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- PDB-5es2: The crystal structure of a functionally uncharacterized protein L... -

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Basic information

Entry
Database: PDB / ID: 5es2
TitleThe crystal structure of a functionally uncharacterized protein LPG0634 from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
ComponentsUncharacterized protein LPG0634
KeywordsStructural Genomics / Unknown Function / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG
Function / homologyPutative substrate of the Dot/Icm secretion system superfamily / Putative substrate of the Dot/Icm secretion system / Substrate of the Dot/Icm secretion system, putative / ACETATE ION / Type IV secretion protein Dot
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsTan, K. / Xu, X. / Cui, H. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM074942 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094585 United States
CitationJournal: To Be Published
Title: The crystal structure of a functionally uncharacterized protein LPG0634 from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Authors: Tan, K. / Xu, X. / Cui, H. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionNov 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein LPG0634
B: Uncharacterized protein LPG0634
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,22725
Polymers99,3412
Non-polymers1,88523
Water93752
1
A: Uncharacterized protein LPG0634
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,98917
Polymers49,6711
Non-polymers1,31816
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein LPG0634
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2388
Polymers49,6711
Non-polymers5677
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.070, 97.322, 100.447
Angle α, β, γ (deg.)90.00, 96.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized protein LPG0634


Mass: 49670.625 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: lpg0634 / Plasmid: p15TvLic / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZXU7
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.88 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.2M LiSO4, 0.1M HEPES, 25% PEG335

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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: Apr 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.6→36.5 Å / Num. all: 35558 / Num. obs: 35558 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 24.7
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 3.06 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→36.202 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2532 1800 5.19 %Random selection
Rwork0.191 ---
obs0.1942 34711 99.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→36.202 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5980 0 106 52 6138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0016143
X-RAY DIFFRACTIONf_angle_d0.3428285
X-RAY DIFFRACTIONf_dihedral_angle_d9.9352252
X-RAY DIFFRACTIONf_chiral_restr0.015966
X-RAY DIFFRACTIONf_plane_restr0.0021057
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.67030.34181430.27482526X-RAY DIFFRACTION100
2.6703-2.74890.361300.26132521X-RAY DIFFRACTION100
2.7489-2.83760.29161200.24982577X-RAY DIFFRACTION100
2.8376-2.93890.32651360.24282537X-RAY DIFFRACTION100
2.9389-3.05660.32871340.25562525X-RAY DIFFRACTION100
3.0566-3.19560.26961480.24792514X-RAY DIFFRACTION100
3.1956-3.3640.27741410.2282532X-RAY DIFFRACTION100
3.364-3.57450.26421320.21342542X-RAY DIFFRACTION100
3.5745-3.85030.22271600.17952516X-RAY DIFFRACTION100
3.8503-4.23720.20521230.15752575X-RAY DIFFRACTION100
4.2372-4.84910.20651530.15222513X-RAY DIFFRACTION100
4.8491-6.10460.24761630.17852532X-RAY DIFFRACTION100
6.1046-36.20580.25761170.1542501X-RAY DIFFRACTION95
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)
13.62541.3919-0.72254.27580.01121.7914-0.05740.1220.0721-0.1277-0.03030.1045-0.0768-0.01510.09050.26540.006-0.05170.37460.00860.368944.380928.9262131.6661
22.484-0.3749-0.21472.0134-0.66723.18130.09450.169-0.0095-0.12470.04080.17590.2474-0.3479-0.14030.2835-0.0232-0.0190.4257-0.05550.4816.643610.0312146.9667
35.2366-0.0589-1.63642.0449-0.29634.42320.09150.1370.263-0.04930.0788-0.0443-0.1492-0.2045-0.14440.3058-0.04950.00540.2713-0.02950.412926.061518.7277142.3565
41.69831.0877-0.87983.9878-1.29084.3971-0.0026-0.42320.19771.250.34970.3035-0.80460.1479-0.31241.24610.1848-0.02490.7694-0.25520.809727.450949.835296.8159
52.1869-0.3789-1.79336.7564-1.77674.56930.23050.3215-0.0708-0.10920.1143-0.037-0.6081-0.0021-0.25440.77860.078-0.04830.5376-0.1770.55931.324946.70988.3274
64.69541.7921-2.27089.0029-1.12445.62360.1131-0.35940.20310.72210.1308-0.8222-0.32350.8744-0.27620.68420.0836-0.14530.6469-0.30660.720138.004840.067389.9064
71.3506-1.9676-1.40963.64040.77022.7328-0.195-0.3734-0.08460.71790.11760.10570.04870.00190.06220.6655-0.005-0.07560.7478-0.22970.632933.488628.532491.0641
82.241-0.0723-0.41065.24482.47316.8649-0.1232-0.3197-0.27050.60740.0875-0.21850.13920.06990.03360.47280.15450.00360.49390.00560.406239.54033.293878.8095
95.73080.66853.91853.47960.00477.0323-0.2659-0.9892-0.10780.94090.3099-0.29870.03020.318-0.05390.59670.1877-0.05330.687-0.10450.437140.740510.637785.5307
104.90330.57452.62964.6012-0.26526.930.0169-0.99-0.17991.14320.19110.80340.1054-0.9099-0.11370.54920.11260.13850.5665-0.01690.489726.61679.561679.4858
115.38331.1356-1.43336.33410.54595.8206-0.0259-0.34310.37180.49350.4846-1.0971-0.56480.8604-0.47510.59120.1253-0.1490.7279-0.20650.574746.736220.136682.8418
124.8438-2.1462-3.11584.30511.9876.0956-0.2453-0.3130.25880.69690.06390.54270.319-0.59330.15130.6112-0.00220.0970.6759-0.13270.604223.966524.972188.2954
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 180 )
2X-RAY DIFFRACTION2chain 'A' and (resid 181 through 317 )
3X-RAY DIFFRACTION3chain 'A' and (resid 318 through 398 )
4X-RAY DIFFRACTION4chain 'B' and (resid 6 through 62 )
5X-RAY DIFFRACTION5chain 'B' and (resid 63 through 107 )
6X-RAY DIFFRACTION6chain 'B' and (resid 108 through 136 )
7X-RAY DIFFRACTION7chain 'B' and (resid 137 through 202 )
8X-RAY DIFFRACTION8chain 'B' and (resid 203 through 254 )
9X-RAY DIFFRACTION9chain 'B' and (resid 255 through 288 )
10X-RAY DIFFRACTION10chain 'B' and (resid 289 through 317 )
11X-RAY DIFFRACTION11chain 'B' and (resid 318 through 365 )
12X-RAY DIFFRACTION12chain 'B' and (resid 366 through 400 )

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