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- PDB-2r7f: Crystal structure of ribonuclease II family protein from Deinococ... -

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Basic information

Entry
Database: PDB / ID: 2r7f
TitleCrystal structure of ribonuclease II family protein from Deinococcus radiodurans, hexagonal crystal form. NorthEast Structural Genomics target DrR63
ComponentsRibonuclease II family protein
KeywordsHYDROLASE / Ribonuclease II family protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


3'-5'-RNA exonuclease activity / RNA binding / metal ion binding
Similarity search - Function
RNase II-type exonuclease, C-terminal S1 domain / RNase II-type exonuclease C-terminal S1 domain / DNA polymerase; domain 6 / Ribonuclease II/R / RNB domain / RNB / Rhinovirus 14, subunit 4 / Nucleic acid-binding proteins / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Few Secondary Structures ...RNase II-type exonuclease, C-terminal S1 domain / RNase II-type exonuclease C-terminal S1 domain / DNA polymerase; domain 6 / Ribonuclease II/R / RNB domain / RNB / Rhinovirus 14, subunit 4 / Nucleic acid-binding proteins / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Few Secondary Structures / Irregular / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Ribonuclease II family protein
Similarity search - Component
Biological speciesDeinococcus radiodurans R1 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsSeetharaman, J. / Neely, H. / Forouhar, F. / Wang, D. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Xia, R. / Liu, J. / Baran, M.C. ...Seetharaman, J. / Neely, H. / Forouhar, F. / Wang, D. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Xia, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Mol.Biol. / Year: 2012
Title: The Structure and Enzymatic Properties of a Novel RNase II Family Enzyme from Deinococcus radiodurans.
Authors: Schmier, B.J. / Seetharaman, J. / Deutscher, M.P. / Hunt, J.F. / Malhotra, A.
History
DepositionSep 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 11, 2012Group: Database references
Revision 1.3Feb 1, 2012Group: Database references
Revision 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease II family protein


Theoretical massNumber of molelcules
Total (without water)52,2021
Polymers52,2021
Non-polymers00
Water2,576143
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.143, 92.143, 118.562
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Ribonuclease II family protein


Mass: 52201.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans R1 (radioresistant)
Species: Deinococcus radiodurans / Strain: R1, DSM 20539, IFO 15346, LMG 4051 / Gene: DR_0020 / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9RYD0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.78 Å3/Da / Density % sol: 55.81 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Tri-Ammonium citrate, Bis-Tris propane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 34287 / Num. obs: 34287 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 36.3 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.068 / Net I/σ(I): 13.3
Reflection shellResolution: 2.7→2.79 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 12.1 / Num. unique all: 3393 / Rsym value: 0.411 / % possible all: 96.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→30.16 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 74753.87 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: The Friedel pairs were used for phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.244 705 2.5 %RANDOM
Rwork0.201 ---
obs0.201 28452 91.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.4868 Å2 / ksol: 0.355713 e/Å3
Displacement parametersBiso mean: 34.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.42 Å27.21 Å20 Å2
2---2.42 Å20 Å2
3---4.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.7→30.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3545 0 0 143 3688
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d2.04
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.334 86 2.1 %
Rwork0.27 3924 -
obs--77.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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