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- PDB-3rjs: Crystal structure of Dynein Light Chain 8a (DLC8) from Toxoplasma... -

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Basic information

Entry
Database: PDB / ID: 3rjs
TitleCrystal structure of Dynein Light Chain 8a (DLC8) from Toxoplasma gondii at 1.5 A resolution
ComponentsDynein light chain motor protein
KeywordsMOTOR PROTEIN / Parasite / dynein light chain / LC8 / DLC8 / TgDLC8 / DYNEIN / LIGHT CHAIN / PIN / DLC1 / DYNLL1 / TRANSPORT PROTEIN
Function / homology
Function and homology information


cytoplasmic dynein complex / dynein intermediate chain binding / microtubule-based process / microtubule / cytoplasm
Similarity search - Function
Protein Inhibitor Of Neuronal Nitric Oxide Synthase / Protein Inhibitor Of Neuronal Nitric Oxide Synthase; / Dynein light chain, type 1/2, conserved site / Dynein light chain type 1 signature. / Dynein light chain, type 1/2 / Dynein light chain type 1 / Dynein light chain type 1 / Dynein light chain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsQureshi, B. / Hoehne, W. / Scheerer, P.
CitationJournal: Faseb J. / Year: 2013
Title: Dynein light chain 8a of Toxoplasma gondii, a unique conoid-localized beta-strand-swapped homodimer, is required for an efficient parasite growth.
Authors: Qureshi, B.M. / Hofmann, N.E. / Arroyo-Olarte, R.D. / Nickl, B. / Hoehne, W. / Jungblut, P.R. / Lucius, R. / Scheerer, P. / Gupta, N.
History
DepositionApr 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dynein light chain motor protein


Theoretical massNumber of molelcules
Total (without water)10,3181
Polymers10,3181
Non-polymers00
Water2,036113
1
A: Dynein light chain motor protein

A: Dynein light chain motor protein


Theoretical massNumber of molelcules
Total (without water)20,6352
Polymers20,6352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area1950 Å2
ΔGint-7 kcal/mol
Surface area8790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.025, 75.025, 85.081
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-175-

HOH

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Components

#1: Protein Dynein light chain motor protein


Mass: 10317.735 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Plasmid: pET28b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A1YTN0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.23 Å3/Da / Density % sol: 44.87 %
Crystal growTemperature: 295 K / pH: 4.6
Details: 16% polyethylene glycol 4000, 0.2 M (NH4)2SO4, 0.1 M CH3COONa, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 23, 2007 / Details: MIRRORS
RadiationMonochromator: SI-111 CRYSTAL - DOUBLE CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.5→51.62 Å / Num. obs: 14931 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.035 / Rsym value: 0.035 / Net I/σ(I): 46
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 6 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 6.2 / Rsym value: 0.252 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8_1060refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMAC5.5.0109refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CMI

1cmi


Resolution: 1.5→18.756 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU ML: 0.13 / σ(F): 1.36 / Phase error: 22.88 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2186 754 5.05 %
Rwork0.1926 --
obs0.1938 14929 99.87 %
all-14921 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.147 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å2-0.16 Å20 Å2
2---0.33 Å20 Å2
3---0.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0 Å0 Å
Luzzati d res low-0 Å
Luzzati sigma a0 Å0 Å
Refinement stepCycle: LAST / Resolution: 1.5→18.756 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms714 0 0 113 827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008761
X-RAY DIFFRACTIONf_angle_d1.151035
X-RAY DIFFRACTIONf_dihedral_angle_d13.613278
X-RAY DIFFRACTIONf_chiral_restr0.08109
X-RAY DIFFRACTIONf_plane_restr0.004137
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.61580.30041490.24162799X-RAY DIFFRACTION100
1.6158-1.77830.21351830.21482775X-RAY DIFFRACTION100
1.7783-2.03530.22191420.19932830X-RAY DIFFRACTION100
2.0353-2.56330.20781460.19462840X-RAY DIFFRACTION100
2.5633-18.75770.20991340.17762931X-RAY DIFFRACTION99
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)
11.83970.21990.29341.73430.25680.52270.1527-0.1518-0.2679-0.0245-0.04480.08280.2608-0.0004-0.03080.53620.0586-0.11520.13140.02340.055423.165914.5167-8.9376
22.62320.1486-0.27422.7461-0.35821.82070.11590.0253-0.3402-0.3372-0.11630.18390.26250.26330.02470.16090.0617-0.03650.14030.01730.148625.966915.99563.3338
31.2398-0.58940.23480.7679-0.15991.24770.27610.1113-0.329-0.3331-0.08350.22350.21810.16210.06630.16840.0259-0.07670.079-0.00760.175719.456822.3133-3.521
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 14 )
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 50 )
3X-RAY DIFFRACTION3chain 'A' and (resid 51 through 89 )

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