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- PDB-5w4d: C. japonica N-domain, Selenomethionine mutant -

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Basic information

Entry
Database: PDB / ID: 5w4d
TitleC. japonica N-domain, Selenomethionine mutant
ComponentsP-granule scaffold protein
KeywordsRNA BINDING PROTEIN / P-granule scaffold protein
Function / homologyIMIDAZOLE / DI(HYDROXYETHYL)ETHER / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / TRIETHYLENE GLYCOL / Uncharacterized protein / :
Function and homology information
Biological speciesCaenorhabditis japonica (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.599 Å
AuthorsAoki, S.T. / Bingman, C.A. / Kimble, J.
CitationJournal: Nat Commun / Year: 2021
Title: C. elegans germ granules require both assembly and localized regulators for mRNA repression.
Authors: Aoki, S.T. / Lynch, T.R. / Crittenden, S.L. / Bingman, C.A. / Wickens, M. / Kimble, J.
History
DepositionJun 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: P-granule scaffold protein
B: P-granule scaffold protein
C: P-granule scaffold protein
D: P-granule scaffold protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,30927
Polymers98,0084
Non-polymers2,30123
Water11,836657
1
A: P-granule scaffold protein
C: P-granule scaffold protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,30415
Polymers49,0042
Non-polymers1,30013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: P-granule scaffold protein
D: P-granule scaffold protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,00512
Polymers49,0042
Non-polymers1,00110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.300, 94.800, 72.500
Angle α, β, γ (deg.)90.00, 91.40, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-557-

HOH

21C-533-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
P-granule scaffold protein


Mass: 24501.994 Da / Num. of mol.: 4 / Fragment: N-domain (UNP residues 1-216) / Mutation: I63M, I212M
Source method: isolated from a genetically manipulated source
Details: codon optimized version / Source: (gene. exp.) Caenorhabditis japonica (invertebrata) / Tissue: germline / Plasmid: pET21a / Details (production host): IPTG inducible / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Variant (production host): Rosetta2 / References: UniProt: H2W791, UniProt: A0A2H2IB89*PLUS

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Non-polymers , 8 types, 680 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H5N2
#8: Chemical ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE


Mass: 178.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 657 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.34 Å3/Da / Density % sol: 47.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Imidazole pH 7.5, 40-45% PEG 400, 1 mM TCEP pH 7.4
PH range: 7.5-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 7, 2016 / Details: MD2 Micro Diffractometer
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.599→48.466 Å / Num. obs: 227476 / % possible obs: 97.06 % / Redundancy: 7.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.0469 / Rpim(I) all: 0.01827 / Net I/σ(I): 24.44
Reflection shellResolution: 1.599→1.656 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.8775 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 11239 / CC1/2: 0.74 / Rpim(I) all: 0.348 / % possible all: 95.16

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.599→48.466 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.54
RfactorNum. reflection% reflectionSelection details
Rfree0.1898 2817 1.24 %random selection
Rwork0.1574 ---
obs0.1577 227474 96.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.599→48.466 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6683 0 153 657 7493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017015
X-RAY DIFFRACTIONf_angle_d1.0049421
X-RAY DIFFRACTIONf_dihedral_angle_d10.1174337
X-RAY DIFFRACTIONf_chiral_restr0.051074
X-RAY DIFFRACTIONf_plane_restr0.0061222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5989-1.62650.2831420.274410787X-RAY DIFFRACTION94
1.6265-1.65610.25751130.244611146X-RAY DIFFRACTION96
1.6561-1.68790.26121540.230811155X-RAY DIFFRACTION96
1.6879-1.72240.22791390.214311111X-RAY DIFFRACTION96
1.7224-1.75980.25871400.202311101X-RAY DIFFRACTION96
1.7598-1.80080.22881440.189911233X-RAY DIFFRACTION97
1.8008-1.84580.19291440.17211207X-RAY DIFFRACTION97
1.8458-1.89570.19061340.166411271X-RAY DIFFRACTION97
1.8957-1.95150.19681500.155711189X-RAY DIFFRACTION97
1.9515-2.01450.18141480.147911294X-RAY DIFFRACTION97
2.0145-2.08650.1831400.144911268X-RAY DIFFRACTION97
2.0865-2.170.16121500.135811264X-RAY DIFFRACTION98
2.17-2.26880.21181320.133911315X-RAY DIFFRACTION98
2.2688-2.38840.17821440.135511363X-RAY DIFFRACTION98
2.3884-2.5380.15141480.135511392X-RAY DIFFRACTION98
2.538-2.7340.18281300.138311320X-RAY DIFFRACTION98
2.734-3.00910.1551430.145311417X-RAY DIFFRACTION98
3.0091-3.44440.2171480.156211344X-RAY DIFFRACTION98
3.4444-4.33910.16541420.145111359X-RAY DIFFRACTION98
4.3391-48.48780.20631320.180911121X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: -33.8159 Å / Origin y: -13.2379 Å / Origin z: 17.9354 Å
111213212223313233
T0.1298 Å2-0.0022 Å20.0006 Å2-0.1252 Å2-0.0064 Å2--0.1437 Å2
L0.1987 °2-0.0452 °20.0045 °2-0.3141 °2-0.0221 °2--0.3272 °2
S0.0074 Å °-0.0033 Å °0.0362 Å °0.0041 Å °-0.0046 Å °-0.0439 Å °-0.0068 Å °-0.005 Å °-0 Å °
Refinement TLS groupSelection details: all

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