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- PDB-4kun: Crystal structure of Legionella pneumophila Lpp1115 / KaiB -

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Basic information

Entry
Database: PDB / ID: 4kun
TitleCrystal structure of Legionella pneumophila Lpp1115 / KaiB
ComponentsHypothetical protein Lpp1115
KeywordsUNKNOWN FUNCTION / Midwest Center for Structural Genomics / MCSG / PSI-Biology / Alpha and beta proteins (a/b) / thioredoxin fold
Function / homologyGlutaredoxin / Glutaredoxin / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsPetit, P. / Stogios, P.J. / Stein, A. / Wawrzak, Z. / Skarina, T. / Daniels, C. / Di Leo, R. / Buchrieser, C. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Environ Microbiol / Year: 2014
Title: The Legionella pneumophila kai operon is implicated in stress response and confers fitness in competitive environments.
Authors: Loza-Correa, M. / Sahr, T. / Rolando, M. / Daniels, C. / Petit, P. / Skarina, T. / Gomez Valero, L. / Dervins-Ravault, D. / Honore, N. / Savchenko, A. / Buchrieser, C.
History
DepositionMay 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Structure summary
Revision 1.2Oct 23, 2013Group: Database references / Structure summary
Revision 1.3Oct 8, 2014Group: Database references
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein Lpp1115
B: Hypothetical protein Lpp1115


Theoretical massNumber of molelcules
Total (without water)20,3382
Polymers20,3382
Non-polymers00
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-11 kcal/mol
Surface area10110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.830, 46.050, 45.079
Angle α, β, γ (deg.)90.00, 105.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hypothetical protein Lpp1115


Mass: 10168.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Strain: Paris / Gene: lpp1115 / Plasmid: p15Tv-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIPL / References: UniProt: Q5X655
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M sodium acetate, 0.1 M bis-Tris pH 6.5, 35% w/v PEG 8K, 1 mM zinc acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.2828144 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 16, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2828144 Å / Relative weight: 1
ReflectionResolution: 1.95→29.91 Å / Num. obs: 11748 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 7.3 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 21.7
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 5.1 / Num. unique all: 1686 / % possible all: 97.9

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Processing

Software
NameVersionClassification
HKL-3000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.95→27.379 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2467 557 4.75 %random
Rwork0.1906 ---
obs0.1935 11730 98.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→27.379 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1396 0 0 150 1546
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031404
X-RAY DIFFRACTIONf_angle_d0.8011883
X-RAY DIFFRACTIONf_dihedral_angle_d12.066569
X-RAY DIFFRACTIONf_chiral_restr0.05236
X-RAY DIFFRACTIONf_plane_restr0.003235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9501-2.14620.28691480.22982724X-RAY DIFFRACTION98
2.1462-2.45660.30531350.22532780X-RAY DIFFRACTION99
2.4566-3.09440.22821390.21762802X-RAY DIFFRACTION99
3.0944-27.38130.22911350.16192867X-RAY DIFFRACTION99
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)
14.83141.4875-1.76129.2313-2.35665.2230.1448-0.00230.2851-0.4235-0.062-0.3346-0.16370.3789-0.04530.1637-0.05850.03850.2772-0.01840.121714.030428.7188-0.2893
23.88920.222-0.39965.79150.21387.15190.4832-0.26670.2920.1448-0.405-0.1876-0.50170.1475-0.0290.2142-0.12560.03420.3105-0.05670.158110.735131.76846.4853
33.816-0.2235-0.55043.3350.36998.2483-0.0278-0.107-0.23580.0682-0.1073-0.07960.52920.86180.15840.17340.042-0.03350.21380.02620.13382.857115.077925.7747
41.85163.02643.17777.33965.40277.4378-0.1921-0.14710.08860.15110.03810.63150.0303-0.18080.15860.14160.0496-0.0120.21620.00820.1571-7.214215.844224.5394
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 0:34
2X-RAY DIFFRACTION2chain A and resi 35:90
3X-RAY DIFFRACTION3chain B and resi 1:64
4X-RAY DIFFRACTION4chain B and resi 65:90

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