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- PDB-4psh: Structure of holo ArgBP from T. maritima -

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Basic information

Entry
Database: PDB / ID: 4psh
TitleStructure of holo ArgBP from T. maritima
ComponentsABC-type transporter, periplasmic subunit family 3
KeywordsPROTEIN TRANSPORT / alpha/beta / arg binding protein
Function / homology
Function and homology information


ligand-gated monoatomic ion channel activity / amino acid binding / outer membrane-bounded periplasmic space / membrane
Similarity search - Function
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.
Similarity search - Domain/homology
ARGININE / Amino acid ABC transporter, periplasmic amino acid-binding protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsRuggiero, A. / Dattelbaum, J.D. / Staiano, M. / Berisio, R. / D'Auria, S. / Vitagliano, L.
CitationJournal: Plos One / Year: 2014
Title: A loose domain swapping organization confers a remarkable stability to the dimeric structure of the arginine binding protein from Thermotoga maritima
Authors: Ruggiero, A. / Dattelbaum, J.D. / Staiano, M. / Berisio, R. / D'Auria, S. / Vitagliano, L.
History
DepositionMar 7, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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: ABC-type transporter, periplasmic subunit family 3
B: ABC-type transporter, periplasmic subunit family 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9464
Polymers50,5962
Non-polymers3502
Water8,503472
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-21 kcal/mol
Surface area20370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.482, 79.482, 434.232
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-450-

HOH

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Components

#1: Protein ABC-type transporter, periplasmic subunit family 3 / Amino acid ABC transporter / periplasmic amino acid-binding protein


Mass: 25297.967 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM_0593 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZ62
#2: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 472 / 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: 3.91 Å3/Da / Density % sol: 68.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.2M Potassium acetate, 20%(w/v) Polyethylene glycol 3350, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.9799 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9799 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 30065 / Num. obs: 29302 / % possible obs: 97.46 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.6→2.62 Å / % possible all: 75.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.6→15 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.912 / SU B: 7.816 / SU ML: 0.167 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.33 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1288 5.1 %RANDOM
Rwork0.16928 ---
obs0.17249 23890 95.99 %-
all-24888 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.771 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20.11 Å20 Å2
2--0.22 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3533 0 24 472 4029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223628
X-RAY DIFFRACTIONr_angle_refined_deg1.8351.9844897
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6965451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72624.051158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.27915665
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7071526
X-RAY DIFFRACTIONr_chiral_restr0.1290.2575
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212666
X-RAY DIFFRACTIONr_mcbond_it0.8581.52254
X-RAY DIFFRACTIONr_mcangle_it1.66123658
X-RAY DIFFRACTIONr_scbond_it2.72431374
X-RAY DIFFRACTIONr_scangle_it4.5954.51239
LS refinement shellResolution: 2.598→2.664 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 52 -
Rwork0.222 1410 -
obs--78.6 %

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