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- PDB-3lu2: Structure of lmo2462, a Listeria monocytogenes amidohydrolase fam... -

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Basic information

Entry
Database: PDB / ID: 3lu2
TitleStructure of lmo2462, a Listeria monocytogenes amidohydrolase family putative dipeptidase
ComponentsLmo2462 protein
KeywordsHYDROLASE / dipeptidase / metallo-dependent hydrolase / Lysteria / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


metallodipeptidase activity
Similarity search - Function
Peptidase M19 / Membrane dipeptidase (Peptidase family M19) / Renal dipeptidase family profile. / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsAnderson, S.M. / Wawrzak, Z. / Onopriyenko, O. / Hasseman, J. / Edwards, A. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Structure of lmo2462, a Listeria monocytogenes amidohydrolase family putative dipeptidase
Authors: Anderson, S.M. / Wawrzak, Z. / Onopriyenko, O. / Hasseman, J. / Edwards, A. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionFeb 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 7, 2011Group: Structure summary
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lmo2462 protein
B: Lmo2462 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0846
Polymers70,8222
Non-polymers2624
Water5,062281
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Lmo2462 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5423
Polymers35,4111
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Lmo2462 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5423
Polymers35,4111
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)179.088, 179.088, 46.412
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Lmo2462 protein


Mass: 35411.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD-e / Gene: lmo2462 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q8Y4H9
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 3.03 Å3/Da / Density % sol: 59.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 25% PEG 3350, 200mM Na Tartrate, 100mM Tris, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.18072 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 4, 2009 / Details: beryllium lens
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18072 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 43887 / Num. obs: 43794 / % possible obs: 99.7 % / Observed criterion σ(I): 2.5 / Redundancy: 5.4 % / Rmerge(I) obs: 0.09 / Χ2: 1.025 / Net I/σ(I): 14.6
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 2.5 / Num. unique all: 4278 / Χ2: 1.031 / % possible all: 99.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6_289refinement
PDB_EXTRACT3.005data extraction
BLU-MAXdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→35.6 Å / Occupancy max: 1 / Occupancy min: 0.38 / FOM work R set: 0.897 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.185 1907 4.55 %RANDOM
Rwork0.152 ---
obs0.154 41868 95.4 %-
all-43887 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.615 Å2 / ksol: 0.359 e/Å3
Displacement parametersBiso max: 147.38 Å2 / Biso mean: 47.039 Å2 / Biso min: 16.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.428 Å2-0 Å2-0 Å2
2--0.428 Å20 Å2
3----0.856 Å2
Refinement stepCycle: LAST / Resolution: 2.2→35.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4908 0 4 281 5193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085085
X-RAY DIFFRACTIONf_angle_d1.0526872
X-RAY DIFFRACTIONf_chiral_restr0.071751
X-RAY DIFFRACTIONf_plane_restr0.004895
X-RAY DIFFRACTIONf_dihedral_angle_d18.3311872
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.198-2.2760.2461710.1833578374987
2.276-2.3670.2211770.1733731390890
2.367-2.4750.2131850.1683805399092
2.475-2.6060.1981870.1633918410594
2.606-2.7690.2251870.1714029421697
2.769-2.9820.2191990.184075427498
2.982-3.2820.212000.1724130433099
3.282-3.7570.1781990.1464148434799
3.757-4.7320.1492010.11742334434100
4.732-35.5860.1542010.1434314451599
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)
12.7084-0.0090.88210.42950.19171.33920.4980.5207-1.4824-0.11670.08830.16540.70910.1486-0.58690.60060.0825-0.39230.3189-0.21220.919120.69847.247-0.1028
21.8797-0.15360.76150.7111-0.63081.89750.2397-0.2152-0.6059-0.11640.10650.52190.3146-0.2407-0.33780.2383-0.015-0.21090.24150.0460.536613.051960.55879.0611
33.67230.50580.81341.2647-0.38281.07880.18270.2506-0.371-0.1799-0.06910.13050.16990.2083-0.12250.28890.1064-0.13960.2785-0.00190.298832.621661.34949.5267
43.10830.44030.2012.33740.75211.91080.03270.285-0.32040.12740.06230.07120.16610.0653-0.09150.1613-0.0501-0.07040.2714-0.01110.1889-17.581273.1956-11.8083
51.8551-0.0151.3580.99790.27351.6403-0.03230.3019-0.0480.04930.0915-0.25760.01280.3505-0.04770.1363-0.0287-0.08050.3815-0.00460.2654-0.206880.1696-5.4226
62.5076-0.53310.14761.54070.29331.332-0.069-0.05310.21030.40450.0694-0.1076-0.05170.07890.02760.2365-0.0446-0.05720.22240.07370.1611-18.235590.5421-0.749
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 0:89)A0 - 89
2X-RAY DIFFRACTION2(chain A and resid 90:182)A90 - 182
3X-RAY DIFFRACTION3(chain A and resid 183:308)A183 - 308
4X-RAY DIFFRACTION4(chain B and resid 0:116)B0 - 116
5X-RAY DIFFRACTION5(chain B and resid 117:191)B117 - 191
6X-RAY DIFFRACTION6(chain B and resid 192:308)B192 - 308

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