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- PDB-5h0m: Crystal structure of deep-sea thermophilic bacteriophage GVE2 HNH... -

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Basic information

Entry
Database: PDB / ID: 5h0m
TitleCrystal structure of deep-sea thermophilic bacteriophage GVE2 HNH endonuclease with zinc ion
ComponentsHNH endonuclease
KeywordsHYDROLASE / Thermophilic bacteriophage / HNH Endonuclease / DNA nicking
Function / homologyHNH endonuclease / HNH endonuclease / HNH nucleases / HNH nuclease / endonuclease activity / nucleic acid binding / zinc ion binding / HNH endonuclease
Function and homology information
Biological speciesGeobacillus virus E2
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.52 Å
AuthorsZhang, L.K. / Xu, D.D. / Huang, Y.C. / Gong, Y.
Funding support China, 1items
OrganizationGrant numberCountry
China
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 5, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)15,8202
Polymers15,7541
Non-polymers651
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.264, 66.264, 51.484
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 1.79 Å3/Da / Density % sol: 31.43 %
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: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.52→50 Å / Num. obs: 18179 / % possible obs: 99.7 % / Redundancy: 13.7 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 65.2
Reflection shellResolution: 1.52→1.55 Å / Rmerge(I) obs: 0.541 / Mean I/σ(I) obs: 6.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXv1.0phasing
RefinementMethod to determine structure: SAD / Resolution: 1.52→50 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.967 / Cross valid method: FREE R-VALUE / ESU R: 0.072 / ESU R Free: 0.06
RfactorNum. reflection% reflectionSelection details
Rfree0.16809 925 5.1 %RANDOM
Rwork0.14403 ---
obs0.14521 17215 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.52→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms780 0 1 146 927
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.019794
X-RAY DIFFRACTIONr_bond_other_d00.02769
X-RAY DIFFRACTIONr_angle_refined_deg1.1281.9331065
X-RAY DIFFRACTIONr_angle_other_deg3.4631759
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.999591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54422.88945
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.81815157
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8231510
X-RAY DIFFRACTIONr_chiral_restr0.0710.2111
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02893
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02203
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.941.723367
X-RAY DIFFRACTIONr_mcbond_other0.9381.716366
X-RAY DIFFRACTIONr_mcangle_it0.9812.58457
X-RAY DIFFRACTIONr_mcangle_other0.9822.582458
X-RAY DIFFRACTIONr_scbond_it1.6862.21427
X-RAY DIFFRACTIONr_scbond_other1.6652.206427
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5783.136608
X-RAY DIFFRACTIONr_long_range_B_refined2.20617.0391074
X-RAY DIFFRACTIONr_long_range_B_other1.71415.289983
X-RAY DIFFRACTIONr_rigid_bond_restr2.99331563
X-RAY DIFFRACTIONr_sphericity_free17.996533
X-RAY DIFFRACTIONr_sphericity_bonded4.14151663
LS refinement shellResolution: 1.52→1.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.17 66 -
Rwork0.144 1231 -
obs--99.16 %

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