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- PDB-6ggv: Structure of the arginine-bound form of truncated (residues 20-23... -

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Basic information

Entry
Database: PDB / ID: 6ggv
TitleStructure of the arginine-bound form of truncated (residues 20-233) ArgBP 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.
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 / MOLECULAR REPLACEMENT / Resolution: 2.69 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 4, 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 ...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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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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
B: Amino acid ABC transporter, periplasmic amino acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,96926
Polymers47,1462
Non-polymers2,82324
Water4,234235
1
A: Amino acid ABC transporter, periplasmic amino acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,21015
Polymers23,5731
Non-polymers1,63714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Amino acid ABC transporter, periplasmic amino acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,76011
Polymers23,5731
Non-polymers1,18710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.700, 52.139, 221.343
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11B-305-

CD

21B-309-

CD

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Components

#1: Protein Amino acid ABC transporter, periplasmic amino acid-binding protein


Mass: 23573.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima / 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: Chemical...
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: Cd
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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 % sol: 34.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: The crystals were obtained using a protein concentration of 16 mg/mL and in 0.1 M Cadmium chloride hydrate, 0.1 M Sodium acetate trihydrate (pH 4.6), 30% (v/v) Polyethylene glycol 400. ...Details: The crystals were obtained using a protein concentration of 16 mg/mL and in 0.1 M Cadmium chloride hydrate, 0.1 M Sodium acetate trihydrate (pH 4.6), 30% (v/v) Polyethylene glycol 400. Crystal quality was enhanced in presence of 2.0 M Sodium Thiocyanate or 1.0 M Sodium Bromide.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.5418 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: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 9570 / % possible obs: 85.6 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 20.7
Reflection shellResolution: 2.6→2.64 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: 4PSH

4psh


Resolution: 2.69→15 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.901 / SU B: 12.537 / SU ML: 0.263 / Cross valid method: THROUGHOUT / ESU R Free: 0.461 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22599 378 4.7 %RANDOM
Rwork0.1748 ---
obs0.17723 7711 76.76 %-
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: 19.371 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.28 Å20 Å2
3----0.32 Å2
Refinement stepCycle: 1 / Resolution: 2.69→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3311 0 46 235 3592
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223381
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.9864563
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2885423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55224.054148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.22615620
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9641526
X-RAY DIFFRACTIONr_chiral_restr0.0950.2543
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212484
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.5011.52117
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.96323434
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.66631264
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8264.51129
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.692→2.76 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 24 -
Rwork0.187 503 -
obs--69.16 %

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