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- PDB-4rxi: Structure of C-terminal domain of uncharacterized protein from Le... -

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Basic information

Entry
Database: PDB / ID: 4rxi
TitleStructure of C-terminal domain of uncharacterized protein from Legionella pneumophila
Componentshypothetical protein lpg0944
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / MCSG / PSI-Biology / Midwest Center for Structural Genomics
Function / homologysymbiont-mediated perturbation of host actin cytoskeleton via actin filament reorganization / : / RavJ, Peptidase domain / Domain of unknown function DUF5617 / Domain of unknown function (DUF5617) / Uncharacterized protein
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsCuff, M. / Nocek, B. / 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 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references
Revision 1.2Nov 6, 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 / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein lpg0944
B: hypothetical protein lpg0944


Theoretical massNumber of molelcules
Total (without water)37,8762
Polymers37,8762
Non-polymers00
Water3,567198
1
A: hypothetical protein lpg0944


Theoretical massNumber of molelcules
Total (without water)18,9381
Polymers18,9381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: hypothetical protein lpg0944


Theoretical massNumber of molelcules
Total (without water)18,9381
Polymers18,9381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.353, 60.715, 57.524
Angle α, β, γ (deg.)90.00, 104.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein hypothetical protein lpg0944


Mass: 18938.182 Da / Num. of mol.: 2 / Fragment: UNP residues 230-391
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Gene: lpg0944 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q5ZWY9
#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

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.6M NH4Sulfate, 0.1M NaCl, 0.1M Hepes pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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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 210r / Detector: CCD / Date: Mar 12, 2012 / 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: 1.9→38.5 Å / Num. all: 22850 / Num. obs: 22413 / % possible obs: 97.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 35
Reflection shellResolution: 1.9→1.93 Å / % possible all: 95.4

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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: 1.9→38.491 Å / SU ML: 0.15 / σ(F): 1.36 / σ(I): 2 / Phase error: 19.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1832 1700 5.2 %RANDOM
Rwork0.1558 ---
all0.16 2 --
obs0.1573 19905 89.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→38.491 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1919 0 0 198 2117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072009
X-RAY DIFFRACTIONf_angle_d0.9652727
X-RAY DIFFRACTIONf_dihedral_angle_d13.664723
X-RAY DIFFRACTIONf_chiral_restr0.041291
X-RAY DIFFRACTIONf_plane_restr0.004348
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.95530.2076520.17181044X-RAY DIFFRACTION29
1.9553-2.01840.1963730.16521361X-RAY DIFFRACTION39
2.0184-2.09060.1891010.15911686X-RAY DIFFRACTION48
2.0906-2.17430.1521390.15062009X-RAY DIFFRACTION57
2.1743-2.27320.20371570.15682307X-RAY DIFFRACTION67
2.2732-2.3930.21181270.15982745X-RAY DIFFRACTION76
2.393-2.54290.22611460.16422950X-RAY DIFFRACTION83
2.5429-2.73920.19871670.16583242X-RAY DIFFRACTION91
2.7392-3.01480.21081560.16113421X-RAY DIFFRACTION96
3.0148-3.45080.18511720.15693484X-RAY DIFFRACTION98
3.4508-4.34670.15232150.13513426X-RAY DIFFRACTION97
4.3467-38.4990.17881950.16173289X-RAY DIFFRACTION94
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)
12.77992.0189-0.06984.1216-1.1011.60810.22780.2056-0.1328-0.2386-0.333-0.4440.05340.3097-0.03920.11680.02710.05560.18570.00460.168218.29531.998151.8075
21.2739-0.2459-0.42492.32130.20061.9138-0.19460.28160.3229-0.66350.0884-0.2284-0.4630.24510.03940.1902-0.05460.00090.17310.0710.197715.768145.166450.9451
35.48582.626-3.21473.2493-3.33033.5096-0.28390.8085-0.3645-1.07660.295-0.26710.51510.27730.0660.52-0.06230.06650.2978-0.00460.142411.795928.079944.8625
40.7289-0.36860.62634.43280.29512.1513-0.04720.01270.04160.31390.02880.1535-0.0795-0.02840.0340.09390.00210.0050.10140.01080.128810.656738.459660.0035
51.17710.3874-0.35981.7437-0.43662.27930.1622-0.0961-0.13450.4075-0.2687-0.62550.22370.38820.14580.1602-0.0417-0.06250.24160.02520.246220.142334.137862.3594
61.88520.95120.71562.95431.14422.1241-0.04880.11540.18150.18820.14140.423-0.1916-0.38620.00250.14070.05350.01740.20560.0420.167411.359645.787980.3469
71.1093-0.40410.0782.82340.04521.8453-0.26180.1806-0.1153-0.17840.28220.35480.5899-0.4101-0.00720.2064-0.0924-0.01750.17610.00440.163712.96830.395977.6258
83.17443.82281.22625.49782.69512.290.20260.39680.3539-0.05470.01790.2551-0.6773-0.023-0.07430.365-0.0365-0.02870.20270.00090.13417.404846.758971.991
90.38890.16110.04537.4802-2.31041.6128-0.013-0.07040.00430.41290.0194-0.4803-0.05180.2451-0.0350.2268-0.0052-0.05810.1202-0.01070.167722.615141.321985.3931
101.49110.1174-0.13372.7781-0.15371.2010.047-0.1464-0.07370.52470.06350.50860.2235-0.2739-0.04610.3804-0.01310.07360.20620.02040.086912.647436.452490.9877
111.5881.62931.28711.82030.53245.1107-0.0159-0.4715-0.25250.42-0.39060.6839-0.0679-0.90820.01270.2237-0.09180.07720.4477-0.00830.47462.984835.156983.965
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 251 through 276 )
2X-RAY DIFFRACTION2chain 'A' and (resid 277 through 306 )
3X-RAY DIFFRACTION3chain 'A' and (resid 307 through 315 )
4X-RAY DIFFRACTION4chain 'A' and (resid 316 through 348 )
5X-RAY DIFFRACTION5chain 'A' and (resid 349 through 371 )
6X-RAY DIFFRACTION6chain 'B' and (resid 251 through 272 )
7X-RAY DIFFRACTION7chain 'B' and (resid 273 through 306 )
8X-RAY DIFFRACTION8chain 'B' and (resid 307 through 315 )
9X-RAY DIFFRACTION9chain 'B' and (resid 316 through 333 )
10X-RAY DIFFRACTION10chain 'B' and (resid 334 through 363 )
11X-RAY DIFFRACTION11chain 'B' and (resid 364 through 371 )

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