[English] 日本語
Yorodumi
- PDB-4xig: Crystal structure of bacterial alginate ABC transporter determine... -

+
Open data


ID or keywords:

Loading...

-
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
  • 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. (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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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

-
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 / 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 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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more