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- PDB-4mu6: Crystal Structure of the N-terminal domain of Effector Protein Le... -

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Basic information

Entry
Database: PDB / ID: 4mu6
TitleCrystal Structure of the N-terminal domain of Effector Protein LegC3 from Legionella pneumophila
ComponentsKinectin 1 (Kinesin receptor)
KeywordsUNKNOWN FUNCTION / structural genomics
Function / homologyLegC3 N-terminal, Legionellaceae / LegC3 N-terminal coiled-coil domain / membrane / Kinectin 1 (Kinesin receptor)
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.082 Å
AuthorsYao, D. / Cherney, M. / Cygler, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure of the N-terminal domain of the effector protein LegC3 from Legionella pneumophila.
Authors: Yao, D. / Cherney, M. / Cygler, M.
History
DepositionSep 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Sep 24, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Nov 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

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Assembly

Deposited unit
A: Kinectin 1 (Kinesin receptor)


Theoretical massNumber of molelcules
Total (without water)42,7891
Polymers42,7891
Non-polymers00
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.874, 150.246, 24.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Kinectin 1 (Kinesin receptor)


Mass: 42789.262 Da / Num. of mol.: 1 / Fragment: UNP residues 1-367
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Strain: Philadelphia 1 / Gene: legC3, lpg1701 / Plasmid: pZL922 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q5ZUU1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.32 Å3/Da / Density % sol: 46.91 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG3300, 0.1MTris-HCl pH8.5, 0.2M tri-potassium citrate, 30mM Di-ammonium hydrogen phosphate, vapor diffusion, hanging drop, temperature 295K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97887 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97887 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. obs: 23598 / % possible obs: 94.9 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.144 / Net I/σ(I): 7.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.08-2.1810.30.932184.9
2.18-2.2690.789186.1
2.26-2.379.80.58191.4
2.37-2.4910.30.477193.9
2.49-2.65110.33199
2.65-2.8511.20.279197
2.85-3.14120.178198.5
3.14-3.5912.70.127199.1
3.59-4.5212.70.093198.9
4.52-5013.10.07199.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.082→45.499 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.27 / σ(F): 1.33 / Phase error: 29.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2753 1624 8.69 %
Rwork0.2075 --
obs0.2133 22962 91.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.082→45.499 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2250 0 0 195 2445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072278
X-RAY DIFFRACTIONf_angle_d0.9853052
X-RAY DIFFRACTIONf_dihedral_angle_d14.721901
X-RAY DIFFRACTIONf_chiral_restr0.069349
X-RAY DIFFRACTIONf_plane_restr0.004389
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.082-2.1340.30041040.24261091X-RAY DIFFRACTION69
2.134-2.19170.32881270.27881334X-RAY DIFFRACTION82
2.1917-2.25620.50681140.36211200X-RAY DIFFRACTION76
2.2562-2.3290.33371350.27221412X-RAY DIFFRACTION89
2.329-2.41220.32521400.2371466X-RAY DIFFRACTION90
2.4122-2.50880.33231380.22731462X-RAY DIFFRACTION93
2.5088-2.6230.29361500.21671568X-RAY DIFFRACTION97
2.623-2.76130.27271450.2261528X-RAY DIFFRACTION94
2.7613-2.93420.31821530.22731605X-RAY DIFFRACTION99
2.9342-3.16070.31231500.21851573X-RAY DIFFRACTION97
3.1607-3.47870.26741580.20921661X-RAY DIFFRACTION99
3.4787-3.98180.26651550.18151620X-RAY DIFFRACTION98
3.9818-5.01570.19491580.14971655X-RAY DIFFRACTION99
5.0157-45.50990.221690.18441791X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 5.9159 Å / Origin y: 36.0438 Å / Origin z: 13.7062 Å
111213212223313233
T0.2601 Å2-0.0498 Å20.0019 Å2-0.2137 Å20.0202 Å2--0.1904 Å2
L0.1316 °20.0466 °2-0.0644 °2--0.0116 °2-0.1015 °2---0.0047 °2
S-0.0348 Å °0.0511 Å °-0.0167 Å °-0.0173 Å °0.0816 Å °0.0143 Å °-0.0067 Å °-0.04 Å °-0 Å °
Refinement TLS groupSelection details: all

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