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- PDB-6aa1: Crystal structure of putative amino acid binding periplasmic ABC ... -

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Basic information

Entry
Database: PDB / ID: 6aa1
TitleCrystal structure of putative amino acid binding periplasmic ABC transporter protein from Candidatus Liberibacter asiaticus bound with citrate
ComponentsPutative amino acid-binding periplasmic ABC transporter protein
KeywordsTRANSPORT PROTEIN / Candidatus Liberibacter asiaticus / periplasmic / ABC transporter / Solute binding / Citrate
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
CITRIC ACID / DI(HYDROXYETHYL)ETHER / Putative amino acid-binding periplasmic ABC transporter protein
Similarity search - Component
Biological speciesLiberibacter asiaticus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 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 16, 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)58,60148
Polymers55,2312
Non-polymers3,36946
Water4,702261
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)46.070, 86.960, 121.800
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, 307 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.21 Å3/Da / Density % sol: 44.31 % / Description: Cubic
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 20% PEG 550, 0.1 M Sodium Citrate pH 5.0

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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: Mar 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 1.857→70.773 Å / Num. obs: 42127 / % possible obs: 99.9 % / Redundancy: 8.9 % / Biso Wilson estimate: 25.3 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.05 / Net I/σ(I): 12.5
Reflection shellResolution: 1.857→1.889 Å / Redundancy: 8.8 % / Rmerge(I) obs: 1.14 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2069 / CC1/2: 0.664 / Rpim(I) all: 0.407 / Rrim(I) all: 1.213 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
XDSVersion June 1, 2017data reduction
autoPROC1.1.7data scaling
MoRDa22(2018-05-05)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YLN

2yln


Resolution: 1.86→70.77 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.224 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22517 2016 4.8 %RANDOM
Rwork0.18641 ---
obs0.18826 40111 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.019 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å20 Å20 Å2
2--0.45 Å2-0 Å2
3----1.33 Å2
Refinement stepCycle: 1 / Resolution: 1.86→70.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3760 0 219 261 4240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0194276
X-RAY DIFFRACTIONr_bond_other_d0.0010.024090
X-RAY DIFFRACTIONr_angle_refined_deg1.8071.985726
X-RAY DIFFRACTIONr_angle_other_deg0.8893.0029460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg22.3325.353539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.29623.194191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38215732
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9351537
X-RAY DIFFRACTIONr_chiral_restr0.1160.2631
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214984
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02897
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_it1.7962.1352018
X-RAY DIFFRACTIONr_mcbond_other1.7962.1342017
X-RAY DIFFRACTIONr_mcangle_it2.6443.1882568
X-RAY DIFFRACTIONr_mcangle_other2.6433.1882569
X-RAY DIFFRACTIONr_scbond_it2.9972.6822258
X-RAY DIFFRACTIONr_scbond_other2.9952.6822258
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5663.7623159
X-RAY DIFFRACTIONr_long_range_B_refined6.7827.6954781
X-RAY DIFFRACTIONr_long_range_B_other6.75627.5234747
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.857→1.905 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.449 145 -
Rwork0.411 2908 -
obs--99.93 %

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