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- PDB-5ym9: Crystal Structure of the Deamidase from Legionella pneumophila -

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Basic information

Entry
Database: PDB / ID: 5ym9
TitleCrystal Structure of the Deamidase from Legionella pneumophila
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / Deamidase / CIF
Function / homology: / MvcA insertion domain / MvcA insertion domain-containing protein
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsZhu, Z.L. / Zhu, M.
CitationJournal: To Be Published
Title: Crystal Structure of the Deamidase from Legionella pneumophila
Authors: Zhu, Z.L. / Zhu, M.
History
DepositionOct 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)88,0902
Polymers88,0902
Non-polymers00
Water3,873215
1
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)44,0451
Polymers44,0451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)44,0451
Polymers44,0451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.101, 135.895, 64.578
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Uncharacterized protein / Deamidase


Mass: 44044.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg2148 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5ZTL3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 3.04 Å3/Da / Density % sol: 59.55 % / Mosaicity: 1.065 °
Crystal growTemperature: 289 K / Method: evaporation / Details: pentaerythritol propoxylate (5/4 PO/OH)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. obs: 37412 / % possible obs: 98.4 % / Redundancy: 6.4 % / Biso Wilson estimate: 59.39 Å2 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.034 / Rrim(I) all: 0.087 / Χ2: 1.371 / Net I/σ(I): 13.8 / Num. measured all: 238747
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRrim(I) all
2.5-2.545.90.93818340.8430.4121.51398.1
2.54-2.595.90.81918360.8340.361.57498.30.897
2.59-2.6460.74818200.8560.3261.604980.819
2.64-2.6960.65418690.9110.2851.62897.60.715
2.69-2.756.10.57917820.9240.251.55897.60.632
2.75-2.826.10.44718520.9520.1941.61697.60.489
2.82-2.896.10.35718200.9620.1531.57697.50.389
2.89-2.966.20.318280.9740.1281.56897.80.327
2.96-3.056.30.24718490.980.1051.59498.10.268
3.05-3.156.30.19618410.9860.0831.5597.70.213
3.15-3.266.40.16618460.9910.071.50298.20.181
3.26-3.396.50.13218880.9950.0551.44698.70.143
3.39-3.556.50.10618690.9960.0451.38699.20.115
3.55-3.736.60.08818880.9970.0361.28599.30.095
3.73-3.976.70.08318890.9960.0351.20499.80.09
3.97-4.276.70.07219150.9970.031.03899.80.078
4.27-4.716.80.06719200.9980.0280.96199.90.073
4.71-5.396.80.05519520.9980.0231.03899.90.06
5.39-6.7970.04919440.9990.021.02499.80.053
6.79-1006.60.04119700.9980.0181.11794.30.045

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
DENZOdata collection
HKL-2000data scaling
PHASESphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.5→46.809 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 28.66
RfactorNum. reflection% reflection
Rfree0.2517 1798 4.82 %
Rwork0.2007 --
obs0.2031 37317 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 135.69 Å2 / Biso mean: 70.8825 Å2 / Biso min: 42.1 Å2
Refinement stepCycle: final / Resolution: 2.5→46.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6190 0 0 215 6405
Biso mean---67.57 -
Num. residues----768
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126322
X-RAY DIFFRACTIONf_angle_d1.5818524
X-RAY DIFFRACTIONf_chiral_restr0.094922
X-RAY DIFFRACTIONf_plane_restr0.011114
X-RAY DIFFRACTIONf_dihedral_angle_d16.8592418
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4996-2.56720.34421500.29462651280197
2.5672-2.64270.29781320.28022671280398
2.6427-2.7280.31891280.27492706283497
2.728-2.82550.32721390.25372655279497
2.8255-2.93860.33761320.25382696282898
2.9386-3.07230.29561320.24042716284898
3.0723-3.23420.31021320.22872685281798
3.2342-3.43680.29071460.21882697284399
3.4368-3.70210.23421300.19792759288999
3.7021-4.07440.24521270.186828132940100
4.0744-4.66360.19711470.171827802927100
4.6636-5.87380.25211610.178828252986100
5.8738-46.81760.21431420.17712865300796

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