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- PDB-8gu1: Crystal Structure of putative amino acid binding periplasmic ABC ... -

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Basic information

Entry
Database: PDB / ID: 8gu1
TitleCrystal Structure of putative amino acid binding periplasmic ABC transporter protein from Candidatus Liberibacter asiaticus in complex with Pimozide
ComponentsPutative amino acid-binding periplasmic ABC transporter protein
KeywordsTRANSPORT PROTEIN / amino acid binding receptors / periplasmic amino acid binding protein / Candidatus Liberibacter asiaticus
Function / homologySolute-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 space / membrane / Chem-1II / Putative amino acid-binding periplasmic ABC transporter protein
Function and homology information
Biological speciesCandidatus Liberibacter asiaticus str. psy62 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsLonare, S. / Sharma, M. / Sharma, A.K.
Funding support India, 1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)CRG/2019/001909 India
CitationJournal: J.Struct.Biol. / Year: 2023
Title: Identification and evaluation of potential inhibitor molecules against TcyA from Candidatus Liberibacter asiaticus.
Authors: Lonare, S. / Sharma, M. / Dalal, V. / Gubyad, M. / Kumar, P. / Nath Gupta, D. / Pareek, A. / Tomar, S. / Kumar Ghosh, D. / Kumar, P. / Kumar Sharma, A.
History
DepositionSep 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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)56,1544
Polymers55,2312
Non-polymers9232
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-7 kcal/mol
Surface area20700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.014, 45.795, 115.675
Angle α, β, γ (deg.)90.000, 91.990, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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.) Candidatus Liberibacter asiaticus str. psy62 (bacteria)
Strain: psy62 / Gene: CLIBASIA_05070 / Production host: Escherichia coli (E. coli) / References: UniProt: C6XGT2
#2: Chemical ChemComp-1II / 3-[1-[4,4-bis(4-fluorophenyl)butyl]piperidin-4-yl]-1~{H}-benzimidazol-2-one


Mass: 461.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H29F2N3O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 4.31 Å3/Da / Density % sol: 71.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Sodium citrate, 20% PEG 550, pH 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 HyPix-6000HE / Detector: PIXEL / Date: Nov 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.65→28.8 Å / Num. obs: 29525 / % possible obs: 99.8 % / Redundancy: 4.3 % / CC1/2: 0.97 / Net I/σ(I): 5.5
Reflection shellResolution: 2.65→9.01 Å / Num. unique obs: 3590 / CC1/2: 0.86

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A80

6a80


Resolution: 2.65→28.8 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.821 / SU B: 12.172 / SU ML: 0.255 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.404 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2828 1339 4.8 %RANDOM
Rwork0.2369 ---
obs0.2392 26522 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 117.16 Å2 / Biso mean: 29.724 Å2 / Biso min: 2.49 Å2
Baniso -1Baniso -2Baniso -3
1-4.62 Å2-0 Å20.64 Å2
2---1.28 Å20 Å2
3----3.38 Å2
Refinement stepCycle: final / Resolution: 2.65→28.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3760 0 68 246 4074
Biso mean--83.94 25.6 -
Num. residues----468
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123912
X-RAY DIFFRACTIONr_angle_refined_deg1.9321.6615280
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3225466
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.14921.376218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.45615694
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0241532
X-RAY DIFFRACTIONr_chiral_restr0.1460.2508
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022934
LS refinement shellResolution: 2.65→2.719 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.47 91 -
Rwork0.312 1922 -
all-2013 -
obs--99.7 %

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