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- PDB-6lw4: Structure of Lpg2148/Lpg2149 complex -

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Basic information

Entry
Database: PDB / ID: 6lw4
TitleStructure of Lpg2148/Lpg2149 complex
Components
  • Uncharacterized protein Lpg2148
  • Uncharacterized protein Lpg2149
KeywordsTRANSFERASE / complex / deamidase / transglutaminase
Function / homologyUncharacterized protein / Uncharacterized protein
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsFeng, Y. / Wang, Y. / Huang, Y. / Li, D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31822012 China
CitationJournal: To Be Published
Title: Structure of Lpg2148/Lpg2149 complex
Authors: Feng, Y. / Wang, Y. / Huang, Y. / Li, D.
History
DepositionFeb 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: Uncharacterized protein Lpg2148
B: Uncharacterized protein Lpg2149


Theoretical massNumber of molelcules
Total (without water)56,5302
Polymers56,5302
Non-polymers00
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-12 kcal/mol
Surface area23680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.524, 67.524, 205.355
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Uncharacterized protein Lpg2148


Mass: 43883.719 Da / Num. of mol.: 1 / Mutation: C83A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Gene: lpg2148 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZTL3
#2: Protein Uncharacterized protein Lpg2149


Mass: 12646.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Gene: lpg2149 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZTL2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.39 Å3/Da / Density % sol: 48.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: PEG3350, Magnesium chloride hexahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 13640 / % possible obs: 99.8 % / Redundancy: 18.5 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 31.3
Reflection shellResolution: 2.7→2.798 Å / Rmerge(I) obs: 0.78 / Num. unique obs: 623

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5SUJ, 5DPO

5suj

5dpo


Resolution: 2.7→34.23 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 31.28
RfactorNum. reflection% reflection
Rfree0.2985 722 5.3 %
Rwork0.2426 --
obs0.2456 13617 87.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 102.35 Å2 / Biso mean: 40.4164 Å2 / Biso min: 10.23 Å2
Refinement stepCycle: final / Resolution: 2.7→34.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3948 0 0 38 3986
Biso mean---33.01 -
Num. residues----487
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.910.3906770.28731382145949
2.91-3.20.35261380.2772543268187
3.2-3.660.29281570.245829283085100
3.67-4.610.29521660.217729473113100
4.62-34.230.2711840.24253095327999

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