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- PDB-4fgo: Legionella pneumophila LapG (calcium-bound) -

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Basic information

Entry
Database: PDB / ID: 4fgo
TitleLegionella pneumophila LapG (calcium-bound)
ComponentsPeriplasmic proteinPeriplasm
KeywordsHYDROLASE / DUF920 / protease / calcium binding
Function / homologyTransglutaminase-like cysteine peptidase, predicted / Bacterial transglutaminase-like cysteine proteinase BTLCP / C8orf32 fold - #30 / C8orf32 fold / Roll / metal ion binding / Alpha Beta / Periplasmic protein
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.903 Å
AuthorsChatterjee, D. / Boyd, C.D. / O'Toole, G.A. / Sondermann, H.
CitationJournal: J.Bacteriol. / Year: 2012
Title: Structural characterization of a conserved, calcium-dependent periplasmic protease from Legionella pneumophila.
Authors: Chatterjee, D. / Boyd, C.D. / O'Toole, G.A. / Sondermann, H.
History
DepositionJun 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8182
Polymers21,7781
Non-polymers401
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.951, 59.951, 110.379
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Periplasmic protein / Periplasm


Mass: 21778.174 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia 1 / Gene: lpg0828 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5ZXA4
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.28 Å3/Da / Density % sol: 45.95 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.14 M Ammonium Tartrate dibasic, 20% PEG3350, 2 mM calcium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9771 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 4, 2011
RadiationMonochromator: Horizontal focusing 5.05 asymmetric cut Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9771 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 16508 / Num. obs: 16128 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.9→1.97 Å / % possible all: 81.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.903→33.619 Å / SU ML: 0.31 / σ(F): 0 / Phase error: 34.88 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2667 1549 9.96 %random
Rwork0.2592 ---
all0.2599 16128 --
obs0.2599 15545 94.37 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.846 Å2 / ksol: 0.352 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.8461 Å20 Å2-0 Å2
2--7.8461 Å20 Å2
3----15.6921 Å2
Refinement stepCycle: LAST / Resolution: 1.903→33.619 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1439 0 1 34 1474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081472
X-RAY DIFFRACTIONf_angle_d1.1111992
X-RAY DIFFRACTIONf_dihedral_angle_d16.584546
X-RAY DIFFRACTIONf_chiral_restr0.062221
X-RAY DIFFRACTIONf_plane_restr0.005252
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.903-1.96440.4736980.3923898X-RAY DIFFRACTION68
1.9644-2.03460.43181240.34511138X-RAY DIFFRACTION86
2.0346-2.11610.32741390.32681260X-RAY DIFFRACTION95
2.1161-2.21240.32251430.30281279X-RAY DIFFRACTION97
2.2124-2.3290.3521430.2931281X-RAY DIFFRACTION97
2.329-2.47490.31231410.30281293X-RAY DIFFRACTION97
2.4749-2.66590.34361480.30131323X-RAY DIFFRACTION99
2.6659-2.9340.31221460.30311321X-RAY DIFFRACTION99
2.934-3.35820.29261510.26751350X-RAY DIFFRACTION99
3.3582-4.22970.24521530.22991380X-RAY DIFFRACTION100
4.2297-33.62410.19581630.21771473X-RAY DIFFRACTION100
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)
13.65560.62220.19082.3252.1251.9852-1.0034-1.37961.47080.84250.71280.9506-4.1949-1.6482-0.35811.88560.36050.14481.1464-0.19510.684-22.984814.71620.2945
21.352-0.010.87750.9427-0.98465.032-0.2493-0.18080.31390.18870.4260.8875-1.7248-2.0086-0.36360.60410.52350.23391.04090.12520.2917-25.70550.782821.2716
36.70910.07282.11445.6692-1.39442.2833-0.04870.5969-0.1964-0.09440.3040.7908-0.5062-1.4365-0.45070.64070.07810.06830.65790.13470.359-24.6902-2.24531.6865
42.19120.3306-1.06892.4812-0.92676.5838-0.1442-0.0594-0.263-0.03840.37880.043-0.4282-0.7445-0.04260.09710.01720.03370.35280.07120.1908-17.363-8.729113.0767
52.04770.59253.70296.86848.30711.99930.73340.0655-0.9960.67260.3183-1.02210.83510.6391-0.89050.0794-0.1629-0.080.50150.00960.4221-5.5644-13.62166.3885
68.1209-5.86145.14658.0565-2.89187.4143-0.07450.07190.33690.50680.3339-0.585-0.91791.04290.00570.4444-0.1079-0.03950.4044-0.02380.403-7.1339-2.82375.444
76.6001-5.96810.49915.46290.04264.0473-1.3009-0.85420.46722.07621.4665-0.0637-1.89380.5536-0.07291.51360.0216-0.07520.55170.04260.5858-15.11039.26327.4703
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 59:71)
2X-RAY DIFFRACTION2(chain A and resid 72:114)
3X-RAY DIFFRACTION3(chain A and resid 115:125)
4X-RAY DIFFRACTION4(chain A and resid 126:215)
5X-RAY DIFFRACTION5(chain A and resid 216:220)
6X-RAY DIFFRACTION6(chain A and resid 221:239)
7X-RAY DIFFRACTION7(chain A and resid 240:244)

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