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- PDB-1m0d: Crystal Structure of Bacteriophage T7 Endonuclease I with a Wild-... -

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Basic information

Entry
Database: PDB / ID: 1m0d
TitleCrystal Structure of Bacteriophage T7 Endonuclease I with a Wild-Type Active Site and Bound Manganese Ions
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 / crossover junction DNA endonuclease activity / double-stranded 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: 1.9 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 12, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)65,10216
Polymers64,2784
Non-polymers82412
Water8,521473
1
A: Endodeoxyribonuclease I
B: Endodeoxyribonuclease I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5518
Polymers32,1392
Non-polymers4126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7040 Å2
ΔGint-103 kcal/mol
Surface area14200 Å2
MethodPISA
2
C: Endodeoxyribonuclease I
D: Endodeoxyribonuclease I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5518
Polymers32,1392
Non-polymers4126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-102 kcal/mol
Surface area13970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.810, 133.960, 61.460
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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 473 / 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: 68.96 %
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
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris-HCl1droppH8.0
250 mM1dropNaCl
34 mg/mlprotein1drop
417-19 %PEG40001reservoir
5100 mMammonium sulfate1reservoir
6100 mMTris-HCl1reservoirpH7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 25, 2001
RadiationMonochromator: Diamond (111), Ge (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.9→25.55 Å / Num. all: 81257 / Num. obs: 81257 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rsym value: 0.058 / Net I/σ(I): 7.6
Reflection shellResolution: 1.9→1.99 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 11678 / Rsym value: 0.36 / % possible all: 99.4
Reflection
*PLUS
Num. measured all: 419157 / Rmerge(I) obs: 0.085
Reflection shell
*PLUS
% possible obs: 99.4 %

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Processing

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

1fzr


Resolution: 1.9→24.8 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1676632.53 / Data cutoff high rms absF: 1676632.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Maximum Likelihood target used as implemented in CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.234 4083 5 %RANDOM
Rwork0.21 ---
obs0.21 81189 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.3311 Å2 / ksol: 0.380933 e/Å3
Displacement parametersBiso mean: 40.4 Å2
Baniso -1Baniso -2Baniso -3
1-4.63 Å20 Å20 Å2
2---0.49 Å20 Å2
3----4.14 Å2
Refine analyzeLuzzati coordinate error free: 0.26 Å / Luzzati sigma a free: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.9→24.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4129 0 28 473 4630
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d0.9
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.285 400 5 %
Rwork0.259 7559 -
obs-7559 99 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 1.9 Å / % reflection Rfree: 5 % / Rfactor obs: 0.21 / Rfactor Rfree: 0.234 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.38
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9
LS refinement shell
*PLUS
Rfactor Rfree: 0.285 / Rfactor Rwork: 0.259

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