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- PDB-5l1a: Crystal structure of uncharacterized protein LPG2271 from Legione... -

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Basic information

Entry
Database: PDB / ID: 5l1a
TitleCrystal structure of uncharacterized protein LPG2271 from Legionella pneumophila
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / Structural Genomics / Midwest Center for Structural Genomics / MCSG / PSI-Biology
Function / homologyDomain of unknown function DUF5638 / Family of unknown function (DUF5638) / membrane / Chem-I3C / DUF5638 domain-containing protein
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsChang, C. / Xu, X. / Cui, H. / Yim, V. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115586 United States
CitationJournal: To Be Published
Title: Crystal structure of uncharacterized protein LPG2271 from Legionella pneumophila
Authors: Chang, C. / Xu, X. / Cui, H. / Yim, V. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionJul 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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
Revision 1.3Mar 6, 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

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6796
Polymers12,8851
Non-polymers2,7945
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.154, 44.657, 54.136
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized protein / LPG2271


Mass: 12885.265 Da / Num. of mol.: 1 / Fragment: UNP residues 1-110
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: lpg2271 / Plasmid: p15Tv lic
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q5ZT91
#2: Chemical
ChemComp-I3C / 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid / 5-Amino-2,4,6-triiodoisophthalic acid


Mass: 558.835 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H4I3NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 1.94 Å3/Da / Density % sol: 36.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.5 / Details: 0.1M Citric acid, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.7712 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 15, 2013
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7712 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 4158 / % possible obs: 98.1 % / Redundancy: 5.8 % / Biso Wilson estimate: 20.24 Å2 / Rmerge(I) obs: 0.097 / Χ2: 0.791 / Net I/av σ(I): 15.524 / Net I/σ(I): 15.6 / Num. measured all: 24051
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.4-2.443.10.196180.9
2.44-2.493.50.179187.3
2.49-2.533.90.159196.2
2.53-2.594.80.142198.5
2.59-2.645.20.1371100
2.64-2.75.90.1231100
2.7-2.776.20.12199.5
2.77-2.856.30.1121100
2.85-2.936.50.1091100
2.93-3.026.30.0971100
3.02-3.136.50.1011100
3.13-3.266.30.0931100
3.26-3.416.50.0961100
3.41-3.586.40.091100
3.58-3.816.20.0941100
3.81-4.16.50.0951100
4.1-4.526.50.092199.5
4.52-5.176.30.0981100
5.17-6.516.20.0721100
6.51-505.50.068198.4

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Processing

Software
NameVersionClassification
PHENIXdev_2386refinement
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→34.449 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 21.49
RfactorNum. reflection% reflection
Rfree0.2464 333 4.55 %
Rwork0.1915 --
obs0.1937 7314 96.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.5 Å2 / Biso mean: 21.4159 Å2 / Biso min: 4.68 Å2
Refinement stepCycle: final / Resolution: 2.4→34.449 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms880 0 80 65 1025
Biso mean--47.71 30.17 -
Num. residues----108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003972
X-RAY DIFFRACTIONf_angle_d0.5151320
X-RAY DIFFRACTIONf_chiral_restr0.033133
X-RAY DIFFRACTIONf_plane_restr0.002174
X-RAY DIFFRACTIONf_dihedral_angle_d12.818553
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3972-3.01990.25231980.19833344354294
3.0199-34.45240.24161350.18836373772100
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)
11.07650.37321.45350.5778-0.22096.1746-0.0248-0.09680.1850.156-0.10190.1748-0.1563-0.45420.17330.15940.0080.05790.1302-0.02820.2472-7.004841.04616.4535
21.5446-0.15741.0040.85970.09752.1934-0.07610.08890.05680.015-0.034-0.0026-0.18340.16540.07690.108-0.01730.00140.09990.02150.12491.530142.32466.9383
31.2461.0176-0.98612.9152-1.78373.08480.012-0.0738-0.0812-0.2769-0.1328-0.2212-0.00190.38910.16110.150.0288-0.00410.11580.00010.176513.224434.90889.8577
47.23671.49-1.67856.46761.05963.7608-0.25810.15230.4990.18680.0549-0.4895-0.36080.28280.09480.1028-0.0019-0.04750.2041-0.01880.195211.415342.801313.5723
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 31 )A0 - 31
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 76 )A32 - 76
3X-RAY DIFFRACTION3chain 'A' and (resid 77 through 95 )A77 - 95
4X-RAY DIFFRACTION4chain 'A' and (resid 96 through 110 )A96 - 110

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