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- PDB-5bq9: Crystal structure of uncharacterized protein lpg1496 Legionella p... -

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Basic information

Entry
Database: PDB / ID: 5bq9
TitleCrystal structure of uncharacterized protein lpg1496 Legionella pneumophila subsp. pneumophila
ComponentsUncharacterized protein
KeywordsUnknown Function / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology: / lpg1496 N-terminal domain / SidE, PDE domain / SidE phosphodiesterase (PDE) domain / Uncharacterized protein
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2785 Å
AuthorsChang, C. / Morar, M. / Evdokimova, E. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Proteins / Year: 2015
Title: Crystal structure of the Legionella pneumophila lem10 effector reveals a new member of the HD protein superfamily.
Authors: Morar, M. / Evdokimova, E. / Chang, C. / Ensminger, A.W. / Savchenko, A.
History
DepositionMay 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references
Revision 1.2Jan 27, 2016Group: Database references
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)136,0152
Polymers136,0152
Non-polymers00
Water3,567198
1
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)68,0071
Polymers68,0071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)68,0071
Polymers68,0071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.439, 76.625, 76.688
Angle α, β, γ (deg.)90.000, 96.660, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized protein


Mass: 68007.406 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: lpg1496 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q5ZVE4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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

Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: 0.15M Magnesium Chloride, 0.1M Tris, 24% PEG 3350, 5% DMSO. 0.5M Calcium Chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 27, 2013
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.278→50 Å / Num. all: 38964 / Num. obs: 38820 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 26.78 Å2 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.039 / Rrim(I) all: 0.103 / Χ2: 0.803 / Net I/av σ(I): 21.768 / Net I/σ(I): 8.3 / Num. measured all: 265782
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.278-2.346.50.86119280.8390.3630.9360.88198.8
2.34-2.386.60.71619240.8780.30.7770.86899.7
2.38-2.436.60.59619030.9030.2490.6470.87499
2.43-2.486.70.57319550.9110.2380.6210.84499.4
2.48-2.536.70.51419170.9120.2130.5570.85799.7
2.53-2.596.80.43319350.9440.1790.4690.84199.4
2.59-2.666.80.36419260.9590.150.3940.84899.5
2.66-2.736.90.3119300.9730.1270.3360.851100
2.73-2.816.90.25719300.9720.1050.2780.85599.6
2.81-2.96.90.20319310.9820.0820.2190.86499.7
2.9-370.16519360.9870.0670.1780.83599.8
3-3.1270.13319400.9880.0540.1430.83399.8
3.12-3.2670.11119480.9870.0450.120.84999.9
3.26-3.446.90.08619330.9890.0350.0930.85899.9
3.44-3.656.90.06719430.9930.0270.0720.83799.9
3.65-3.936.90.05419570.9950.0220.0580.80799.8
3.93-4.336.80.04219460.9950.0170.0460.66699.9
4.33-4.9570.03719660.9960.0150.040.59699.9
4.95-6.247.30.03819680.9950.0150.0410.58399.9
6.24-506.80.03620040.9960.0150.0390.64999

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
SBC-Collectdata collection
HKL-3000phasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.2785→32.363 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.36 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2263 3470 4.96 %
Rwork0.18 66472 -
obs0.1822 38572 90.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 162.99 Å2 / Biso mean: 45.2715 Å2 / Biso min: 6.01 Å2
Refinement stepCycle: final / Resolution: 2.2785→32.363 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6738 0 0 198 6936
Biso mean---36.76 -
Num. residues----866
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026931
X-RAY DIFFRACTIONf_angle_d0.5949395
X-RAY DIFFRACTIONf_chiral_restr0.0241010
X-RAY DIFFRACTIONf_plane_restr0.0031209
X-RAY DIFFRACTIONf_dihedral_angle_d10.112494
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2785-2.30970.2518590.20661364142345
2.3097-2.34270.2497880.21831906199466
2.3427-2.37760.28781180.20542141225973
2.3776-2.41480.2681310.20612161229275
2.4148-2.45430.25851250.21542315244079
2.4543-2.49670.27641010.21292360246181
2.4967-2.5420.28611490.21072545269486
2.542-2.59090.27051250.20722615274089
2.5909-2.64380.2441550.21242743289892
2.6438-2.70120.25481060.21292779288596
2.7012-2.7640.27681660.19382891305798
2.764-2.83310.23371460.19712879302599
2.8331-2.90970.24381550.187729263081100
2.9097-2.99520.2341530.19412889304299
2.9952-3.09180.25961560.188629313087100
3.0918-3.20220.23861770.191328783055100
3.2022-3.33030.22061630.190729453108100
3.3303-3.48170.24712020.179228523054100
3.4817-3.66510.21411600.16642885304599
3.6651-3.89430.15851750.15432899307499
3.8943-4.19440.22031310.15042902303399
4.1944-4.61550.18781450.14752890303599
4.6155-5.28080.26141180.163429663084100
5.2808-6.64380.18551530.194629083061100
6.6438-32.36630.19241130.1682902301598
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)
10.31210.123-0.01940.20570.0940.0657-0.0864-0.03030.31430.0285-0.18630.15390.45550.1828-0.00580.84270.0704-0.08210.6503-0.03010.3385142.2483-14.741443.9709
20.0365-0.0111-0.08120.02260.0750.3524-0.0806-0.03860.0036-0.0719-0.0578-0.0580.11-0.2582-0.37640.5426-0.0175-0.11430.36480.02460.0663139.1949-9.017432.4134
30.6854-0.0205-0.35751.00170.28180.6517-0.0958-0.02380.01260.01920.05730.09340.0911-0.0258-0.01440.04430.02320.00350.04680.01290.1214138.69145.26242.74
40.8752-0.20360.13840.3260.18690.21470.75190.03760.05590.1159-0.39170.0264-0.54470.08870.17880.6181-0.12540.0750.6320.00480.2525120.406623.1776-34.3969
51.0715-0.15640.27490.92540.03340.544-0.093-0.00260.0067-0.02020.08550.0052-0.1028-0.0106-0.00080.0668-0.0178-0.00050.0714-0.00230.0421102.70648.6801-3.3533
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 99 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 100 through 302 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 303 through 590 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid -5 through 124 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 125 through 590 )B0

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