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- PDB-1fzr: CRYSTAL STRUCTURE OF BACTERIOPHAGE T7 ENDONUCLEASE I -

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Basic information

Entry
Database: PDB / ID: 1fzr
TitleCRYSTAL STRUCTURE OF BACTERIOPHAGE T7 ENDONUCLEASE I
ComponentsENDONUCLEASE I
KeywordsHYDROLASE / Holliday junction resolvase / Homodimer / Domain swapped / Composite active site
Function / homology
Function and homology information


degradation of host chromosome by virus / deoxyribonuclease IV / deoxyribonuclease IV (phage-T4-induced) activity / double-stranded DNA endonuclease activity / crossover junction DNA endonuclease activity / DNA integration / symbiont-mediated suppression of host gene expression / DNA binding
Similarity search - Function
Bacteriophage T7, Gp3, endodeoxynuclease I / Phage endonuclease I / Restriction Endonuclease - #30 / Restriction Endonuclease / Restriction endonuclease type II-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEnterobacteria phage T7 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsHadden, J.M. / Convery, M.A. / Declais, A.C. / Lilley, D.M.J. / Phillips, S.E.V.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Crystal structure of the Holliday junction resolving enzyme T7 endonuclease I.
Authors: Hadden, J.M. / Convery, M.A. / Declais, A.C. / Lilley, D.M. / Phillips, S.E.
History
DepositionOct 4, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_sheet.number_strands
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENDONUCLEASE I
B: ENDONUCLEASE I
C: ENDONUCLEASE I
D: ENDONUCLEASE I


Theoretical massNumber of molelcules
Total (without water)64,2784
Polymers64,2784
Non-polymers00
Water8,737485
1
A: ENDONUCLEASE I
B: ENDONUCLEASE I


Theoretical massNumber of molelcules
Total (without water)32,1392
Polymers32,1392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-43 kcal/mol
Surface area14470 Å2
MethodPISA
2
C: ENDONUCLEASE I
D: ENDONUCLEASE I


Theoretical massNumber of molelcules
Total (without water)32,1392
Polymers32,1392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-45 kcal/mol
Surface area14490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.660, 135.190, 61.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsEndonuclease I is active as a homodimer. There are 2 homodimers in the asymmetric unit. Chains A and B form one homodimer. / Endonuclease I is active as a homodimer. There are 2 homodimers in the asymmetric unit. Chains C and D form the other homodimer

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Components

#1: Protein
ENDONUCLEASE I / ENDODEOXYRIBONUCLEASE I


Mass: 16069.557 Da / Num. of mol.: 4 / Fragment: RESIDUES 12-149 / Mutation: E65K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T7 (virus) / Genus: T7-like viruses / Plasmid: PET19B / Production host: Escherichia coli (E. coli) / References: UniProt: P00641, deoxyribonuclease IV
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
1469.26
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2911vapor diffusion, hanging drop7.2PEG 4000, ammonium sulphate, sodium chloride, Tris.HCL, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
2912also used cross seeding using non-semet substituted proteinPEG 4000, ammonium sulphate, sodium chloride, Tris.HCL, Also used cross seeding using non-Semet substituted protein, temperature 291K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14 mg/mlprotein1drop
220 mMTris-HCl1drop
350 mM1dropNaCl
417-19 %(w/v)PEG40001reservoir
5100 mMammonium sulfate1reservoir
6100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.933
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 12, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.1→29.88 Å / Num. all: 229942 / Num. obs: 61020 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 38.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.7
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.488 / Num. unique all: 8761 / % possible all: 99.6
Reflection
*PLUS
Num. measured all: 229942 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 99.6 % / Mean I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS0.9refinement
MOSFLMdata reduction
CCP4(TRUNCATE)data scaling
RefinementResolution: 2.1→28.81 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2004036.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Maximum likelihood target used. The structure was solved using the Semet MAD technique at 3.0A, an optimised anomalous data set at 2.5A and a native data set at 2.1A. See paper for details.
RfactorNum. reflection% reflectionSelection details
Rfree0.235 6061 10 %RANDOM
Rwork0.198 ---
all0.202 60471 --
obs0.202 60471 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 72.05 Å2 / ksol: 0.353 e/Å3
Displacement parametersBiso mean: 54.1 Å2
Baniso -1Baniso -2Baniso -3
1-7.64 Å20 Å20 Å2
2---2.28 Å20 Å2
3----5.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-29 Å
Luzzati sigma a0.25 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.1→28.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4217 0 0 485 4702
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d1.08
X-RAY DIFFRACTIONc_mcbond_it4.721.5
X-RAY DIFFRACTIONc_mcangle_it5.62
X-RAY DIFFRACTIONc_scbond_it7.582
X-RAY DIFFRACTIONc_scangle_it9.582.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.324 960 10.1 %
Rwork0.284 8545 -
obs--94.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 54.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.08
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.324 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.284

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