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- PDB-6q3u: Gly52Ala mutant of arginine-bound ArgBP from T. maritima -

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Basic information

Entry
Database: PDB / ID: 6q3u
TitleGly52Ala mutant of arginine-bound ArgBP from T. maritima
ComponentsAmino acid ABC transporter, periplasmic amino acid-binding protein
KeywordsTRANSPORT PROTEIN / Gly52Ala mutation / protein stability / local strains / helix insertion motif
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: 1.64 Å
AuthorsBalasco, N. / Smaldone, G. / Ruggiero, A. / Vitagliano, L.
CitationJournal: Sci Rep / Year: 2019
Title: The characterization of Thermotoga maritima Arginine Binding Protein variants demonstrates that minimal local strains have an important impact on protein stability.
Authors: Balasco, N. / Smaldone, G. / Vigorita, M. / Del Vecchio, P. / Graziano, G. / Ruggiero, A. / Vitagliano, L.
History
DepositionDec 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8583
Polymers23,5871
Non-polymers2712
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-12 kcal/mol
Surface area10050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.572, 52.238, 59.889
Angle α, β, γ (deg.)90.00, 117.39, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-586-

HOH

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Components

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


Mass: 23587.039 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: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.73 Å3/Da / Density % sol: 54.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2.0 M ammonium sulfate, 0.1 M TRIS hydrochloride buffer pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 30030 / % possible obs: 96.1 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 30.3
Reflection shellResolution: 1.64→1.7 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: 6GGV

6ggv


Resolution: 1.64→14.8 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.585 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.084 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18923 1512 5 %RANDOM
Rwork0.16334 ---
obs0.16466 28469 96.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.561 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0.01 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.64→14.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1662 0 17 272 1951
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0191726
X-RAY DIFFRACTIONr_bond_other_d0.0010.021712
X-RAY DIFFRACTIONr_angle_refined_deg2.2341.9872336
X-RAY DIFFRACTIONr_angle_other_deg0.94333942
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4365218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.5462475
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1615315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6331513
X-RAY DIFFRACTIONr_chiral_restr0.1310.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021922
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02367
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_it1.4031.243866
X-RAY DIFFRACTIONr_mcbond_other1.4041.243865
X-RAY DIFFRACTIONr_mcangle_it1.9541.861083
X-RAY DIFFRACTIONr_mcangle_other1.9531.861084
X-RAY DIFFRACTIONr_scbond_it2.7431.58860
X-RAY DIFFRACTIONr_scbond_other2.7461.577856
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1212.2221247
X-RAY DIFFRACTIONr_long_range_B_refined6.10311.9082098
X-RAY DIFFRACTIONr_long_range_B_other5.77511.0681972
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.644→1.686 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 99 -
Rwork0.209 1807 -
obs--84.3 %

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