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- PDB-2yyz: Crystal structure of Sugar ABC transporter, ATP-binding protein -

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Basic information

Entry
Database: PDB / ID: 2yyz
TitleCrystal structure of Sugar ABC transporter, ATP-binding protein
ComponentsSugar ABC transporter, ATP-binding protein
KeywordsTRANSPORT PROTEIN / Sugar transport / ATP binding / Alpha and beta proteins (a/b) class / TM0421 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / transmembrane transport / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Transport-associated OB, type 2 / TOBE domain / 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. ...Transport-associated OB, type 2 / TOBE domain / 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 / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Sugar ABC transporter, ATP-binding protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsEthayathullah, A.S. / Bessho, Y. / Padmanabhan, B. / Singh, T.P. / Kaur, P. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of Sugar ABC transporter, ATP-binding protein
Authors: Ethayathullah, A.S. / Bessho, Y. / Padmanabhan, B. / Singh, T.P. / Kaur, P. / Yokoyama, S.
History
DepositionMay 2, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sugar ABC transporter, ATP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7384
Polymers40,4401
Non-polymers2983
Water4,972276
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.063, 86.774, 105.681
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 Sugar ABC transporter, ATP-binding protein


Mass: 40439.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q9WYQ2
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.55 Å3/Da / Density % sol: 51.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2M Li Sulfate, 21% PEG3350, 0.1M HEPES, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD
RadiationMonochromator: Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50.12 Å / Num. all: 24672 / Num. obs: 24616 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Redundancy: 7 % / Rmerge(I) obs: 0.06
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 7 % / Rmerge(I) obs: 0.302 / Num. unique all: 2405 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2D62

2d62


Resolution: 2.11→50.12 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.879 / SU B: 5.28 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.259 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27973 1250 5.1 %RANDOM
Rwork0.22322 ---
obs0.22622 23314 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.401 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2---0.63 Å20 Å2
3---0.81 Å2
Refinement stepCycle: LAST / Resolution: 2.11→50.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2835 0 17 276 3128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222915
X-RAY DIFFRACTIONr_angle_refined_deg1.3861.9923947
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5055361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.82124.252127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.47715537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1451521
X-RAY DIFFRACTIONr_chiral_restr0.0920.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022155
X-RAY DIFFRACTIONr_nbd_refined0.220.21406
X-RAY DIFFRACTIONr_nbtor_refined0.310.21957
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2244
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.218
X-RAY DIFFRACTIONr_mcbond_it0.7671.51858
X-RAY DIFFRACTIONr_mcangle_it1.24722943
X-RAY DIFFRACTIONr_scbond_it1.7831170
X-RAY DIFFRACTIONr_scangle_it2.8754.51002
LS refinement shellResolution: 2.107→2.162 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 71 -
Rwork0.223 1641 -
obs--95.11 %

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