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- PDB-5bu0: Structure of the C-terminal domain of lpg1496 from Legionella pne... -

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Basic information

Entry
Database: PDB / ID: 5bu0
TitleStructure of the C-terminal domain of lpg1496 from Legionella pneumophila
Componentslpg1496
KeywordsUNKNOWN FUNCTION / bacterial effector / nucleotide-binding / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
Function / homology:
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila ATCC 43290 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsWong, K. / Kozlov, G. / Gehring, K. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)GSP-48370 Canada
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structure of the Legionella Effector, lpg1496, Suggests a Role in Nucleotide Metabolism.
Authors: Wong, K. / Kozlov, G. / Zhang, Y. / Gehring, K.
History
DepositionJun 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2Oct 21, 2015Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: lpg1496
B: lpg1496


Theoretical massNumber of molelcules
Total (without water)71,4832
Polymers71,4832
Non-polymers00
Water3,963220
1
A: lpg1496


Theoretical massNumber of molelcules
Total (without water)35,7411
Polymers35,7411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: lpg1496


Theoretical massNumber of molelcules
Total (without water)35,7411
Polymers35,7411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.976, 77.232, 109.378
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein lpg1496


Mass: 35741.301 Da / Num. of mol.: 2 / Fragment: UNP residue 293-598
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila ATCC 43290 (bacteria)
Gene: lp12_1434 / Production host: Escherichia coli (E. coli) / References: UniProt: G8UY02
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 0.1 M Bicine, 20% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 26043 / Num. obs: 25991 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13 % / Rsym value: 0.169 / Net I/σ(I): 42.5
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 11.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.35→37.931 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2933 1318 5.07 %RANDOM
Rwork0.2391 ---
obs0.2418 25991 98.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→37.931 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4653 0 0 220 4873
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024775
X-RAY DIFFRACTIONf_angle_d0.6516464
X-RAY DIFFRACTIONf_dihedral_angle_d12.2251742
X-RAY DIFFRACTIONf_chiral_restr0.045676
X-RAY DIFFRACTIONf_plane_restr0.004835
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.43540.31921270.25582491X-RAY DIFFRACTION91
2.4354-2.54620.30441450.26032720X-RAY DIFFRACTION100
2.5462-2.68040.3461610.26032718X-RAY DIFFRACTION100
2.6804-2.84830.32631470.25632749X-RAY DIFFRACTION100
2.8483-3.06820.33421560.25582725X-RAY DIFFRACTION100
3.0682-3.37680.31491300.2512784X-RAY DIFFRACTION100
3.3768-3.8650.27321360.23242783X-RAY DIFFRACTION100
3.865-4.86780.26091620.21662791X-RAY DIFFRACTION100
4.8678-37.93630.26871540.22652912X-RAY DIFFRACTION99

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