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- PDB-6a8s: Crystal Structure of the putative amino acid-binding periplasmic ... -

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Basic information

Entry
Database: PDB / ID: 6a8s
TitleCrystal Structure of the putative amino acid-binding periplasmic ABC transporter protein from Candidatus Liberibacter asiaticus in complex with Cysteine
ComponentsPutative amino acid-binding periplasmic ABC transporter protein
KeywordsTRANSPORT PROTEIN / Candidatus Liberibacter asiaticus / Periplasmic / Solute Binding / Cysteine
Function / homology
Function and homology information


periplasmic space / membrane
Similarity search - Function
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
ACETATE ION / CYSTEINE / Putative amino acid-binding periplasmic ABC transporter protein
Similarity search - Component
Biological speciesLiberibacter asiaticus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsKumar, P. / Kesari, P. / Ghosh, D.K. / Kumar, P. / Sharma, A.K.
CitationJournal: Febs J. / Year: 2019
Title: Crystal structures of a putative periplasmic cystine-binding protein from Candidatus Liberibacter asiaticus: insights into an adapted mechanism of ligand binding.
Authors: Kumar, P. / Kesari, P. / Kokane, S. / Ghosh, D.K. / Kumar, P. / Sharma, A.K.
History
DepositionJul 10, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: 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: Putative amino acid-binding periplasmic ABC transporter protein
B: Putative amino acid-binding periplasmic ABC transporter protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,61135
Polymers55,2312
Non-polymers2,37933
Water3,153175
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.791, 87.049, 122.164
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 27615.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Liberibacter asiaticus (strain psy62) (bacteria)
Strain: psy62 / Gene: CLIBASIA_05070 / Plasmid: pET28C / Production host: Escherichia coli (E. coli) / References: UniProt: C6XGT2

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Non-polymers , 7 types, 208 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-CYS / CYSTEINE / Cysteine


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO2S
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.22 Å3/Da / Density % sol: 44.51 % / Description: Cubic
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 2M Ammonium sulphate, 0.1M Sodium acetate Trihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976251 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 2.05→70.89 Å / Num. obs: 31433 / % possible obs: 99.8 % / Redundancy: 5.2 % / Biso Wilson estimate: 35 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.071 / Rrim(I) all: 0.147 / Net I/σ(I): 8.5
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3028 / CC1/2: 0.702 / Rpim(I) all: 0.452 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSversion June1, 2017data reduction
Aimless0.5.32data scaling
MoRDa22(2018-05-05)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YLN

2yln


Resolution: 2.05→36.885 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2583 1503 4.79 %RANDOM
Rwork0.1971 ---
obs0.2001 31364 99.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→36.885 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3760 0 149 175 4084
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074093
X-RAY DIFFRACTIONf_angle_d0.8865489
X-RAY DIFFRACTIONf_dihedral_angle_d5.7723354
X-RAY DIFFRACTIONf_chiral_restr0.054602
X-RAY DIFFRACTIONf_plane_restr0.005711
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.11620.36561490.28822662X-RAY DIFFRACTION100
2.1162-2.19180.36011450.25012646X-RAY DIFFRACTION100
2.1918-2.27950.29031280.24012690X-RAY DIFFRACTION100
2.2795-2.38330.27911400.23082652X-RAY DIFFRACTION100
2.3833-2.50890.33151300.23352698X-RAY DIFFRACTION100
2.5089-2.6660.27681370.22222690X-RAY DIFFRACTION100
2.666-2.87180.30221250.22332705X-RAY DIFFRACTION100
2.8718-3.16070.31371220.20032722X-RAY DIFFRACTION100
3.1607-3.61770.19421360.17662745X-RAY DIFFRACTION100
3.6177-4.55660.22911490.15092755X-RAY DIFFRACTION100
4.5566-36.89090.22611420.18692896X-RAY DIFFRACTION100

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