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- PDB-1vk0: X-ray Structure of Gene Product from Arabidopsis Thaliana At5g06450 -

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Basic information

Entry
Database: PDB / ID: 1vk0
TitleX-ray Structure of Gene Product from Arabidopsis Thaliana At5g06450
Componentshypothetical protein
Keywordsstructural genomics / unknown function / Protein / homohexamer / Arabidopsis thaliana / At5g06450 / Protein Structure Initiative / 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 / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsWesenberg, G.E. / Smith, D.W. / Phillips Jr., G.N. / Johnson, K.A. / Bingman, C.A. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: To be published
Title: X-ray Structure of Gene Product from Arabidopsis Thaliana At5g06450
Authors: Center for Eukaryotic Structural Genomics
History
DepositionApr 12, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2004Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein
B: hypothetical protein
C: hypothetical protein
D: hypothetical protein
E: hypothetical protein
F: hypothetical protein


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 area16780 Å2
ΔGint-79 kcal/mol
Surface area44900 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)120.831, 120.831, 185.222
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
hypothetical protein /


Mass: 23243.074 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g06450 / Production host: Escherichia coli (E. coli) / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Sodium Citrate, Polyethylene glycol 2000, hepes, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9792, 0.9800, 0.9641
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 26, 2003 / Details: Bent flat mirror and sagitally bent second crystal
RadiationMonochromator: Double crystal silicon 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.981
30.96411
ReflectionResolution: 2.1→35 Å / Num. obs: 91738 / % possible obs: 100 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 29
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.1-2.148.60.4795.8199.8
2.14-2.180.3671100
2.18-2.220.3321100
2.22-2.260.3251100
2.26-2.310.2641100
2.31-2.370.2451100
2.37-2.420.211100
2.42-2.490.1751100
2.49-2.560.1481100
2.56-2.650.1371100
2.65-2.740.1211100
2.74-2.850.11100
2.85-2.980.0851100
2.98-3.140.0671100
3.14-3.330.0521100
3.33-3.590.0421100
3.59-3.950.0361100
3.95-4.520.0311100
4.52-5.690.0321100
5.69-350.0311100

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MADD res high: 3.5 Å / D res low: 20 Å / FOM : 0.78 / Reflection: 20131
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
1110.97952.15-9.76
1120.97925.46-7.51
1130.96413.96-4.16
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
140.6418.7131.894SE48.40.36
235.24172.87728.131SE26.80.3
312.99347.1089.779SE450.34
4107.18610.2520.959SE39.90.35
53.14814.19426.837SE40.60.34
673.90716.66118.707SE39.10.31
Phasing MAD shell
Resolution (Å)FOM Reflection
11.16-200.871180
7.54-11.160.871732
6.04-7.540.852157
5.18-6.040.822480
4.61-5.180.82773
4.19-4.610.773016
3.87-4.190.723297
3.61-3.870.673496
Phasing dmFOM : 0.88 / FOM acentric: 0.89 / FOM centric: 0.79 / Reflection: 20132 / Reflection acentric: 17801 / Reflection centric: 2331
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
10-19.990.970.970.92827603224
6.3-100.930.950.8527732313460
5-6.30.90.920.7833852964421
4.4-50.90.920.8134263058368
3.8-4.40.870.880.7660105454556
3.5-3.80.780.80.6137113409302

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Processing

Software
NameVersionClassificationNB
SOLVE2.02phasing
RESOLVE2.02phasing
REFMACrefmac_5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT1data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.1→34.922 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.249 / SU ML: 0.114 / SU R Cruickshank DPI: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.17
RfactorNum. reflection% reflectionSelection details
Rfree0.2326 4592 5.009 %RANDOM
Rwork0.1803 ---
all0.183 ---
obs0.1829 87085 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 30.501 Å2
Baniso -1Baniso -2Baniso -3
1--0.008 Å2-0.004 Å20 Å2
2---0.008 Å20 Å2
3---0.011 Å2
Refinement stepCycle: LAST / Resolution: 2.1→34.922 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9546 0 0 645 10191
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0219770
X-RAY DIFFRACTIONr_angle_refined_deg1.7771.94813236
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.71651188
X-RAY DIFFRACTIONr_chiral_restr0.1380.21491
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027346
X-RAY DIFFRACTIONr_nbd_refined0.210.24278
X-RAY DIFFRACTIONr_nbtor_refined0.3170.26709
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2653
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.212
X-RAY DIFFRACTIONr_mcbond_it1.98225943
X-RAY DIFFRACTIONr_mcangle_it3.56949555
X-RAY DIFFRACTIONr_scbond_it5.82663827
X-RAY DIFFRACTIONr_scangle_it8.02983681
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.15440.3033160.2356377670399.85
2.154-2.21320.2823340.261866520
2.213-2.27710.2752990.20460386337
2.277-2.34680.2733310.258276158
2.347-2.42350.2672960.19556865982
2.423-2.50810.2522900.18454785768
2.508-2.60220.2472870.17853335620
2.602-2.70790.2942710.18951145385
2.708-2.82750.2372340.17749655199
2.828-2.96450.2432520.18346784930
2.965-3.12370.2442430.19144884731
3.124-3.31150.2382310.18542644495
3.311-3.53780.2152140.17640124227
3.538-3.8180.2351940.1837433939
3.818-4.17750.1811850.14634803665
4.177-4.66220.1611890.14231113300
4.662-5.36750.2021370.15628092946
5.368-6.53540.2751240.19324092534
6.535-9.08470.2111010.18619042005
9.085-34.92150.207640.21211831247

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