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- PDB-3tai: Crystal structure of NurA -

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Basic information

Entry
Database: PDB / ID: 3tai
TitleCrystal structure of NurA
ComponentsDNA double-strand break repair protein nurA
KeywordsHYDROLASE / Recombination
Function / homology
Function and homology information


exonuclease activity / endonuclease activity / Hydrolases; Acting on ester bonds / DNA repair / metal ion binding
Similarity search - Function
DNA double-strand break repair nuclease NurA-like / NurA domain / NurA domain / NurA
Similarity search - Domain/homology
DNA double-strand break repair nuclease NurA
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.82 Å
AuthorsChae, J. / Kim, Y.C. / Cho, Y.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Crystal structure of the NurA-dAMP-Mn2+ complex
Authors: Chae, J. / Kim, Y.C. / Cho, Y.
History
DepositionAug 4, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA double-strand break repair protein nurA
B: DNA double-strand break repair protein nurA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,2019
Polymers108,5562
Non-polymers6457
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8990 Å2
ΔGint-32 kcal/mol
Surface area38180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.000, 114.210, 122.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA double-strand break repair protein nurA / Putative uncharacterized protein


Mass: 54278.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF1168 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U1N8
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.09 Å3/Da / Density % sol: 41.17 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 21% PEG 400, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.97947 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 13, 2010
RadiationMonochromator: Si 4-crystal channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 42436 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 75.29 Å2
Reflection shellResolution: 2.5→2.54 Å / % possible all: 99.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.autosol: 1.7_650)model building
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7_650phasing
RefinementMethod to determine structure: SAD / Resolution: 2.82→29.552 Å / SU ML: 0.33 / σ(F): 0 / Phase error: 31.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2755 2006 4.95 %RANDOM
Rwork0.2018 ---
obs0.2056 40529 95.71 %-
all-42337 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.588 Å2 / ksol: 0.299 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.8652 Å20 Å2-0 Å2
2--6.1992 Å2-0 Å2
3----2.334 Å2
Refinement stepCycle: LAST / Resolution: 2.82→29.552 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6941 0 42 19 7002
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017092
X-RAY DIFFRACTIONf_angle_d1.4259556
X-RAY DIFFRACTIONf_dihedral_angle_d17.3032739
X-RAY DIFFRACTIONf_chiral_restr0.091098
X-RAY DIFFRACTIONf_plane_restr0.0111197
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.82-2.89050.41071100.3016245285
2.8905-2.96860.36461290.2908253188
2.9686-3.05580.43671340.2965259590
3.0558-3.15440.35361170.2721267192
3.1544-3.2670.37991450.237273295
3.267-3.39760.25371650.219274497
3.3976-3.5520.31911580.2059281498
3.552-3.73890.28511360.2024283399
3.7389-3.97260.28321410.1899287299
3.9726-4.27850.23251820.1715279999
4.2785-4.70760.24341560.1639286799
4.7076-5.38520.26561390.17752882100
5.3852-6.77130.29481490.22882849100
6.7713-29.55360.23391450.18882882100
Refinement TLS params.Method: refined / Origin x: 56.317 Å / Origin y: 64.8981 Å / Origin z: 91.7156 Å
111213212223313233
T0.2504 Å20.0347 Å2-0.0189 Å2-0.1826 Å2-0.0432 Å2--0.3083 Å2
L0.9842 °20.3337 °20.1257 °2-0.3171 °2-0.0501 °2--1.5116 °2
S-0.044 Å °-0.1242 Å °0.1977 Å °-0.0232 Å °-0.0948 Å °-0.0116 Å °-0.1077 Å °0.0501 Å °0.0569 Å °
Refinement TLS groupSelection details: all

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