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- PDB-2aja: X-Ray structure of an ankyrin repeat family protein Q5ZSV0 from L... -

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Basic information

Entry
Database: PDB / ID: 2aja
TitleX-Ray structure of an ankyrin repeat family protein Q5ZSV0 from Legionella pneumophila. Northeast Structural Genomics Consortium target LgR21.
Componentsankyrin repeat family protein
KeywordsPROTEIN BINDING / NESG / Q5ZSV0 / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologyAnkyrin repeat-containing domain / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha / Ankyrin repeat family protein
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsKuzin, A.P. / Chen, Y. / Acton, T. / Xiao, R. / Conover, K. / Ma, C. / Kellie, R. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: X-Ray structure of an ankyrin repeat family protein Q5ZSV0 from Legionella pneumophila.
Authors: Kuzin, A.P. / Chen, Y. / Acton, T. / Xiao, R. / Conover, K. / Ma, C. / Kellie, R. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionAug 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ankyrin repeat family protein
B: ankyrin repeat family protein


Theoretical massNumber of molelcules
Total (without water)86,5312
Polymers86,5312
Non-polymers00
Water2,504139
1
A: ankyrin repeat family protein


Theoretical massNumber of molelcules
Total (without water)43,2651
Polymers43,2651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ankyrin repeat family protein


Theoretical massNumber of molelcules
Total (without water)43,2651
Polymers43,2651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.610, 90.457, 118.719
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ankyrin repeat family protein


Mass: 43265.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) + Magic / References: UniProt: Q5ZSV0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M potassium thiocyanate, 20% PEG 3350, 20 mM EDTA, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 12, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 40286 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.95 % / Biso Wilson estimate: 28.2 Å2 / Rsym value: 0.07
Reflection shellResolution: 2.8→2.9 Å / Rsym value: 0.235 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→19.92 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 287667.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1848 5 %RANDOM
Rwork0.221 ---
obs0.221 37160 92.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 13.9618 Å2 / ksol: 0.27268 e/Å3
Displacement parametersBiso mean: 35.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20 Å2
2--0.66 Å20 Å2
3----0.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5505 0 0 139 5644
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20.9
X-RAY DIFFRACTIONc_improper_angle_d0.79
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.297 258 5.1 %
Rwork0.261 4781 -
obs--74.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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