUANTUM 315r / Detector: CCD / Date: May 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 37120 / % possible obs: 99.8 % / Redundancy: 7.2 % / Net I/σ(I): 12.7
Reflection shellResolution: 3.4→3.46 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.536 / % possible all: 100

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.402→37.559 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2895 1846 5 %
Rwork0.2357 --
obs0.2383 36945 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.402→37.559 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14218 0 48 0 14266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314599
X-RAY DIFFRACTIONf_angle_d0.8219823
X-RAY DIFFRACTIONf_dihedral_angle_d12.8185370
X-RAY DIFFRACTIONf_chiral_restr0.0312244
X-RAY DIFFRACTIONf_plane_restr0.0032524
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4021-3.4940.32651330.27062604X-RAY DIFFRACTION98
3.494-3.59680.30131180.25322701X-RAY DIFFRACTION100
3.5968-3.71280.32071350.25612667X-RAY DIFFRACTION100
3.7128-3.84530.29741320.24352672X-RAY DIFFRACTION100
3.8453-3.99910.33461370.2562699X-RAY DIFFRACTION100
3.9991-4.18090.30581510.2442642X-RAY DIFFRACTION100
4.1809-4.4010.27661560.23012658X-RAY DIFFRACTION100
4.401-4.67630.28761460.22462687X-RAY DIFFRACTION100
4.6763-5.03660.29021800.23032678X-RAY DIFFRACTION100
5.0366-5.5420.33471420.26152712X-RAY DIFFRACTION100
5.542-6.34060.32181340.26682740X-RAY DIFFRACTION100
6.3406-7.97580.3051440.24622777X-RAY DIFFRACTION100
7.9758-37.56130.23351380.2032862X-RAY DIFFRACTION98
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)
12.36120.81080.26481.997-0.9472.59210.49630.7121-0.8021-0.6603-0.18820.05551.07660.5389-0.30761.26740.4057-0.46491.0582-0.2381.0158-29.8802-20.294517.6936
24.1118-0.76584.34461.7158-0.47358.8573-0.15480.0540.6549-0.3305-0.2212-0.0144-1.23460.7750.33350.7762-0.0643-0.12060.73560.04330.6806-23.32165.197827.1382
34.9493-1.84352.9285.5945-0.92083.32360.13250.7209-0.3317-0.33810.3118-0.34980.83081.2924-0.34481.08030.4212-0.2891.3683-0.26810.7581-24.6476-12.292111.1581
48.8701-1.25851.13278.52810.56316.5935-0.2988-1.36230.3001-0.0392-0.2395-1.5396-1.1242-0.07260.37621.1069-0.1266-0.07510.5158-0.1450.5592-23.82814.791833.58
52.7643-0.51161.29561.9031-1.36965.1760.47550.0151-0.5341-0.49760.16290.30090.7159-0.4242-0.64580.8270.1496-0.28250.76180.0090.9257-42.3059-10.437523.821
61.8251-0.66981.14595.9062-2.99927.04140.3113-0.1760.0262-0.3007-0.05150.52220.3777-0.721-0.22220.50180.0327-0.21960.7810.05160.7429-44.2055-0.640722.1644
77.1352-1.8234-0.77326.63790.8959.04310.05740.12850.47490.4311-0.0071-0.2405-1.22881.0970.00050.7718-0.1022-0.12580.88040.07090.6485-12.3394.01262.7369
85.75130.8029-1.10624.8767-1.92817.901-0.7890.25-1.14550.18580.4298-1.00251.97462.75510.29280.63690.214-0.07841.3618-0.21030.8211-5.5741-12.185961.5171
92.08470.5852-4.71850.7414-0.09567.0632-0.0855-0.57810.39850.61940.1610.57030.0857-0.1049-0.06891.03810.10950.1991.083-0.00150.8958-26.4579-4.70787.9421
102.9757-0.0604-0.40398.69984.83444.43580.7769-0.52290.07020.6591-0.5611-0.02490.06990.1848-0.09141.0977-0.02150.3391.37830.05170.7415-33.1788-18.210492.9305
111.8179-0.271.50463.6968-0.86865.90220.79010.1993-0.8719-0.026-0.1212-0.16231.2580.2112-0.72041.45570.2076-0.56941.166-0.05731.0561-56.409-5.9242-13.3695
123.8822-0.64632.79631.6280.67354.20180.29331.2750.6533-0.7198-0.4429-0.6885-0.73690.68610.19571.56790.2099-0.17631.78980.52921.102-35.638118.745-16.6761
132.6732-0.69050.47184.226-0.54085.07060.11781.41970.1369-0.1467-0.163-0.0085-0.51150.5218-0.09391.2579-0.0602-0.24961.55290.29061.0013-33.087115.5746-14.4559
144.77340.84372.27032.89171.77924.09380.06360.98320.6716-1.1873-0.34430.5138-0.416-0.03820.09111.47370.2692-0.41531.35340.38180.9135-55.077611.0511-17.2
152.156-0.7860.07353.74510.16764.2901-0.00771.3306-0.2323-0.28040.2499-0.00710.41771.1051-0.14281.3440.3657-0.17832.42410.06040.944-30.89270.8632-22.457
164.03271.7676-0.27942.96070.06256.6921-0.4679-0.0914-1.6289-0.92690.2310.02591.78361.1464-0.29522.51590.4609-0.1690.57730.22450.8201-34.1054-44.146560.0993
172.63121.29690.78662.80311.26188.34860.14020.4150.6549-0.69290.00490.89410.0496-0.0481-0.15281.17730.1348-0.0320.78940.26351.0839-44.0384-27.453363.2725
188.49040.60180.98781.6943-1.84884.17460.0645-1.2818-1.28350.16070.11720.23071.26610.6332-0.23061.72110.42980.10421.1140.21790.8006-16.6318-37.816675.6652
194.3609-0.71481.82692.6691-0.4043.387-0.00330.0494-0.47310.73780.0895-0.33580.59010.9093-0.04361.14840.35590.07351.38230.11940.7699-6.7191-31.880384.1989
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'M' and (resid 25 through 122 )
2X-RAY DIFFRACTION2chain 'M' and (resid 123 through 251 )
3X-RAY DIFFRACTION3chain 'M' and (resid 252 through 323 )
4X-RAY DIFFRACTION4chain 'N' and (resid 2 through 41 )
5X-RAY DIFFRACTION5chain 'N' and (resid 42 through 178 )
6X-RAY DIFFRACTION6chain 'N' and (resid 179 through 291 )
7X-RAY DIFFRACTION7chain 'S' and (resid 1 through 107 )
8X-RAY DIFFRACTION8chain 'S' and (resid 108 through 183 )
9X-RAY DIFFRACTION9chain 'S' and (resid 184 through 278 )
10X-RAY DIFFRACTION10chain 'S' and (resid 279 through 363 )
11X-RAY DIFFRACTION11chain 'Q' and (resid 1 through 117 )
12X-RAY DIFFRACTION12chain 'Q' and (resid 118 through 210 )
13X-RAY DIFFRACTION13chain 'Q' and (resid 211 through 280 )
14X-RAY DIFFRACTION14chain 'Q' and (resid 281 through 401 )
15X-RAY DIFFRACTION15chain 'Q' and (resid 402 through 492 )
16X-RAY DIFFRACTION16chain 'T' and (resid 1 through 31 )
17X-RAY DIFFRACTION17chain 'T' and (resid 32 through 194 )
18X-RAY DIFFRACTION18chain 'T' and (resid 195 through 260 )
19X-RAY DIFFRACTION19chain 'T' and (resid 261 through 363 )

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