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- PDB-5cv3: C. remanei PGL-1 Dimerization Domain - Hg -

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Basic information

Entry
Database: PDB / ID: 5cv3
TitleC. remanei PGL-1 Dimerization Domain - Hg
ComponentsPutative uncharacterized protein
KeywordsHYDROLASE / guanosine endonuclease / P-granule / dimer
Function / homologyribonuclease T1 activity / ribonuclease T1 / oogenesis / RNA endonuclease activity / lyase activity / RNA binding / identical protein binding / ETHYL MERCURY ION / Guanyl-specific ribonuclease pgl-1
Function and homology information
Biological speciesCaenorhabditis remanei (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.17014754005 Å
AuthorsAoki, S.T. / Bingman, C.A. / Wickens, M. / Kimble, J.E.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)5F32HD071692 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: PGL germ granule assembly protein is a base-specific, single-stranded RNase.
Authors: Aoki, S.T. / Kershner, A.M. / Bingman, C.A. / Wickens, M. / Kimble, J.
History
DepositionJul 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2Apr 6, 2016Group: Source and taxonomy
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 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: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8293
Polymers28,3701
Non-polymers4592
Water00
1
A: Putative uncharacterized protein
hetero molecules

A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6586
Polymers56,7392
Non-polymers9194
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area3880 Å2
ΔGint-15 kcal/mol
Surface area19880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.312, 87.312, 45.059
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number152
Space group name H-MP3121
Space group name HallP312"

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Components

#1: Protein Putative uncharacterized protein


Mass: 28369.695 Da / Num. of mol.: 1 / Fragment: UNP Residues 203-464 / Mutation: deletion, residues 321-335
Source method: isolated from a genetically manipulated source
Details: codon optimized for E.coli, ordered synthetic / Source: (gene. exp.) Caenorhabditis remanei (invertebrata) / Gene: CRE_08178 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta2 / References: UniProt: E3M3V1
#2: Chemical ChemComp-EMC / ETHYL MERCURY ION


Mass: 229.651 Da / Num. of mol.: 2 / Fragment: UNP Residues 203-464 / Mutation: deletion, residues 321-335
Source method: isolated from a genetically manipulated source
Formula: C2H5Hg

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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

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 100 mM PIPES pH 6.0, 24-27% PEG 4K, 200 mM LiSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.004 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 19, 2013
RadiationMonochromator: Double-crystal Si(111) and multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.004 Å / Relative weight: 1
ReflectionResolution: 3.17→38.71 Å / Num. obs: 3523 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 49.2662019395 Å2 / Rmerge(I) obs: 0.1257 / Net I/σ(I): 28.62
Reflection shell

Diffraction-ID: 1 / Rejects: _ / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2
3.17-3.2817.30.23829.972710.78
2.75-2.813.50.5572890.785
2.8-2.85140.5492650.801
2.85-2.9114.20.5042710.814
2.91-2.9714.50.3242880.829
2.97-3.0414.40.3252710.846
3.04-3.1214.60.2922610.843
3.12-3.214.50.2362880.96
3.2-3.314.40.2212720.989
3.3-3.414.50.22651.056
3.4-3.5214.30.2012831.543
3.52-3.6614.30.1642821.408
3.66-3.8314.30.1332761.104
3.83-4.0314.10.1412791.505
4.03-4.2914.50.1182771.181
4.29-4.62140.1142871.129
4.62-5.0814.10.1192781.281
5.08-5.8113.60.1242881.262
5.81-7.3213.70.1022921.1
7.32-5012.90.0833110.756

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data collection
SCALEPACKdata scaling
SHARPphasing
PDB_EXTRACT3.15data extraction
Cootmodel building
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 3.17014754005→38.707528789 Å / SU ML: 0.363675624193 / Cross valid method: FREE R-VALUE / σ(F): 1.35527198586 / Phase error: 23.4818993775
RfactorNum. reflection% reflection
Rfree0.266615923133 630 9.77957156163 %
Rwork0.218789337419 5812 -
obs0.223656523372 6442 98.7128409439 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.2063949052 Å2
Refinement stepCycle: LAST / Resolution: 3.17014754005→38.707528789 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1904 0 0 0 1904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002790634091861944
X-RAY DIFFRACTIONf_angle_d0.9031512339762628
X-RAY DIFFRACTIONf_chiral_restr0.0297482883416302
X-RAY DIFFRACTIONf_plane_restr0.0047744288316333
X-RAY DIFFRACTIONf_dihedral_angle_d13.5400470733715
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1701-3.4890.2635353760091580.2309145876011419X-RAY DIFFRACTION96.3936430318
3.489-3.99340.2954729289321540.2463428996141443X-RAY DIFFRACTION98.5802469136
3.9934-5.02950.2708603953921650.2072900831581478X-RAY DIFFRACTION99.9391727494
5.0295-38.71040.2401706616731530.2045565126811472X-RAY DIFFRACTION99.938499385
Refinement TLS params.Method: refined / Origin x: -27.3607 Å / Origin y: -11.5855 Å / Origin z: -3.529 Å
111213212223313233
T0.0959 Å2-0.0523 Å20.052 Å2-0.1115 Å20.0517 Å2--0.093 Å2
L5.3311 °2-1.3304 °21.1308 °2-3.8489 °2-1.0137 °2--7.6232 °2
S0.1176 Å °0.1984 Å °-0.1884 Å °-0.0707 Å °-0.0402 Å °0.062 Å °1.0769 Å °0.0879 Å °0.1127 Å °
Refinement TLS groupSelection details: all

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