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- PDB-6ft2: Structure of the periplasmic binding protein LAO-Q122A in complex... -

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Basic information

Entry
Database: PDB / ID: 6ft2
TitleStructure of the periplasmic binding protein LAO-Q122A in complex with arginine.
ComponentsLysine/arginine/ornithine-binding periplasmic protein
KeywordsTRANSPORT PROTEIN / periplasmic binding protein
Function / homology
Function and homology information


amino acid transport / outer membrane-bounded periplasmic space
Similarity search - Function
Specific amino acids and opine-binding periplasmic protein, ABC transporter / Solute-binding protein family 3, conserved site / Bacterial extracellular solute-binding proteins, family 3 signature. / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ARGININE / Lysine/arginine/ornithine-binding periplasmic protein
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsVigouroux, A. / Morera, S.
CitationJournal: To Be Published
Title: Structure of the periplasmic binding protein LAO-Q122A A in complex with arginin
Authors: Vigouroux, A. / Morera, S.
History
DepositionFeb 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 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: Lysine/arginine/ornithine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4967
Polymers27,0911
Non-polymers4066
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-18 kcal/mol
Surface area11110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.410, 58.440, 101.240
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 Lysine/arginine/ornithine-binding periplasmic protein / LAO-binding protein


Mass: 27090.518 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: argT, STM2355 / Production host: Escherichia coli (E. coli) / References: UniProt: P02911
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.11 Å3/Da / Density % sol: 41.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 20% PEG4000; 0.1M Mes pH6.5; 0.1M CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.25→50.62 Å / Num. obs: 62491 / % possible obs: 99.3 % / Redundancy: 8.9 % / Biso Wilson estimate: 15.23 Å2 / CC1/2: 0.99 / Rsym value: 0.093 / Net I/σ(I): 13.27
Reflection shellResolution: 1.25→1.32 Å / Redundancy: 8.5 % / Mean I/σ(I) obs: 1.92 / Num. unique obs: 9589 / CC1/2: 0.96 / Rsym value: 1.149 / % possible all: 96

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LAF

1laf


Resolution: 1.25→50.62 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / Rfactor Rfree error: 0.01 / SU R Cruickshank DPI: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.048 / SU Rfree Blow DPI: 0.049 / SU Rfree Cruickshank DPI: 0.047
RfactorNum. reflection% reflectionSelection details
Rfree0.202 3110 5 %RANDOM
Rwork0.179 ---
obs0.181 62211 99.9 %-
Displacement parametersBiso mean: 21.55 Å2
Baniso -1Baniso -2Baniso -3
1-2.8402 Å20 Å20 Å2
2---0.5013 Å20 Å2
3----2.3389 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å
Refinement stepCycle: 1 / Resolution: 1.25→50.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1828 0 11 281 2120
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011897HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.062560HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d680SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes50HARMONIC2
X-RAY DIFFRACTIONt_gen_planes281HARMONIC5
X-RAY DIFFRACTIONt_it1897HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.96
X-RAY DIFFRACTIONt_other_torsion15.03
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion250SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2474SEMIHARMONIC4
LS refinement shellResolution: 1.25→1.28 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 226 5.01 %
Rwork0.24 4285 -
all0.242 4511 -
obs--99.24 %
Refinement TLS params.Method: refined / Origin x: 7.8267 Å / Origin y: 0.093 Å / Origin z: -12.7266 Å
111213212223313233
T-0.0148 Å20.0021 Å20.0064 Å2-0.0005 Å20.0028 Å2---0.0938 Å2
L1.4601 °20.1171 °2-0.1106 °2-0.7421 °20.0666 °2--0.4819 °2
S-0.0185 Å °0.0895 Å °-0.0946 Å °0.006 Å °-0.0008 Å °-0.0638 Å °0.0106 Å °-0.0109 Å °0.0194 Å °
Refinement TLS groupSelection details: { E|* }

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