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- PDB-3vvf: Crystal structure of TTC0807 complexed with Arginine -

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Basic information

Entry
Database: PDB / ID: 3vvf
TitleCrystal structure of TTC0807 complexed with Arginine
ComponentsAmino acid ABC transporter, binding protein
KeywordsTRANSPORT PROTEIN / Arginine-complex / Periplasm substrate binding protein
Function / homology
Function and homology information


ligand-gated monoatomic ion channel activity / membrane
Similarity search - Function
Solute-binding protein family 3, conserved site / Bacterial extracellular solute-binding proteins, family 3 signature. / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ARGININE / Amino acid ABC transporter, binding protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTomita, T. / Kanemaru, Y. / Hasebe, F. / Kuzuyama, T. / Nishiyama, M.
CitationJournal: J.Bacteriol. / Year: 2013
Title: Two ATP-Binding Cassette Transporters Involved in (S)-2-Aminoethyl-Cysteine Uptake in Thermus thermophilus
Authors: Kanemaru, Y. / Hasebe, F. / Tomita, T. / Kuzuyama, T. / Nishiyama, M.
History
DepositionJul 21, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Nov 8, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Amino acid ABC transporter, binding protein
B: Amino acid ABC transporter, binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2618
Polymers58,5262
Non-polymers7356
Water3,225179
1
A: Amino acid ABC transporter, binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6314
Polymers29,2631
Non-polymers3673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Amino acid ABC transporter, binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6314
Polymers29,2631
Non-polymers3673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.935, 68.838, 104.596
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 Amino acid ABC transporter, binding protein


Mass: 29263.207 Da / Num. of mol.: 2 / Fragment: UNP residues 19-254
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: TTC0807, TT_C0807 / Plasmid: pHIS8-TTC0807 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon Plus (DE3)-RIL / References: UniProt: Q72JG5
#2: Chemical ChemComp-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.12 Å3/Da / Density % sol: 41.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2M Ammonium sulfate, 20% PEG4000, 10mM Arginine, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 1, 2011
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→32.69 Å / Num. all: 40039 / Num. obs: 40039 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.9→1.948 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LST

1lst


Resolution: 1.9→32.69 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.916 / SU B: 2.94 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23976 1978 5 %RANDOM
Rwork0.19107 ---
all0.19347 37501 --
obs0.19347 37501 98.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.347 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→32.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3806 0 44 179 4029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193910
X-RAY DIFFRACTIONr_angle_refined_deg1.3341.9595266
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8995480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.26623.434198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.23415696
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2441542
X-RAY DIFFRACTIONr_chiral_restr0.0910.2572
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212980
LS refinement shellResolution: 1.9→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 140 -
Rwork0.23 2527 -
obs--99.07 %

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