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- PDB-3it7: Crystal Structure of the LasA virulence factor from Pseudomonas a... -

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Basic information

Entry
Database: PDB / ID: 3it7
TitleCrystal Structure of the LasA virulence factor from Pseudomonas aeruginosa
ComponentsProtease lasA
KeywordsHYDROLASE / metallopeptidase / M23 / Beta-protein / Cell membrane / Cell outer membrane / Membrane / Metal-binding / Metalloprotease / Protease / Zymogen
Function / homology
Function and homology information


protein transport by the Sec complex / septum digestion after cytokinesis / protein secretion by the type II secretion system / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / peptidoglycan catabolic process / metalloendopeptidase activity / endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Peptidase M23A, B-lytic metalloendopeptidase / Glucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
L(+)-TARTARIC ACID / Protease LasA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.14 Å
AuthorsSpencer, J. / Murphy, L.M. / Conners, R. / Sessions, R.B. / Gamblin, S.J.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal structure of the LasA virulence factor from Pseudomonas aeruginosa: substrate specificity and mechanism of M23 metallopeptidases.
Authors: Spencer, J. / Murphy, L.M. / Conners, R. / Sessions, R.B. / Gamblin, S.J.
History
DepositionAug 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease lasA
B: Protease lasA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6699
Polymers39,9622
Non-polymers7077
Water7,044391
1
A: Protease lasA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3815
Polymers19,9811
Non-polymers4004
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protease lasA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2884
Polymers19,9811
Non-polymers3083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.964, 58.838, 146.438
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protease lasA / Staphylolytic protease


Mass: 19980.902 Da / Num. of mol.: 2 / Fragment: UNP residues 237-418 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / Strain: PAO1
References: UniProt: P14789, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 1.88 Å3/Da / Density % sol: 34.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: sodium potassium tartrate 400mM, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.28402, 1.28348, 1.2574
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Feb 28, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.284021
21.283481
31.25741
ReflectionRedundancy: 3.5 % / Av σ(I) over netI: 23.39 / Number: 109259 / Rmerge(I) obs: 0.095 / Χ2: 1.06 / D res high: 2.14 Å / D res low: 50 Å / Num. obs: 31654 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.615010010.0451.0733.8
3.664.6110010.0471.0633.7
3.23.6610010.060.9993.7
2.93.210010.0880.9773.7
2.72.910010.130.9843.6
2.542.710010.1861.0173.6
2.412.5410010.2291.0663.5
2.312.4110010.2611.1293.3
2.222.3199.510.2781.1793
2.142.229810.2991.212.6
ReflectionResolution: 2.14→50 Å / Num. obs: 32280 / % possible obs: 100 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.054 / Χ2: 1.027 / Net I/σ(I): 14.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.14-2.223.60.132641.0631100
2.22-2.313.70.09532161.0881100
2.31-2.413.70.08632031.041100
2.41-2.543.70.07932611.0651100
2.54-2.73.70.07132171.0311100
2.7-2.93.70.0632090.9921100
2.9-3.23.70.0532220.9941100
3.2-3.663.70.04232161.0381100
3.66-4.613.70.03732310.9651100
4.61-503.70.03732411199.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.14→37.57 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.189 / WRfactor Rwork: 0.145 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.891 / SU B: 3.684 / SU ML: 0.098 / SU R Cruickshank DPI: 0.322 / SU Rfree: 0.189 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.322 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.195 882 5.1 %RANDOM
Rwork0.149 ---
obs0.151 17436 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 50.75 Å2 / Biso mean: 8.668 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2--0.44 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.14→37.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2826 0 40 391 3257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0213009
X-RAY DIFFRACTIONr_angle_refined_deg1.1381.924117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4095370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.50523.014146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.98415380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2931518
X-RAY DIFFRACTIONr_chiral_restr0.0780.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212442
X-RAY DIFFRACTIONr_mcbond_it0.4251.51839
X-RAY DIFFRACTIONr_mcangle_it0.82322939
X-RAY DIFFRACTIONr_scbond_it1.24931170
X-RAY DIFFRACTIONr_scangle_it2.1354.51177
LS refinement shellResolution: 2.14→2.196 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.175 56 -
Rwork0.142 1231 -
all-1287 -
obs--100 %

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