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- PDB-5zhz: Crystal structure of the apurinic/apyrimidinic endonuclease IV fr... -

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Basic information

Entry
Database: PDB / ID: 5zhz
TitleCrystal structure of the apurinic/apyrimidinic endonuclease IV from Mycobacterium tuberculosis
ComponentsProbable endonuclease 4
KeywordsDNA BINDING PROTEIN / endonuclease IV / TIM fold / DNA repair / apurinic-apyrimidinic (AP)ndonuclease superfamily
Function / homology
Function and homology information


deoxyribonuclease IV / deoxyribonuclease IV (phage-T4-induced) activity / phosphoric diester hydrolase activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision repair / DNA binding / zinc ion binding
Similarity search - Function
AP endonucleases family 2 signature 1. / AP endonucleases family 2 signature 2. / AP endonuclease 2, zinc binding site / AP endonucleases family 2 signature 3. / AP endonucleases family 2 profile. / AP endonuclease 2 / AP endonuclease family 2 / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily
Similarity search - Domain/homology
Probable endonuclease 4
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsZhang, W. / Xu, Y. / Yan, M. / Li, S. / Wang, H. / Yang, H. / Zhou, W. / Rao, Z.
Funding support China, 5items
OrganizationGrant numberCountry
National Key R&D Program of China2017YFC0840300 China
MOST 973 ProjectNo. 2014CB542800 China
MOST 973 ProjectNo. 2014CBA02003 China
CAS SPR program BXDB08020200 China
National Science Foundation of China81330036 and 81520108019 China
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Crystal structure of the apurinic/apyrimidinic endonuclease IV from Mycobacterium tuberculosis.
Authors: Zhang, W. / Xu, Y. / Yan, M. / Li, S. / Wang, H. / Yang, H. / Zhou, W. / Rao, Z.
History
DepositionMar 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable endonuclease 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1937
Polymers27,7091
Non-polymers4846
Water6,918384
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-140 kcal/mol
Surface area10830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.638, 55.269, 102.939
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 Probable endonuclease 4 / Endodeoxyribonuclease IV / Endonuclease IV


Mass: 27709.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: end, nfo, Rv0670, MTCI376.04c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WQ13, deoxyribonuclease IV
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 2.56 Å3/Da / Density % sol: 50.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M Sodium acetate trihydrate pH 4.6, 2.0M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL17A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.18→50 Å / Num. obs: 96805 / % possible obs: 99.7 % / Redundancy: 13.5 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 30.6
Reflection shellResolution: 1.18→1.22 Å / Redundancy: 9.3 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 732 / Rsym value: 0.821 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QTW

1qtw


Resolution: 1.18→21.522 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.12
RfactorNum. reflection% reflection
Rfree0.1594 4529 4.94 %
Rwork0.1393 --
obs0.1403 91766 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.18→21.522 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1887 0 18 384 2289
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141933
X-RAY DIFFRACTIONf_angle_d1.4632631
X-RAY DIFFRACTIONf_dihedral_angle_d10.256692
X-RAY DIFFRACTIONf_chiral_restr0.099297
X-RAY DIFFRACTIONf_plane_restr0.009350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1793-1.19270.2931570.29872698X-RAY DIFFRACTION94
1.1927-1.20680.25211520.24572898X-RAY DIFFRACTION100
1.2068-1.22150.2411530.2182844X-RAY DIFFRACTION100
1.2215-1.2370.20851650.18372866X-RAY DIFFRACTION100
1.237-1.25320.20451370.17652910X-RAY DIFFRACTION100
1.2532-1.27040.18981450.16062881X-RAY DIFFRACTION100
1.2704-1.28850.17421490.15882920X-RAY DIFFRACTION100
1.2885-1.30780.19261440.14562833X-RAY DIFFRACTION100
1.3078-1.32820.19371580.13412877X-RAY DIFFRACTION100
1.3282-1.350.14381680.12732906X-RAY DIFFRACTION100
1.35-1.37320.17551570.12512874X-RAY DIFFRACTION100
1.3732-1.39820.15731380.12612893X-RAY DIFFRACTION100
1.3982-1.42510.1471360.12662926X-RAY DIFFRACTION100
1.4251-1.45420.15691660.12392880X-RAY DIFFRACTION100
1.4542-1.48580.14721600.12452864X-RAY DIFFRACTION100
1.4858-1.52040.1441570.1172923X-RAY DIFFRACTION100
1.5204-1.55840.14981340.11582915X-RAY DIFFRACTION100
1.5584-1.60050.14871450.11622909X-RAY DIFFRACTION100
1.6005-1.64760.15381330.11082913X-RAY DIFFRACTION100
1.6476-1.70070.13861430.11652917X-RAY DIFFRACTION100
1.7007-1.76150.14051500.12072918X-RAY DIFFRACTION100
1.7615-1.8320.15441700.12332913X-RAY DIFFRACTION100
1.832-1.91530.13691570.12722909X-RAY DIFFRACTION100
1.9153-2.01620.14451530.12952922X-RAY DIFFRACTION100
2.0162-2.14240.14531550.13132937X-RAY DIFFRACTION100
2.1424-2.30770.16981480.13462962X-RAY DIFFRACTION100
2.3077-2.53960.1721430.14072977X-RAY DIFFRACTION100
2.5396-2.90630.17731410.15162978X-RAY DIFFRACTION100
2.9063-3.65870.16071600.14123007X-RAY DIFFRACTION100
3.6587-21.5260.14691550.15663067X-RAY DIFFRACTION97

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