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- PDB-6gpc: Crystal structure of the arginine-bound form of domain 1 from TmArgBP -

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Basic information

Entry
Database: PDB / ID: 6gpc
TitleCrystal structure of the arginine-bound form of domain 1 from TmArgBP
ComponentsAmino acid ABC transporter, periplasmic amino acid-binding protein,Amino acid ABC transporter, periplasmic amino acid-binding protein
KeywordsTRANSPORT PROTEIN / Domain-domain communication / Diagnostic tool / Protein dissection / Biosensor / Protein structure-stability.
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 / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSmaldone, G. / Balasco, N. / Ruggiero, A. / Berisio, R. / Vitagliano, L.
CitationJournal: Int. J. Biol. Macromol. / Year: 2018
Title: Domain communication in Thermotoga maritima Arginine Binding Protein unraveled through protein dissection.
Authors: Smaldone, G. / Balasco, N. / Vigorita, M. / Ruggiero, A. / Cozzolino, S. / Berisio, R. / Del Vecchio, P. / Graziano, G. / Vitagliano, L.
History
DepositionJun 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 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,Amino acid ABC transporter, periplasmic amino acid-binding protein
B: Amino acid ABC transporter, periplasmic amino acid-binding protein,Amino acid ABC transporter, periplasmic amino acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0664
Polymers27,7162
Non-polymers3502
Water5,368298
1
A: Amino acid ABC transporter, periplasmic amino acid-binding protein,Amino acid ABC transporter, periplasmic amino acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0332
Polymers13,8581
Non-polymers1751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Amino acid ABC transporter, periplasmic amino acid-binding protein,Amino acid ABC transporter, periplasmic amino acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0332
Polymers13,8581
Non-polymers1751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.530, 45.932, 52.510
Angle α, β, γ (deg.)115.91, 109.53, 90.02
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 13857.786 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / 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: isolated from a genetically manipulated source
Formula: C6H15N4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.58 Å3/Da / Density % sol: 52.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: The best crystals of D1 domain were obtained using a protein concentration of 8 mg/ml in a solution containing 0.2 M NaCl, 0.1M Bis-Tris (pH 5.5), 25% (w/v) polyethylene glycol (PEG) 3,350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 11, 2014
RadiationMonochromator: 1.54 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.75→14.62 Å / Num. obs: 25022 / % possible obs: 89.4 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 22.1
Reflection shellResolution: 1.75→1.81 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PRS

4prs


Resolution: 1.75→14.62 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.12 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20174 1272 5.1 %RANDOM
Rwork0.16241 ---
obs0.1644 23712 89.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.269 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20.01 Å2-0 Å2
2--0.01 Å20 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.75→14.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1942 0 24 298 2264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192026
X-RAY DIFFRACTIONr_bond_other_d0.0010.021981
X-RAY DIFFRACTIONr_angle_refined_deg2.0441.9962736
X-RAY DIFFRACTIONr_angle_other_deg0.89134575
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8515260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.72724.56592
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.40415368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5871514
X-RAY DIFFRACTIONr_chiral_restr0.1210.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022285
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02425
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_it1.4041.4941026
X-RAY DIFFRACTIONr_mcbond_other1.4051.4941025
X-RAY DIFFRACTIONr_mcangle_it2.1072.2351281
X-RAY DIFFRACTIONr_mcangle_other2.1062.2341282
X-RAY DIFFRACTIONr_scbond_it2.6131.7781000
X-RAY DIFFRACTIONr_scbond_other2.6121.7781000
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9672.5461453
X-RAY DIFFRACTIONr_long_range_B_refined5.78313.4752547
X-RAY DIFFRACTIONr_long_range_B_other5.50412.6742390
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.748→1.793 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 69 -
Rwork0.201 1272 -
obs--67.02 %

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