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- PDB-4prs: Structure of apo ArgBP from T. maritima -

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Basic information

Entry
Database: PDB / ID: 4prs
TitleStructure of apo ArgBP from T. maritima
ComponentsABC-type transporter, periplasmic subunit family 3
KeywordsPROTEIN TRANSPORT / alpha/beta / Arginine binding
Function / homologyBacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / ligand-gated monoatomic ion channel activity / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / membrane / Amino acid ABC transporter, periplasmic amino acid-binding protein
Function and homology information
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.47 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 6, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABC-type transporter, periplasmic subunit family 3
B: ABC-type transporter, periplasmic subunit family 3


Theoretical massNumber of molelcules
Total (without water)50,5962
Polymers50,5962
Non-polymers00
Water14,538807
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-23 kcal/mol
Surface area21660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.811, 51.966, 98.997
Angle α, β, γ (deg.)90.00, 122.81, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-626-

HOH

21B-605-

HOH

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Components

#1: Protein ABC-type transporter, periplasmic subunit family 3 / ArgBP / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 807 / 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: 2.5 Å3/Da / Density % sol: 50.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 25%(w/v) PEG 3350, 0.1M Sodium Acetate trihydrate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.9796, 0.9894, 0.9537
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.98941
30.95371
ReflectionResolution: 1.47→50 Å / Num. all: 86978 / Num. obs: 85761 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.47→1.52 Å / % possible all: 87.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.47→14.82 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.694 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20405 3988 5 %RANDOM
Rwork0.14984 ---
all0.15254 75884 --
obs0.15254 75884 93.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.122 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20.09 Å2
2---0.07 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.47→14.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3549 0 0 807 4356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0223696
X-RAY DIFFRACTIONr_angle_refined_deg1.9871.9855010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9185477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.42924.286161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.63215690
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4281525
X-RAY DIFFRACTIONr_chiral_restr0.1640.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212729
X-RAY DIFFRACTIONr_mcbond_it2.3671.52291
X-RAY DIFFRACTIONr_mcangle_it3.30723736
X-RAY DIFFRACTIONr_scbond_it4.71431405
X-RAY DIFFRACTIONr_scangle_it6.6384.51261
X-RAY DIFFRACTIONr_rigid_bond_restr2.7733696
X-RAY DIFFRACTIONr_sphericity_free11.3353812
X-RAY DIFFRACTIONr_sphericity_bonded6.86533627
LS refinement shellResolution: 1.469→1.507 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.327 205
Rwork0.258 3947

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