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- PDB-4fgp: Legionella pneumophila LapG (EGTA-treated) -

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Basic information

Entry
Database: PDB / ID: 4fgp
TitleLegionella pneumophila LapG (EGTA-treated)
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 / MOLECULAR REPLACEMENT / Resolution: 1.73 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
Revision 1.2Feb 28, 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

Downloads & links

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Assembly

Deposited unit
A: Periplasmic protein
B: Periplasmic protein


Theoretical massNumber of molelcules
Total (without water)43,1812
Polymers43,1812
Non-polymers00
Water8,251458
1
A: Periplasmic protein


Theoretical massNumber of molelcules
Total (without water)21,5911
Polymers21,5911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Periplasmic protein


Theoretical massNumber of molelcules
Total (without water)21,5911
Polymers21,5911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)123.835, 43.718, 100.679
Angle α, β, γ (deg.)90.00, 122.08, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Periplasmic protein / Periplasm


Mass: 21590.594 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 2.67 Å3/Da / Density % sol: 53.97 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.14 M Ammonium Tartrate dibasic, 20% PEG3350, 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: 1.73→50 Å / Num. all: 47687 / Num. obs: 45446 / % possible obs: 95.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.73→1.79 Å / % possible all: 69.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→47.766 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 21.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2067 1999 4.4 %random
Rwork0.1767 ---
all0.178 45446 --
obs0.178 45427 94.47 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.869 Å2 / ksol: 0.376 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.1934 Å2-0 Å28.0285 Å2
2---6.561 Å20 Å2
3----2.6324 Å2
Refinement stepCycle: LAST / Resolution: 1.73→47.766 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2931 0 0 458 3389
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063051
X-RAY DIFFRACTIONf_angle_d1.0674151
X-RAY DIFFRACTIONf_dihedral_angle_d14.0161143
X-RAY DIFFRACTIONf_chiral_restr0.081465
X-RAY DIFFRACTIONf_plane_restr0.005529
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7299-1.77320.3066900.26321951X-RAY DIFFRACTION60
1.7732-1.82120.27531150.24752524X-RAY DIFFRACTION78
1.8212-1.87470.28791320.22282867X-RAY DIFFRACTION88
1.8747-1.93530.25931450.20153135X-RAY DIFFRACTION97
1.9353-2.00440.1931500.19033257X-RAY DIFFRACTION100
2.0044-2.08470.22311500.18343273X-RAY DIFFRACTION100
2.0847-2.17960.20931500.17463253X-RAY DIFFRACTION100
2.1796-2.29450.17861510.16513294X-RAY DIFFRACTION100
2.2945-2.43820.2341520.1773282X-RAY DIFFRACTION100
2.4382-2.62650.20311500.17283267X-RAY DIFFRACTION100
2.6265-2.89070.19741520.17943281X-RAY DIFFRACTION100
2.8907-3.30890.2161520.1743308X-RAY DIFFRACTION100
3.3089-4.16850.19231520.15493314X-RAY DIFFRACTION100
4.1685-47.7840.18051580.1713422X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.0819-0.051-0.02250.0883-0.01420.15330.11930.01160.1650.1066-0.11980.183-0.0208-0.206-0.00020.1423-0.00360.01220.1862-0.00770.1995-10.844316.815937.4568
20.41760.0304-0.27090.0223-0.1210.1927-0.02490.0964-0.0335-0.07240.0031-0.03930.053-0.028900.1711-0.00070.02310.1239-0.01080.1327.005217.444531.6399
30.00240.0035-0.00090.0042-0.00360.0037-0.0326-0.02940.02230.0384-0.03430.0584-0.0757-0.05980.00010.51750.04930.09650.22750.00090.448717.50132.308424.154
40.0263-0.03540.00710.0313-0.02030.0322-0.11680.20710.4011-0.2304-0.1549-0.0523-0.310.0819-0.00030.22490.0325-0.06890.2980.00830.2416-0.827423.727719.5528
50.20050.0067-0.05220.3992-0.19870.236-0.02730.3638-0.1216-0.497-0.05020.02650.2635-0.1126-0.07940.1387-0.0106-0.13870.23420.02520.101618.65527.4074-11.9932
60.10160.06910.10090.1545-0.04920.1279-0.0069-0.00530.05860.3678-0.02790.0327-0.0389-0.1476-0.00010.2050.01670.02030.1628-0.00360.146922.602612.95053.7282
70.11010.0722-0.17390.0314-0.11560.285-0.0122-0.02860.00610.08210.00080.05650.0442-0.0661-00.11970.0018-0.00240.1364-0.00650.141522.39523.83538.0957
80.0610.08860.08230.47130.39410.36450.1287-0.2832-0.33150.43080.00760.25840.4038-0.1027-0.01260.1634-0.0453-0.02890.3579-0.00030.271410.289-1.62848.7864
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 56:97)
2X-RAY DIFFRACTION2(chain A and resid 98:217)
3X-RAY DIFFRACTION3(chain A and resid 218:226)
4X-RAY DIFFRACTION4(chain A and resid 227:244)
5X-RAY DIFFRACTION5(chain B and resid 56:94)
6X-RAY DIFFRACTION6(chain B and resid 95:121)
7X-RAY DIFFRACTION7(chain B and resid 122:218)
8X-RAY DIFFRACTION8(chain B and resid 219:244)

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