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- PDB-6aal: Crystal Structure of putative amino acid binding periplasmic ABC ... -

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Basic information

Entry
Database: PDB / ID: 6aal
TitleCrystal Structure of putative amino acid binding periplasmic ABC transporter protein from Candidatus Liberibacter asiaticus in complex with Arginine
ComponentsPutative amino acid-binding periplasmic ABC transporter protein
KeywordsTRANSPORT PROTEIN / Periplasmic / Solute binding / Candidatus Liberibacter asiaticus / ABC transporter
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 / ARGININE / Putative amino acid-binding periplasmic ABC transporter protein
Similarity search - Component
Biological speciesLiberibacter asiaticus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 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 18, 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)56,76923
Polymers55,2312
Non-polymers1,53721
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-30 kcal/mol
Surface area21360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.342, 86.000, 123.832
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 , 5 types, 101 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#5: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.31 Å3/Da / Density % sol: 46.75 % / Description: Cubic
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 2M Ammonium sulphate, 0.1M Sodium acetate trihydrate pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→70.64 Å / Num. obs: 15666 / % possible obs: 98.6 % / Redundancy: 4.2 % / Biso Wilson estimate: 41.5 Å2 / Rsym value: 0.15 / Net I/σ(I): 9.5
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.23 / Num. unique obs: 741 / Rsym value: 0.8 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
HKL-2000v703gdata reduction
HKL-2000v703gdata scaling
MoRDa22(2018-05-05)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YLN

2yln


Resolution: 2.6→70.64 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.869 / SU B: 17.454 / SU ML: 0.36 / Cross valid method: THROUGHOUT / ESU R Free: 0.398 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29013 826 5.3 %RANDOM
Rwork0.20018 ---
obs0.20509 14811 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.787 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2--0.13 Å2-0 Å2
3----0.44 Å2
Refinement stepCycle: 1 / Resolution: 2.6→70.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3760 0 96 80 3936
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193920
X-RAY DIFFRACTIONr_bond_other_d0.0010.023722
X-RAY DIFFRACTIONr_angle_refined_deg1.6181.9695260
X-RAY DIFFRACTIONr_angle_other_deg0.84338599
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4675468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.66223.262187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.07515699
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3141533
X-RAY DIFFRACTIONr_chiral_restr0.0890.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024265
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02824
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_it2.6963.9531883
X-RAY DIFFRACTIONr_mcbond_other2.6953.9511878
X-RAY DIFFRACTIONr_mcangle_it4.1795.9212344
X-RAY DIFFRACTIONr_mcangle_other4.1785.9212345
X-RAY DIFFRACTIONr_scbond_it2.8964.3152037
X-RAY DIFFRACTIONr_scbond_other2.8964.3152038
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.486.3242917
X-RAY DIFFRACTIONr_long_range_B_refined6.56646.3034275
X-RAY DIFFRACTIONr_long_range_B_other6.56746.3044275
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.601→2.669 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 65 -
Rwork0.296 1038 -
obs--97.35 %

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