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- PDB-1v43: Crystal Structure of ATPase subunit of ABC Sugar Transporter -

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Basic information

Entry
Database: PDB / ID: 1v43
TitleCrystal Structure of ATPase subunit of ABC Sugar Transporter
Componentssugar-binding transport ATP-binding protein
KeywordsTRANSPORT PROTEIN / ATPASE / ACTIVE TRANSPORT / SUGAR UPTAKE AND REGULATION
Function / homology
Function and homology information


carbohydrate transport / ABC-type transporter activity / ATP-binding cassette (ABC) transporter complex / ATP hydrolysis activity / ATP binding
Similarity search - Function
MalK, OB fold domain / MalK OB fold domain / ABC transporter, maltose/maltodextrin import, MalK-like / : / Molybdate/tungstate binding, C-terminal / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Nucleic acid-binding proteins / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter ...MalK, OB fold domain / MalK OB fold domain / ABC transporter, maltose/maltodextrin import, MalK-like / : / Molybdate/tungstate binding, C-terminal / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Nucleic acid-binding proteins / 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. / 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 / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
373aa long hypothetical sugar-binding transport ATP-binding protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsOse, T. / Fujie, T. / Yao, M. / Watanabe, N. / Tanaka, I.
CitationJournal: Proteins / Year: 2004
Title: Crystal structure of the ATP-binding cassette of multisugar transporter from Pyrococcus horikoshii OT3
Authors: Ose, T. / Fujie, T. / Yao, M. / Watanabe, N. / Tanaka, I.
History
DepositionNov 8, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: sugar-binding transport ATP-binding protein


Theoretical massNumber of molelcules
Total (without water)41,9961
Polymers41,9961
Non-polymers00
Water1,78399
1
A: sugar-binding transport ATP-binding protein

A: sugar-binding transport ATP-binding protein


Theoretical massNumber of molelcules
Total (without water)83,9922
Polymers83,9922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)79.907, 79.907, 130.569
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein sugar-binding transport ATP-binding protein / Sugar transport protein ATPase


Mass: 41995.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH0022 / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O57758
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 51.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Ethylene glycol, Sucrose, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 17, 2002 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→65 Å / Num. all: 29328 / Num. obs: 29182 / % possible obs: 99.5 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 4.9 % / Biso Wilson estimate: 51.3 Å2 / Rmerge(I) obs: 0.037 / Rsym value: 0.033 / Net I/σ(I): 19
Reflection shellResolution: 2→2.11 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 2.2 / Num. unique all: 4204 / Rsym value: 0.354 / % possible all: 99.5

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Processing

Software
NameVersionClassification
MAR345data collection
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G29

1g29


Resolution: 2.2→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.2863 2176 -RANDOM
Rwork0.2354 ---
all-22137 --
obs-21937 99.1 %-
Displacement parametersBiso mean: 43.0474 Å2
Baniso -1Baniso -2Baniso -3
1--1.569 Å20 Å20 Å2
2---1.569 Å20 Å2
3---3.138 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2797 0 0 99 2896
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008479
X-RAY DIFFRACTIONc_angle_d1.40088
X-RAY DIFFRACTIONc_dihedral_angle_d24.21263
X-RAY DIFFRACTIONc_improper_angle_d0.90637
LS refinement shellResolution: 2.2→2.28 Å
RfactorNum. reflection% reflection
Rfree0.5212 198 -
Rwork0.193 --
obs-2130 90.6 %

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