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- PDB-4rxv: The crystal structure of the N-terminal fragment of uncharacteriz... -

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Basic information

Entry
Database: PDB / ID: 4rxv
TitleThe crystal structure of the N-terminal fragment of uncharacterized protein from Legionella pneumophila
Componentshypothetical protein lpg0944Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / MCSG / PSI-Biology / Midwest Center for Structural Genomics
Function / homologyDomain of unknown function DUF5617 / Domain of unknown function (DUF5617) / DUF5617 domain-containing protein
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.099 Å
AuthorsNocek, B. / Cuff, M. / Evdokimova, E. / Egorova, O. / Joachimiak, A. / Ensminger, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Mol Syst Biol / Year: 2016
Title: Diverse mechanisms of metaeffector activity in an intracellular bacterial pathogen, Legionella pneumophila.
Authors: Urbanus, M.L. / Quaile, A.T. / Stogios, P.J. / Morar, M. / Rao, C. / Di Leo, R. / Evdokimova, E. / Lam, M. / Oatway, C. / Cuff, M.E. / Osipiuk, J. / Michalska, K. / Nocek, B.P. / Taipale, M. ...Authors: Urbanus, M.L. / Quaile, A.T. / Stogios, P.J. / Morar, M. / Rao, C. / Di Leo, R. / Evdokimova, E. / Lam, M. / Oatway, C. / Cuff, M.E. / Osipiuk, J. / Michalska, K. / Nocek, B.P. / Taipale, M. / Savchenko, A. / Ensminger, A.W.
History
DepositionDec 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein lpg0944


Theoretical massNumber of molelcules
Total (without water)25,3631
Polymers25,3631
Non-polymers00
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.515, 68.939, 40.947
Angle α, β, γ (deg.)90.00, 112.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein hypothetical protein lpg0944 / Hypothesis


Mass: 25362.529 Da / Num. of mol.: 1 / Mutation: Q155E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg0944 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZWY9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 1.72 Å3/Da / Density % sol: 28.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.6 M ammonium sulfate, 0.1 M NaCl, 0.1 M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 13, 2013 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.099→37.821 Å / Num. all: 69740 / Num. obs: 62764 / % possible obs: 90.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 30
Reflection shellResolution: 1.09→1.12 Å / Rmerge(I) obs: 0.05 / % possible all: 45.5

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
CCP4model building
PHENIX(phenix.refine: dev_1834)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 1.099→37.821 Å / SU ML: 0.08 / σ(F): 1.39 / Phase error: 14.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1392 3177 5.06 %
Rwork0.1243 --
obs0.1251 62763 89.99 %
all-65940 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.099→37.821 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1782 0 0 297 2079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011921
X-RAY DIFFRACTIONf_angle_d1.3652634
X-RAY DIFFRACTIONf_dihedral_angle_d15.123731
X-RAY DIFFRACTIONf_chiral_restr0.074283
X-RAY DIFFRACTIONf_plane_restr0.008357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0992-1.11560.2413660.2182942X-RAY DIFFRACTION33
1.1156-1.1330.2256580.20351232X-RAY DIFFRACTION43
1.133-1.15160.1905800.16721594X-RAY DIFFRACTION55
1.1516-1.17150.1737980.16011910X-RAY DIFFRACTION67
1.1715-1.19280.17251120.14682326X-RAY DIFFRACTION80
1.1928-1.21570.17461570.13792664X-RAY DIFFRACTION94
1.2157-1.24050.14891360.12492923X-RAY DIFFRACTION100
1.2405-1.26750.16571510.12152833X-RAY DIFFRACTION100
1.2675-1.2970.17211590.12072876X-RAY DIFFRACTION100
1.297-1.32940.14981600.11482863X-RAY DIFFRACTION100
1.3294-1.36540.1511310.11962883X-RAY DIFFRACTION100
1.3654-1.40560.1571710.11112897X-RAY DIFFRACTION100
1.4056-1.45090.14221530.10872846X-RAY DIFFRACTION100
1.4509-1.50280.13641390.10742874X-RAY DIFFRACTION100
1.5028-1.5630.1381430.10192891X-RAY DIFFRACTION100
1.563-1.63410.13751510.1062899X-RAY DIFFRACTION100
1.6341-1.72030.13461560.10522866X-RAY DIFFRACTION100
1.7203-1.8280.12981580.10852871X-RAY DIFFRACTION100
1.828-1.96920.12791500.11082909X-RAY DIFFRACTION100
1.9692-2.16730.13321500.11452871X-RAY DIFFRACTION100
2.1673-2.48090.12581690.12332868X-RAY DIFFRACTION100
2.4809-3.12540.1411680.13592893X-RAY DIFFRACTION100
3.1254-37.84350.13151610.14012855X-RAY DIFFRACTION97

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