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- PDB-2q3s: Ensemble refinement of the protein crystal structure of gene prod... -

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Basic information

Entry
Database: PDB / ID: 2q3s
TitleEnsemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At5g06450
ComponentsProtein At5g06450
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Ensemble Refinement / Refinement Methodology Development / Protein / homohexamer / At5g06450 / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


exoribonuclease II / exoribonuclease II activity / RISC complex binding / plant-type vacuole / single-stranded DNA 3'-5' DNA exonuclease activity / regulatory ncRNA-mediated gene silencing / positive regulation of miRNA metabolic process / : / nucleic acid binding / cytoplasm
Similarity search - Function
Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein RISC-INTERACTING CLEARING 3'-5' EXORIBONUCLEASE 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / Re-refinement using ensemble model / Resolution: 2.1 Å
AuthorsLevin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Structure / Year: 2007
Title: Ensemble refinement of protein crystal structures: validation and application.
Authors: Levin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips, G.N.
History
DepositionMay 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 10, 2011Group: Other
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein At5g06450
B: Protein At5g06450
C: Protein At5g06450
D: Protein At5g06450
E: Protein At5g06450
F: Protein At5g06450


Theoretical massNumber of molelcules
Total (without water)139,4586
Polymers139,4586
Non-polymers00
Water11,620645
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16730 Å2
ΔGint-84 kcal/mol
Surface area45020 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)120.831, 120.831, 185.222
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Number of models8

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Components

#1: Protein
Protein At5g06450


Mass: 23243.074 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: cv. Columbia / Gene: At5g06450, MHF15.3 / Plasmid: PVP13 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q9FNG3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 645 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.04 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 1VK0.

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT2data extraction
CNS1.1phasing
RefinementMethod to determine structure: Re-refinement using ensemble model
Starting model: PDB entry 1VK0

1vk0


Resolution: 2.1→34.88 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3994599 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: maximum likelihood using amplitudes
Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 1vk0 and the first data set in the deposited structure factor file for 1vk0 ...Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 1vk0 and the first data set in the deposited structure factor file for 1vk0 along with the R-free set defined therein. The coordinates were generated by an automated protocol from an initial model consisting of 8 identical copies of the protein and non-water hetero-atoms assigned fractional occupancies adding up to one, and a single copy of the solvent molecules. Refinement was carried out with all the conformers present simultaneously and with the potential energy terms corresponding to interactions between the different conformers excluded. The helix and sheet records were calculated using coordinates from the first conformer only. The structure visualization program PYMOL is well-suited for directly viewing the ensemble model presented in this PDB file.
RfactorNum. reflection% reflectionSelection details
Rfree0.221 4592 5 %RANDOM
Rwork0.155 ---
obs0.155 91677 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.315 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso mean: 25.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å-0.04 Å
Refinement stepCycle: LAST / Resolution: 2.1→34.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9546 0 0 645 10191
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d1.15
X-RAY DIFFRACTIONc_mcbond_it1.561.5
X-RAY DIFFRACTIONc_mcangle_it2.292
X-RAY DIFFRACTIONc_scbond_it2.342
X-RAY DIFFRACTIONc_scangle_it3.112.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.1-2.230.2477344.90.147143530.009151271508799.7
2.23-2.40.22476450.136144000.008151821516499.9
2.4-2.650.2457755.10.141143750.0091515415150100
2.65-3.030.2447384.80.159144910.0091523115229100
3.03-3.810.2377795.10.179145340.008153211531399.9
3.81-34.880.1878025.10.147149320.0071573515734100
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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