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Basic information

Entry
Database: PDB / ID: 5hxl
TitleStructure based function annotation of a hypothetical protein MGG_01005 related to the development of rice blast fungus
Componentsdynein light chain Tctex-1
KeywordsUNKNOWN FUNCTION / dynein light chain Tctex-1
Function / homologyDynein light chain Tctex-1 like / Tctex-1-like superfamily / Tctex-1 family / Tctex-1 family protein
Function and homology information
Biological speciesMagnaporthe oryzae (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.97 Å
AuthorsLiu, J. / Huang, J. / Li, G. / Peng, Y.
CitationJournal: Sci Rep / Year: 2018
Title: Structure based function-annotation of hypothetical protein MGG_01005 from Magnaporthe oryzae reveals it is the dynein light chain orthologue of dynlt1/3.
Authors: Li, G. / Huang, J. / Yang, J. / He, D. / Wang, C. / Qi, X. / Taylor, I.A. / Liu, J. / Peng, Y.L.
History
DepositionJan 31, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 Tctex-1


Theoretical massNumber of molelcules
Total (without water)16,8551
Polymers16,8551
Non-polymers00
Water97354
1
A: dynein light chain Tctex-1

A: dynein light chain Tctex-1


Theoretical massNumber of molelcules
Total (without water)33,7102
Polymers33,7102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_767-x+2,-x+y+1,-z+21
Buried area3370 Å2
ΔGint-24 kcal/mol
Surface area11900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.640, 72.640, 46.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-230-

HOH

21A-234-

HOH

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Components

#1: Protein dynein light chain Tctex-1


Mass: 16854.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnaporthe oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958) (fungus)
Strain: 70-15 / ATCC MYA-4617 / FGSC 8958 / Gene: MGG_01005 / Production host: Escherichia coli (E. coli) / References: UniProt: G4NCW2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.1 Å3/Da / Density % sol: 41.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 1.8M ammonium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.97→46.5 Å / Num. obs: 10166 / % possible obs: 98.5 % / Redundancy: 8.5 % / Net I/σ(I): 17.3

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.97→46.5 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.58
RfactorNum. reflection% reflection
Rfree0.2074 1019 10.02 %
Rwork0.172 --
obs0.1755 10166 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.97→46.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms952 0 0 54 1006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008987
X-RAY DIFFRACTIONf_angle_d1.0191344
X-RAY DIFFRACTIONf_dihedral_angle_d12.534345
X-RAY DIFFRACTIONf_chiral_restr0.043147
X-RAY DIFFRACTIONf_plane_restr0.004173
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9705-2.07440.23741400.18341205X-RAY DIFFRACTION93
2.0744-2.20430.19821450.16511279X-RAY DIFFRACTION97
2.2043-2.37450.22721430.16751304X-RAY DIFFRACTION100
2.3745-2.61350.21691470.17291313X-RAY DIFFRACTION100
2.6135-2.99160.19111460.17441312X-RAY DIFFRACTION100
2.9916-3.76880.21211500.16371335X-RAY DIFFRACTION100
3.7688-46.54310.19741480.17711399X-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)
12.59140.1135-2.59112.60850.5473.17930.3181-0.0460.4740.05960.2956-0.59810.30860.3798-0.53130.28580.0497-0.01590.25670.01180.247316.8531113.590153.5322
21.9094-0.2622-0.90956.60243.10513.7367-0.1245-0.1057-0.45311.14170.16310.00920.59950.2376-0.0380.25430.0299-0.03320.17160.01930.193210.718194.952161.665
34.1182-3.6137-2.72554.80664.79575.3311-0.09510.0294-0.2054-0.0881-0.06830.46880.0353-0.09710.18430.1509-0.0096-0.01280.13880.03940.12893.551497.09455.6327
44.017-4.71082.13076.0247-2.83271.5014-1.0089-0.8321-0.09541.2050.89340.15510.2562-0.55640.02680.34050.07980.05270.2753-0.02440.32-2.8717120.514460.3696
52.3001-2.84380.60665.6701-0.6380.16370.17560.0771-0.0803-0.163-0.1657-0.61290.09370.0574-0.030.1420.00460.04130.123-0.00280.19079.1048102.791851.3263
61.09781.1683-0.71843.1924-3.41454.07150.0962-0.2258-1.11380.0977-0.03230.15130.42650.0509-0.10680.1873-0.0058-0.09630.2050.04090.472621.375499.580847.2267
73.0943-0.85260.60252.9283.9386.6807-0.0462-0.1410.18590.11740.07020.1334-0.49780.1684-0.0940.2173-0.01420.07060.1351-0.01180.181813.0434120.691347.9552
84.9892-1.11671.75184.2497-4.99016.28810.0404-0.0082-0.360.2099-0.1054-0.95070.30790.26930.050.20230.0297-0.00650.1296-0.00630.126715.8476103.974756.6231
95.7741-0.5227-1.02121.70051.82496.1126-0.6774-1.5468-0.291.6610.2322-2.09410.82361.47990.37620.67040.0747-0.19270.53350.13280.992519.916587.174460.2121
103.516-3.27761.38435.0705-3.12092.78080.16030.1194-0.4345-0.1499-0.18520.0669-0.0030.06350.02560.1254-0.027-0.00760.1536-0.02990.174111.4227105.810552.9298
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 10 )
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 33 )
3X-RAY DIFFRACTION3chain 'A' and (resid 34 through 55 )
4X-RAY DIFFRACTION4chain 'A' and (resid 56 through 66 )
5X-RAY DIFFRACTION5chain 'A' and (resid 67 through 77 )
6X-RAY DIFFRACTION6chain 'A' and (resid 78 through 120 )
7X-RAY DIFFRACTION7chain 'A' and (resid 121 through 127 )
8X-RAY DIFFRACTION8chain 'A' and (resid 128 through 134 )
9X-RAY DIFFRACTION9chain 'A' and (resid 135 through 141 )
10X-RAY DIFFRACTION10chain 'A' and (resid 142 through 153 )

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