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- PDB-5btz: Structure of the middle domain of lpg1496 from Legionella pneumop... -

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Basic information

Entry
Database: PDB / ID: 5btz
TitleStructure of the middle domain of lpg1496 from Legionella pneumophila in P212121 space group
Componentslpg1496
KeywordsUNKNOWN FUNCTION / bacterial effector / alpha-beta fold / 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: 1.6 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 1.5Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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


Theoretical massNumber of molelcules
Total (without water)15,5281
Polymers15,5281
Non-polymers00
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.137, 44.066, 77.529
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: 15528.203 Da / Num. of mol.: 1 / Fragment: UNP residues 151-289
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.: 130 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES, 25% (w/v) PEG3350

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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: Mar 31, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 16116 / Num. obs: 16100 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Rsym value: 0.057 / Net I/σ(I): 49.7
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 4.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDEphasing
ARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.6→38.78 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.63 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23125 862 5.1 %RANDOM
Rwork0.19975 ---
obs0.20124 16100 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20 Å20 Å2
2---0.14 Å20 Å2
3----0.61 Å2
Refinement stepCycle: 1 / Resolution: 1.6→38.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1025 0 0 130 1155
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221066
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0311.9511448
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3255138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.77125.30649
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.54915185
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.43154
X-RAY DIFFRACTIONr_chiral_restr0.0710.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02805
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1840.2459
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.2761
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0690.288
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5081.5684
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.82321089
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3743418
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1724.5355
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.638 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 65 -
Rwork0.237 1103 -
obs--93.22 %
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)
15.5387-2.3491-2.83664.04020.48994.1640.08680.0578-0.0204-0.0452-0.0162-0.01470.0437-0.1388-0.07060.0166-0.0033-0.01220.04040.00710.05756.41726.02432.071
21.5746-0.6702-0.0511.9247-0.60592.79250.0470.0288-0.0619-0.2352-0.00320.01580.30310.0455-0.04380.07130.0079-0.0210.0417-0.00480.031112.0164-8.52570.2641
32.4651-0.1326-1.16930.7986-2.43988.8105-0.00340.1743-0.0798-0.18930.1150.22580.2307-0.35-0.11160.0625-0.044-0.03770.0216-0.00140.0573.6341-6.20582.433
42.513-0.50550.08835.74043.150217.2898-0.0226-0.2724-0.08240.530.07360.67920.3833-0.7748-0.05110.0373-0.01090.03280.04180.0220.09032.8168-1.1599.4977
52.5804-0.8756-0.29872.7103-0.52752.1270.0163-0.15420.14430.189-0.0056-0.0929-0.12590.1522-0.01070.0572-0.0245-0.01480.0517-0.0090.010513.86572.048210.9433
61.533-0.36620.84920.9224-0.62433.35620.0758-0.04760.15290.1066-0.0191-0.10070.02320.2411-0.05660.0372-0.0283-0.00360.045-0.01830.034416.49237.1518.9009
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A155 - 169
2X-RAY DIFFRACTION2A170 - 196
3X-RAY DIFFRACTION3A197 - 209
4X-RAY DIFFRACTION4A210 - 223
5X-RAY DIFFRACTION5A224 - 254
6X-RAY DIFFRACTION6A255 - 288

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