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- PDB-5h0o: Crystal structure of deep-sea thermophilic bacteriophage GVE2 HNH... -

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Basic information

Entry
Database: PDB / ID: 5h0o
TitleCrystal structure of deep-sea thermophilic bacteriophage GVE2 HNH endonuclease with manganese ion
ComponentsHNH endonuclease
KeywordsHYDROLASE / Thermophilic bacteriophage / HNH Endonuclease / DNA nicking
Function / homologyHNH endonuclease / HNH endonuclease / HNH nucleases / HNH nuclease / endonuclease activity / nucleic acid binding / metal ion binding / : / HNH endonuclease
Function and homology information
Biological speciesGeobacillus virus E2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsZhang, L.K. / Xu, D.D. / Huang, Y.C. / Gong, Y.
CitationJournal: Sci Rep / Year: 2017
Title: Structural and functional characterization of deep-sea thermophilic bacteriophage GVE2 HNH endonuclease.
Authors: Zhang, L.K. / Xu, D.D. / Huang, Y.C. / Zhu, X.Y. / Rui, M.W. / Wan, T. / Zheng, X. / Shen, Y.L. / Chen, X.D. / Ma, K.S. / Gong, Y.
History
DepositionOct 6, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HNH endonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8092
Polymers15,7541
Non-polymers551
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.847, 66.847, 51.511
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein HNH endonuclease


Mass: 15754.135 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus virus E2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1U7Q1S7*PLUS
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE HAS BEEN DEPOSITED TO DATABASE WITH ACCESSION NUMBER YP_001522898.1.

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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: 1.83 Å3/Da / Density % sol: 32.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES, 0.2M sodium chloride, pH 7.5, 25% (w/v) polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.53→50 Å / Num. obs: 19106 / % possible obs: 99.8 % / Redundancy: 13.4 % / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 21.6
Reflection shellResolution: 1.53→1.55 Å / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11_2567: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H0M

5h0m


Resolution: 1.53→25.856 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1736 922 5.08 %Random selection
Rwork0.1405 ---
obs0.1421 18142 99.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.53→25.856 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms780 0 1 190 971
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008794
X-RAY DIFFRACTIONf_angle_d0.9611065
X-RAY DIFFRACTIONf_dihedral_angle_d20.161311
X-RAY DIFFRACTIONf_chiral_restr0.057111
X-RAY DIFFRACTIONf_plane_restr0.005138
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.61070.19511300.13742421X-RAY DIFFRACTION100
1.6107-1.71160.18611430.12262395X-RAY DIFFRACTION100
1.7116-1.84370.17161390.12052416X-RAY DIFFRACTION100
1.8437-2.02910.1771270.12852433X-RAY DIFFRACTION100
2.0291-2.32260.18611420.12652441X-RAY DIFFRACTION100
2.3226-2.92560.17461170.15212508X-RAY DIFFRACTION100
2.9256-25.85970.16041240.15132606X-RAY DIFFRACTION99

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