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- PDB-4fgq: Legionella pneumophila LapG -

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Basic information

Entry
Database: PDB / ID: 4fgq
TitleLegionella pneumophila LapG
ComponentsPeriplasmic protein
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: 1.645 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
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water9,206511
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)100.929, 105.110, 43.311
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Periplasmic protein


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


Mass: 18.015 Da / Num. of mol.: 511 / 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: 2.66 Å3/Da / Density % sol: 53.73 %
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: Dec 2, 2010
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: 1.645→50 Å / Num. all: 56829 / Num. obs: 55010 / % possible obs: 96.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.65→1.71 Å / % possible all: 88.5

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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
Starting model: model built based on lower resolution SAD dataset

Resolution: 1.645→28.335 Å / SU ML: 0.2 / σ(F): 1.33 / Phase error: 27.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2202 1981 3.63 %random
Rwork0.1889 ---
all0.19 55010 --
obs0.19 54598 96.04 %-
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.362 Å2 / ksol: 0.388 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.0075 Å20 Å2-0 Å2
2--7.7058 Å20 Å2
3----4.6983 Å2
Refinement stepCycle: LAST / Resolution: 1.645→28.335 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2877 0 0 511 3388
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062997
X-RAY DIFFRACTIONf_angle_d1.0954079
X-RAY DIFFRACTIONf_dihedral_angle_d13.3621119
X-RAY DIFFRACTIONf_chiral_restr0.079454
X-RAY DIFFRACTIONf_plane_restr0.005522
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6449-1.6860.34251070.30513210X-RAY DIFFRACTION83
1.686-1.73160.30371450.273678X-RAY DIFFRACTION95
1.7316-1.78260.3161300.25973665X-RAY DIFFRACTION96
1.7826-1.84010.24611500.22843722X-RAY DIFFRACTION96
1.8401-1.90580.26261390.20613708X-RAY DIFFRACTION96
1.9058-1.98210.2511370.19483765X-RAY DIFFRACTION97
1.9821-2.07230.20091410.19553793X-RAY DIFFRACTION97
2.0723-2.18150.19421440.18663799X-RAY DIFFRACTION98
2.1815-2.31810.19981480.16813788X-RAY DIFFRACTION98
2.3181-2.4970.22561390.18493820X-RAY DIFFRACTION98
2.497-2.74810.21341510.1853811X-RAY DIFFRACTION97
2.7481-3.14530.20951470.18423843X-RAY DIFFRACTION97
3.1453-3.96110.21691530.16593951X-RAY DIFFRACTION99
3.9611-28.33880.19831500.17744064X-RAY DIFFRACTION97
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)
11.46261.1349-0.21931.7202-1.60432.53050.0057-0.55030.4220.7149-0.0322-0.1146-0.8560.15070.01520.54050.108-0.12730.3494-0.07810.3236-16.3441-6.7660.9633
21.52620.509-0.44843.212-2.21863.59850.00920.03680.37480.17670.17140.286-0.5209-0.3017-0.11780.15590.0355-0.02660.10020.05530.1821-21.0191-10.9443-7.5647
31.8056-0.62-0.02671.07570.08361.0159-0.0165-0.00850.1154-0.06170.0137-0.1198-0.00450.1228-0.00220.0825-0.01210.0020.09730.03110.092-5.9739-22.8982-5.0718
44.4224-1.73220.06123.796-2.9425.1998-0.0625-0.56150.46381.1652-0.0659-0.6515-0.57990.45910.15190.3664-0.1165-0.05910.2338-0.03030.39730.1047-10.03930.4913
54.30332.96646.00062.22194.22638.4131-0.3733-0.24470.57930.08990.07550.1006-1.0702-0.04330.27180.4892-0.0617-0.0020.41310.04810.378427.9372-8.7351-26.4279
61.7083-0.563-1.00234.41951.5113.46510.1431-0.12130.4786-0.03560.2481-0.2543-0.55340.3449-0.25620.1671-0.04460.02710.1340.00410.210438.0148-10.3654-14.6533
71.64940.53810.00950.9144-0.00230.98780.03450.00230.12910.0483-0.00080.1156-0.0542-0.1031-0.02380.09270.01340.01260.09560.03990.094422.9601-22.8672-16.5426
84.6348-0.3553-0.92978.38330.60084.8138-0.0120.4840.3054-0.85820.110.7616-0.3179-0.41250.03230.25730.0861-0.0160.13290.10960.239516.3631-10.6661-22.8175
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 56:62)
2X-RAY DIFFRACTION2(chain A and resid 63:96)
3X-RAY DIFFRACTION3(chain A and resid 97:218)
4X-RAY DIFFRACTION4(chain A and resid 219:244)
5X-RAY DIFFRACTION5(chain B and resid 53:59)
6X-RAY DIFFRACTION6(chain B and resid 60:96)
7X-RAY DIFFRACTION7(chain B and resid 97:218)
8X-RAY DIFFRACTION8(chain B and resid 219:244)

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