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

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Basic information

Entry
Database: PDB / ID: 8gtu
TitleCrystal Structure of putative amino acid binding periplasmic ABC transporter protein from Candidatus Liberibacter asiaticus in complex with Clidinium
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-KG2 / Putative amino acid-binding periplasmic ABC transporter protein
Function and homology information
Biological speciesLiberibacter asiaticus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 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 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 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)55,9364
Polymers55,2312
Non-polymers7052
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-12 kcal/mol
Surface area20450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.600, 87.440, 123.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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.) Liberibacter asiaticus (strain psy62) (bacteria)
Strain: psy62 / Gene: CLIBASIA_05070 / Production host: Escherichia coli (E. coli) / References: UniProt: C6XGT2
#2: Chemical ChemComp-KG2 / [(3~{S})-1-methyl-1-azoniabicyclo[2.2.2]octan-3-yl] 2-oxidanyl-2,2-diphenyl-ethanoate


Mass: 352.447 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H26NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.23 Å3/Da / Density % sol: 44.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M MES BUFFER, 2.5M AMMONIUM SULFATE, pH 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.56→50.44 Å / Num. obs: 16502 / % possible obs: 99.9 % / Redundancy: 1.9 % / CC1/2: 0.99 / Net I/σ(I): 7.7
Reflection shellResolution: 2.56→2.56 Å / Num. unique obs: 1989 / CC1/2: 0.721

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A80

6a80


Resolution: 2.56→50.44 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.86 / SU B: 27.497 / SU ML: 0.284 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.39 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2915 812 4.9 %RANDOM
Rwork0.2113 ---
obs0.2151 15644 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.95 Å2 / Biso mean: 40.369 Å2 / Biso min: 14.05 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20 Å20 Å2
2--1.15 Å2-0 Å2
3----2.16 Å2
Refinement stepCycle: final / Resolution: 2.56→50.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3770 0 52 97 3919
Biso mean--73.36 38.74 -
Num. residues----470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0124114
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.6495596
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9645515
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.3695.2737
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.36310729
X-RAY DIFFRACTIONr_chiral_restr0.1210.2622
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023126
LS refinement shellResolution: 2.564→2.63 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 58 -
Rwork0.294 1136 -
all-1194 -
obs--99.92 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.680.75210.77132.51230.62782.577-0.008-0.0326-0.09930.0088-0.0432-0.05750.05140.0250.05120.01690.01570.01850.01730.03010.105517.5999-17.7075-13.3984
22.6301-0.40640.48991.4663-0.17472.0555-0.00910.12680.11670.0979-0.0669-0.006-0.126-0.01440.07590.0552-0.01880.01520.0513-0.00940.106224.0542-21.286-44.9977
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 301
2X-RAY DIFFRACTION2B8 - 301

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