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- PDB-3l4e: 1.5A Crystal Structure of a Putative Peptidase E Protein from Lis... -

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Basic information

Entry
Database: PDB / ID: 3l4e
Title1.5A Crystal Structure of a Putative Peptidase E Protein from Listeria monocytogenes EGD-e
ComponentsUncharacterized peptidase Lmo0363
KeywordsHYDROLASE / hypothetical protein lmo0363 / CSGID / similar to peptidase E / Protease / Serine protease / Structural Genomics / National Institute of Allergy and Infectious Diseases / National Institutes of Health / Department of Health and Human Services / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity
Similarity search - Function
Peptidase S51 / Peptidase family S51 / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized peptidase Lmo0363
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsBrunzelle, J.S. / Onopriyenko, O. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 1.5A Crystal Structure of a Putative Peptidase E Protein from Listeria monocytogenes EGD-e
Authors: Brunzelle, J.S. / Onopriyenko, O. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized peptidase Lmo0363
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1563
Polymers22,9641
Non-polymers1922
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.821, 67.821, 155.169
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-213-

HOH

21A-340-

HOH

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Components

#1: Protein Uncharacterized peptidase Lmo0363


Mass: 22963.889 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD-e / Gene: lmo0363 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic
References: UniProt: P58495, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.24 Å3/Da / Density % sol: 45.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 2.5M NH4 Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 21-ID-D10.97857
SYNCHROTRONAPS 21-ID-D20.77487
Detector
TypeIDDetectorDateDetails
RAYONIX MX-3001CCDNov 12, 2009Mirrors
RAYONIX MX-3002CCDDec 10, 2009Mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111SINGLE WAVELENGTHMx-ray1
2Si 111SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.978571
20.774871
ReflectionResolution: 1.5→30 Å / Num. all: 34751 / Num. obs: 34751 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 9.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 36.4
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.646 / Mean I/σ(I) obs: 2.57 / Num. unique all: 1689 / % possible all: 99.7

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Processing

Software
NameVersionClassification
BLU-MAXdata collection
PHENIX(phenix.autosol)model building
PHENIX(phenix.refine: 1.4_115)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→23.415 Å / SU ML: 0.18 / Isotropic thermal model: Ansiotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2222 2571 7.67 %RANDOM
Rwork0.1692 ---
all0.1733 33512 --
obs0.1692 33512 96.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.361 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.1387 Å20 Å20 Å2
2--0 Å2-0.1387 Å2
3---0.2774 Å2
Refinement stepCycle: LAST / Resolution: 1.5→23.415 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1589 0 10 185 1784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051686
X-RAY DIFFRACTIONf_angle_d0.9832292
X-RAY DIFFRACTIONf_dihedral_angle_d16.341615
X-RAY DIFFRACTIONf_chiral_restr0.07273
X-RAY DIFFRACTIONf_plane_restr0.005289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4992-1.55280.24882100.18022834X-RAY DIFFRACTION90
1.5528-1.6150.26772220.16612909X-RAY DIFFRACTION92
1.615-1.68840.23892390.15342959X-RAY DIFFRACTION94
1.6884-1.77740.20032610.14283017X-RAY DIFFRACTION96
1.7774-1.88880.22822780.14863042X-RAY DIFFRACTION97
1.8888-2.03450.20672790.14423090X-RAY DIFFRACTION99
2.0345-2.23910.20752550.14693179X-RAY DIFFRACTION99
2.2391-2.56280.21582700.15633202X-RAY DIFFRACTION99
2.5628-3.22750.23362600.17643270X-RAY DIFFRACTION100
3.2275-23.41730.21352970.17973439X-RAY DIFFRACTION99

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