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- PDB-4h9d: Crystal Structure of Mn-dependent Gme HNH nicking endonuclease fr... -

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Basic information

Entry
Database: PDB / ID: 4h9d
TitleCrystal Structure of Mn-dependent Gme HNH nicking endonuclease from Geobacter metallireducens GS-15, Northeast Structural Genomics Consortium (NESG) Target GmR87
ComponentsHNH endonuclease
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium (NESG) / nicking endonuclease
Function / homology
Function and homology information


endonuclease activity / metal ion binding
Similarity search - Function
DNA Binding (I), subunit A - #50 / HNH endonuclease 5 / HNH endonuclease / HNH nucleases / DNA Binding (I), subunit A / HNH nuclease / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HNH endonuclease family protein
Similarity search - Component
Biological speciesGeobacter metallireducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.599 Å
AuthorsKuzin, A. / Chen, Y. / Seetharaman, J. / Fang, F. / Xiao, R. / Cunningham, K. / Ma, L. / Owens, L. / Chen, C.X. / Everett, J.K. ...Kuzin, A. / Chen, Y. / Seetharaman, J. / Fang, F. / Xiao, R. / Cunningham, K. / Ma, L. / Owens, L. / Chen, C.X. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target GmR87
Authors: Kuzin, A. / Chen, Y. / Seetharaman, J. / Fang, F. / Xiao, R. / Cunningham, K. / Ma, L. / Owens, L. / Chen, C.X. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionSep 24, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionOct 10, 2012ID: 2QGP
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HNH endonuclease
B: HNH endonuclease
C: HNH endonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3697
Polymers40,1483
Non-polymers2214
Water23413
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-12 kcal/mol
Surface area13430 Å2
Unit cell
Length a, b, c (Å)40.674, 83.385, 225.116
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Detailsdimer,23.9 kD,91%

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Components

#1: Protein HNH endonuclease


Mass: 13382.799 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Geobacter metallireducens (bacteria) / Strain: GS-15 / ATCC 53774 / DSM 7210 / References: UniProt: Q39X46
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.38 Å3/Da / Density % sol: 48.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution: MG-sulfate 0.2M, PEG 8000 20% (v/v), Tris-HCl 0.1M, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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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: Apr 27, 2007 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. obs: 22466 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 10.6 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 29

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Processing

Software
NameVersionClassificationNB
PHENIXdev_988refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.599→39.097 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.37 / σ(F): 1.34 / Phase error: 29.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.251 580 4.79 %
Rwork0.2334 --
obs0.2342 12105 98.28 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.108 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--23.6698 Å20 Å2-0 Å2
2--44.1332 Å2-0 Å2
3----20.4634 Å2
Refinement stepCycle: LAST / Resolution: 2.599→39.097 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2228 0 4 13 2245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072281
X-RAY DIFFRACTIONf_angle_d1.2973073
X-RAY DIFFRACTIONf_dihedral_angle_d17.332900
X-RAY DIFFRACTIONf_chiral_restr0.094314
X-RAY DIFFRACTIONf_plane_restr0.008400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5989-2.86040.38391320.33162756X-RAY DIFFRACTION96
2.8604-3.27410.28791480.27282831X-RAY DIFFRACTION99
3.2741-4.12430.23511430.24042898X-RAY DIFFRACTION99
4.1243-39.1010.22321570.19773040X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -3.8005 Å / Origin y: -21.7128 Å / Origin z: -28.3897 Å
111213212223313233
T0.3313 Å2-0.0003 Å2-0.0252 Å2-0.3374 Å20.0637 Å2--0.359 Å2
L0.0865 °20.0028 °2-0.0703 °2-0.3864 °20.5011 °2--0.7037 °2
S-0.0047 Å °-0.1243 Å °0.227 Å °0.1406 Å °0.0427 Å °-0.0468 Å °0.3031 Å °-0.0834 Å °0.0076 Å °
Refinement TLS groupSelection details: all

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