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- PDB-6ggp: Structure of the ligand-free form of truncated ArgBP (residues 20... -

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Basic information

Entry
Database: PDB / ID: 6ggp
TitleStructure of the ligand-free form of truncated ArgBP (residues 20-233) from T. maritima
ComponentsAmino acid ABC transporter, periplasmic amino acid-binding protein
KeywordsTRANSPORT PROTEIN / Domain swapping / Biosensors / Argininemia diagnosis / Protein structure-stability / Calorimetry.
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. / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Amino acid ABC transporter, periplasmic amino acid-binding protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.03 Å
AuthorsSmaldone, G. / Berisio, R. / Balasco, N. / D'Auria, S. / Vitagliano, L. / Ruggiero, A.
CitationJournal: Biochim. Biophys. Acta / Year: 2018
Title: Domain swapping dissection in Thermotoga maritima arginine binding protein: How structural flexibility may compensate destabilization.
Authors: Smaldone, G. / Berisio, R. / Balasco, N. / D'Auria, S. / Vitagliano, L. / Ruggiero, A.
History
DepositionMay 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: 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: Amino acid ABC transporter, periplasmic amino acid-binding protein


Theoretical massNumber of molelcules
Total (without water)23,4441
Polymers23,4441
Non-polymers00
Water8,485471
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.707, 71.063, 88.386
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, periplasmic amino acid-binding protein


Mass: 23443.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Gene: TM_0593 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZ62
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 2.32 Å3/Da / Density % sol: 47.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Crystals grew in 16-20 mg/mL protein solution and in 30 % w/v PEG 8,000, 0.1 M Sodium cacodylate trihydrate (pH 6.5) and 0.2 M Sodium Acetate trihydrate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9464 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9464 Å / Relative weight: 1
ReflectionResolution: 1.03→20 Å / Num. obs: 104443 / % possible obs: 95.9 % / Redundancy: 13.7 % / Net I/σ(I): 41.3
Reflection shellResolution: 1.03→1.05 Å

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PRS

4prs


Resolution: 1.03→15 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.594 / SU ML: 0.014 / Cross valid method: THROUGHOUT / ESU R: 0.024 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.171 969 0.9 %RANDOM
Rwork0.137 ---
obs0.138 103364 95.8 %-
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: 8.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.03→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1651 0 0 471 2122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0221839
X-RAY DIFFRACTIONr_bond_other_d0.0080.021276
X-RAY DIFFRACTIONr_angle_refined_deg2.1831.9862521
X-RAY DIFFRACTIONr_angle_other_deg1.13433154
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2565258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.2524.05179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9515351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.4541514
X-RAY DIFFRACTIONr_chiral_restr0.1380.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022080
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02382
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9621.51142
X-RAY DIFFRACTIONr_mcbond_other0.9821.5463
X-RAY DIFFRACTIONr_mcangle_it2.84921887
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.413697
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.1334.5613
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.11833115
X-RAY DIFFRACTIONr_sphericity_free12.6973480
X-RAY DIFFRACTIONr_sphericity_bonded4.73333065
LS refinement shellResolution: 1.03→1.06 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 79 -
Rwork0.264 6602 -
obs--84.24 %

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