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

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Basic information

Entry
Database: PDB / ID: 4tqv
TitleCrystal structure of a bacterial ABC transporter involved in the import of the acidic polysaccharide alginate
Components
  • AlgM1
  • AlgM2
  • 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 / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
: / Transport-associated OB, type 1 / TOBE domain / 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 ...: / Transport-associated OB, type 1 / TOBE domain / 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. / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
AlgM2 / AlgM1 / AlgS
Similarity search - Component
Biological speciesSphingomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 4.504 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 1.4Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AlgM1
B: AlgM2
C: AlgS
D: AlgS
E: AlgM1
F: AlgM2
G: AlgS
H: AlgS
I: AlgM1
J: AlgM2
K: AlgS
L: AlgS
M: AlgM1
N: AlgM2
O: AlgS
P: AlgS


Theoretical massNumber of molelcules
Total (without water)591,72916
Polymers591,72916
Non-polymers00
Water00
1
A: AlgM1
B: AlgM2
C: AlgS
D: AlgS


Theoretical massNumber of molelcules
Total (without water)147,9324
Polymers147,9324
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14190 Å2
ΔGint-119 kcal/mol
Surface area57620 Å2
MethodPISA
2
E: AlgM1
F: AlgM2
G: AlgS
H: AlgS


Theoretical massNumber of molelcules
Total (without water)147,9324
Polymers147,9324
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14120 Å2
ΔGint-119 kcal/mol
Surface area58250 Å2
MethodPISA
3
I: AlgM1
J: AlgM2
K: AlgS
L: AlgS


Theoretical massNumber of molelcules
Total (without water)147,9324
Polymers147,9324
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14220 Å2
ΔGint-121 kcal/mol
Surface area57620 Å2
MethodPISA
4
M: AlgM1
N: AlgM2
O: AlgS
P: AlgS


Theoretical massNumber of molelcules
Total (without water)147,9324
Polymers147,9324
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14170 Å2
ΔGint-116 kcal/mol
Surface area57630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.245, 151.187, 162.406
Angle α, β, γ (deg.)68.66, 81.76, 90.10
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
AlgM1


Mass: 34286.555 Da / Num. of mol.: 4 / 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.: 4
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.: 8 / 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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.4 Å3/Da / Density % sol: 72.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PEG4000, sodium potassium tartrate, N-(2-acetamido)iminodiacetic acid

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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: Apr 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.5→30 Å / Num. obs: 57115 / % possible obs: 96.2 % / Redundancy: 2 % / Net I/σ(I): 14.7
Reflection shellResolution: 4.5→4.58 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 1.3 / % possible all: 91.4

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementResolution: 4.504→29.816 Å / SU ML: 0.84 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 43.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3201 1989 3.5 %
Rwork0.2786 --
obs0.28 56880 95.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.504→29.816 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms40472 0 0 0 40472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00441320
X-RAY DIFFRACTIONf_angle_d1.1256148
X-RAY DIFFRACTIONf_dihedral_angle_d15.17615108
X-RAY DIFFRACTIONf_chiral_restr0.0436620
X-RAY DIFFRACTIONf_plane_restr0.0057100
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.5042-4.61640.37391330.36063618X-RAY DIFFRACTION87
4.6164-4.74080.38541340.35623744X-RAY DIFFRACTION92
4.7408-4.87970.3651380.33913805X-RAY DIFFRACTION93
4.8797-5.03650.41841380.3423838X-RAY DIFFRACTION93
5.0365-5.21550.42641420.33613864X-RAY DIFFRACTION94
5.2155-5.42320.38751410.33973896X-RAY DIFFRACTION95
5.4232-5.66840.41961410.32743886X-RAY DIFFRACTION96
5.6684-5.9650.40521470.33224030X-RAY DIFFRACTION98
5.965-6.33540.41450.32834025X-RAY DIFFRACTION98
6.3354-6.81910.37681460.30264052X-RAY DIFFRACTION98
6.8191-7.49550.31981470.26473997X-RAY DIFFRACTION98
7.4955-8.55760.32061460.23114043X-RAY DIFFRACTION98
8.5576-10.69820.22661470.19864074X-RAY DIFFRACTION99
10.6982-29.81620.28331440.28174019X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 32.1965 Å / Origin y: -26.0895 Å / Origin z: 12.7038 Å
111213212223313233
T0.8142 Å2-0.0427 Å20.141 Å2-1.0365 Å2-0.2192 Å2--0.8572 Å2
L0.1164 °2-0.0844 °2-0.3609 °2--0.1108 °20.1538 °2--0.4905 °2
S0.0314 Å °-0.1171 Å °0.075 Å °0.1068 Å °0.0681 Å °0.0274 Å °-0.0809 Å °0.1704 Å °-0.1048 Å °
Refinement TLS groupSelection details: all

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