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- PDB-1m0i: Crystal Structure of Bacteriophage T7 Endonuclease I with a Wild-... -

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Basic information

Entry
Database: PDB / ID: 1m0i
TitleCrystal Structure of Bacteriophage T7 Endonuclease I with a Wild-Type Active Site
Componentsendodeoxyribonuclease 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 / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsHadden, J.M. / Declais, A.C. / Phillips, S.E. / Lilley, D.M.
CitationJournal: Embo J. / Year: 2002
Title: Metal ions bound at the active site of the junction-resolving enzyme T7 endonuclease I
Authors: Hadden, J.M. / Declais, A.C. / Phillips, S.E. / Lilley, D.M.
History
DepositionJun 13, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: endodeoxyribonuclease I
B: endodeoxyribonuclease I
C: endodeoxyribonuclease I
D: endodeoxyribonuclease I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5667
Polymers64,2784
Non-polymers2883
Water95553
1
A: endodeoxyribonuclease I
B: endodeoxyribonuclease I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3314
Polymers32,1392
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6420 Å2
ΔGint-76 kcal/mol
Surface area14320 Å2
MethodPISA
2
C: endodeoxyribonuclease I
D: endodeoxyribonuclease I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2353
Polymers32,1392
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-59 kcal/mol
Surface area14240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.440, 134.550, 61.390
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.

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Components

#1: Protein
endodeoxyribonuclease I / endonuclease


Mass: 16069.490 Da / Num. of mol.: 4 / Fragment: Residues 12-149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T7 (virus) / Genus: T7-like viruses / Gene: Endonuclease I / Plasmid: pET 19B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P00641, deoxyribonuclease IV
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 3.96 Å3/Da / Density % sol: 68.97 %
Crystal growTemperature: 291 K
Method: vapor diffusion, hanging drop. seeds of e65k mutant used.
pH: 7.2
Details: PEG 4000, Ammonium sulphate, Sodium chloride, Tris HCL, pH 7.2, Vapor diffusion, hanging drop. Seeds of E65K mutant used., temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 27, 2001
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.55→33.13 Å / Num. all: 34014 / Num. obs: 34014 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 49.8 Å2 / Rsym value: 0.063 / Net I/σ(I): 9.5
Reflection shellResolution: 2.55→2.68 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 4893 / Rsym value: 0.305 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M0D

1m0d


Resolution: 2.55→33.13 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1192014.82 / Data cutoff high rms absF: 1192014.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Maximum Likelhood target used as implemented in CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1686 5 %RANDOM
Rwork0.222 ---
obs0.222 33984 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.1648 Å2 / ksol: 0.357219 e/Å3
Displacement parametersBiso mean: 46.9 Å2
Baniso -1Baniso -2Baniso -3
1-5.67 Å20 Å20 Å2
2---2.71 Å20 Å2
3----2.96 Å2
Refine analyzeLuzzati coordinate error free: 0.41 Å / Luzzati sigma a free: 0.35 Å
Refinement stepCycle: LAST / Resolution: 2.55→33.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4097 0 15 53 4165
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d1.08
LS refinement shellResolution: 2.55→2.64 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.373 175 5.2 %
Rwork0.321 3175 -
obs-3175 99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMION.TOP

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