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- PDB-1ygt: Dynein Light Chain TcTex-1 -

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Basic information

Entry
Database: PDB / ID: 1ygt
TitleDynein Light Chain TcTex-1
ComponentsCytoplasmic dynein light chainDynein
KeywordsPROTEIN TRANSPORT / Domain Swapping
Function / homology
Function and homology information


Neutrophil degranulation / dynein complex / cytoplasmic dynein complex / dynein light intermediate chain binding / retrograde axonal transport / dynein intermediate chain binding / microtubule-based movement / spermatid development / axon cytoplasm / determination of adult lifespan ...Neutrophil degranulation / dynein complex / cytoplasmic dynein complex / dynein light intermediate chain binding / retrograde axonal transport / dynein intermediate chain binding / microtubule-based movement / spermatid development / axon cytoplasm / determination of adult lifespan / disordered domain specific binding / mitotic cell cycle / microtubule / protein homodimerization activity / protein-containing complex / identical protein binding / cytoplasm
Similarity search - Function
Tctex-1 / Dynein light chain Tctex-1 like / Tctex-1-like superfamily / Tctex-1 family / Ribosomal protein S3 C-terminal domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Dynein light chain Tctex-type
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsWilliams, J.C. / Xie, H. / Hendrickson, W.A.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Crystal structure of dynein light chain TcTex-1.
Authors: Williams, J.C. / Xie, H. / Hendrickson, W.A.
History
DepositionJan 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytoplasmic dynein light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5872
Polymers12,4911
Non-polymers961
Water2,666148
1
A: Cytoplasmic dynein light chain
hetero molecules

A: Cytoplasmic dynein light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1744
Polymers24,9822
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3500 Å2
ΔGint-53 kcal/mol
Surface area11610 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)60.598, 60.598, 48.485
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-169-

HOH

21A-184-

HOH

31A-256-

HOH

DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit by the operations:y,x,-z.

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Components

#1: Protein Cytoplasmic dynein light chain / Dynein / TCTEX-1 protein homolog


Mass: 12491.021 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Dlc90F, Tctex / Plasmid: pET24d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q94524
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.245
22.245
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion9.50.1M CHES, pH 9.5, 2.4 M (NH4)2SO4 and 0.1M Li2SO4, vapor diffusion, temperature 293K
2932vapor diffusion9.50.1M CHES, pH 9.5, 2.4 M (NH4)2SO4 and 0.1M Li2SO4, vapor diffusion, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X4A10.99187, 0.97950, 0.97897, 0.96672
SYNCHROTRONNSLS X4A20.99187, 0.97950, 0.97897, 0.96672
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDSep 4, 2000
ADSC QUANTUM 42CCDSep 7, 2000
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.991871
20.97951
30.978971
40.966721
ReflectionResolution: 1.7→50 Å / Num. all: 10932 / Num. obs: 10932 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Rmerge(I) obs: 0.055 / Χ2: 1.613 / Net I/σ(I): 37.6
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 8 % / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 12 / Num. unique all: 1122 / Χ2: 1.183 / % possible all: 96.9

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 1.7 Å / D res low: 26.21 Å / FOM acentric: 0.723 / FOM centric: 0.592 / Reflection acentric: 10133 / Reflection centric: 1302
Phasing MAD set

Highest resolution: 1.76 Å

IDR cullis acentricR cullis centricR kraut acentricR kraut centricPower acentricPower centric
ISO01000.0160.11200
ANO010.95300.0210.1521.0380
ISO020.4630.5220.030.2183.5432.195
ANO020.7800.0210.1481.9280
ISO030.4470.4910.0250.1813.6142.537
ANO030.51800.0340.2453.1670
ISO040.7510.7660.0360.2571.7070.982
ANO040.6400.0390.2772.7090
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricR kraut acentricR kraut centricPower acentricPower centric
ISO016.194-26.21000.010.03400
ISO013.884-6.194000.010.05700
ISO013.028-3.884000.0110.07800
ISO012.561-3.028000.0140.13200
ISO012.26-2.561000.0160.17100
ISO012.047-2.26000.020.27300
ISO011.886-2.047000.030.48500
ISO011.757-1.886000.0460.7700
ANO016.194-26.210.85200.0120.0432.0310
ANO013.884-6.1940.91700.0110.0611.4550
ANO013.028-3.8840.93800.0140.0991.6110
ANO012.561-3.0280.93400.0160.1581.5550
ANO012.26-2.5610.96100.0220.2291.1340
ANO012.047-2.260.97100.0280.3740.8030
ANO011.886-2.0470.98200.0460.740.6490
ANO011.757-1.8860.99500.0821.3720.4070
ISO026.194-26.210.4790.5260.0410.144.5872.399
ISO023.884-6.1940.4670.5420.0250.1383.6322.13
ISO023.028-3.8840.4960.5180.0280.2093.7022.4
ISO022.561-3.0280.4770.5240.0310.2963.7242.545
ISO022.26-2.5610.4430.480.0270.2863.8572.36
ISO022.047-2.260.4180.5040.0280.3783.5961.754
ISO021.886-2.0470.4330.5140.0330.5293.3891.758
ISO021.757-1.8860.4720.5170.0450.732.872.057
ANO026.194-26.210.53700.0130.0434.7390
ANO023.884-6.1940.68200.0120.0682.5190
ANO023.028-3.8840.67400.0140.1012.9370
ANO022.561-3.0280.71400.0170.1652.5670
ANO022.26-2.5610.81700.020.2092.1140
ANO022.047-2.260.87200.0250.3451.6110
ANO021.886-2.0470.95300.0430.6881.1230
ANO021.757-1.8860.97600.0721.1570.8310
ISO036.194-26.210.4350.4750.0310.1054.7623.003
ISO033.884-6.1940.4160.4690.0180.0964.2162.906
ISO033.028-3.8840.4450.450.020.1484.2612.902
ISO032.561-3.0280.4170.4840.0230.2194.4892.94
ISO032.26-2.5610.4120.4660.0230.2424.0232.496
ISO032.047-2.260.4240.5460.0260.3453.7332.142
ISO031.886-2.0470.4880.6050.0380.5912.9642.082
ISO031.757-1.8860.5830.6510.0620.9922.221.444
ANO036.194-26.210.3300.0220.0766.4160
ANO033.884-6.1940.42700.020.1084.4030
ANO033.028-3.8840.3800.0230.1674.7760
ANO032.561-3.0280.41700.0290.2784.3620
ANO032.26-2.5610.52500.0350.3633.3280
ANO032.047-2.260.6200.0440.5812.7030
ANO031.886-2.0470.75500.0681.0732.0320
ANO031.757-1.8860.90200.1171.8751.3880
ISO046.194-26.210.7340.8030.0340.1171.9571.728
ISO043.884-6.1940.6540.6960.020.1082.1631.434
ISO043.028-3.8840.70.7420.0250.1882.2281.062
ISO042.561-3.0280.7220.7440.030.2892.7381.248
ISO042.26-2.5610.7220.7280.0330.3412.4590.742
ISO042.047-2.260.740.7670.040.531.5950.775
ISO041.886-2.0470.8210.8110.0681.0540.9960.344
ISO041.757-1.8860.8790.9110.1191.9140.5310.254
ANO046.194-26.210.33900.0180.0616.5950
ANO043.884-6.1940.4500.0160.094.4270
ANO043.028-3.8840.4500.0210.1574.2740
ANO042.561-3.0280.53400.030.2913.6990
ANO042.26-2.5610.64600.0390.4112.8310
ANO042.047-2.260.77300.0540.7222.1320
ANO041.886-2.0470.90700.0971.4991.4020
ANO041.757-1.8860.97900.1542.4720.9510
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
126.1753.53543.483X4001
218.77730.19946.979X4001
3-2.7836.39542.733X4001
413.89925.4611.455X4001
Phasing MAD shell
Resolution (Å)FOM acentricFOM centricReflection acentricReflection centric
4.74-26.210.90.768418164
3.38-4.740.8450.742793169
2.77-3.380.8540.7011063164
2.4-2.770.8420.651264170
2.15-2.40.7980.5541426176
1.96-2.150.7330.4911620167
1.82-1.960.6140.4021723156
1.7-1.820.5060.3841826136

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
SHARPphasing
DM4phasing
ARP/wARPmodel building
DENZOdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.7→6 Å / WRfactor Rfree: 0 / WRfactor Rwork: 0.21751 / FOM work R set: 0.81783 / σ(F): 0 / Stereochemistry target values: mon_lib of CCP4-refmac
RfactorNum. reflection% reflectionSelection details
Rfree0.235 501 5 %Random
Rwork0.19304 ---
all0.2 10140 --
obs0.2 10140 --
Refinement stepCycle: LAST / Resolution: 1.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms813 0 5 148 966
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_angle_deg1.7
X-RAY DIFFRACTIONo_bond_d0.014
X-RAY DIFFRACTIONo_angle_d0.033

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