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- PDB-2wsh: Structure of bacteriophage T4 EndoII E118A mutant -

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Basic information

Entry
Database: PDB / ID: 2wsh
TitleStructure of bacteriophage T4 EndoII E118A mutant
ComponentsENDONUCLEASE II
KeywordsHYDROLASE / GIY-YIG / NUCLEASE
Function / homology
Function and homology information


T4 deoxyribonuclease II / degradation of host chromosome by virus / symbiont-mediated suppression of host gene expression / endonuclease activity / DNA binding / metal ion binding
Similarity search - Function
GIY-YIG endonuclease - #40 / Bacteriophage T4, DenA, endonuclease II / GIY-YIG endonuclease / GIY-YIG type nucleases (URI domain) / GIY-YIG endonuclease / GIY-YIG catalytic domain / GIY-YIG domain profile. / GIY-YIG endonuclease superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Endonuclease II
Similarity search - Component
Biological speciesENTEROBACTERIA PHAGE T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAndersson, C.E. / Lagerback, P. / Carlson, K.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structure of Bacteriophage T4 Endonuclease II Mutant E118A, a Tetrameric Giy-Yig Enzyme.
Authors: Andersson, C.E. / Lagerback, P. / Carlson, K.
History
DepositionSep 7, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENDONUCLEASE II
B: ENDONUCLEASE II
C: ENDONUCLEASE II
D: ENDONUCLEASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9677
Polymers67,6594
Non-polymers3073
Water6,720373
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-47.4 kcal/mol
Surface area27020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.417, 104.974, 57.865
Angle α, β, γ (deg.)90.00, 113.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ENDONUCLEASE II /


Mass: 16914.846 Da / Num. of mol.: 4 / Fragment: RESIDUES 9-144 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROBACTERIA PHAGE T4 (virus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS
References: UniProt: P07059, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 126 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 126 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, GLU 126 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 126 TO ALA ENGINEERED RESIDUE IN CHAIN C, GLU 126 TO ALA ENGINEERED RESIDUE IN CHAIN D, GLU 126 TO ALA
Sequence detailsTHE SUBMITTED SEQUENCE IN THIS ENTRY IS 8 AMINO ACIDS SHORTER IN THE N-TERMINUS COMPARED TO OTHER ...THE SUBMITTED SEQUENCE IN THIS ENTRY IS 8 AMINO ACIDS SHORTER IN THE N-TERMINUS COMPARED TO OTHER DATABASE ENTRIES. THE SEQUENCE IS DESCRIBED IN CARLSON ET AL. (1999) , MOL. MICROBIOLOGY, 31(5)., P 1295

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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: 2.6 Å3/Da / Density % sol: 52.9 %
Description: THE STARTING MODEL USED FOR MOLECULAR REPLACEMENT AS A PARTIAL MODEL OF ENDOII SOLVED PREVIOUSLY BY SAD.
Crystal growTemperature: 293 K / Method: microbatch / pH: 7
Details: CRYSTALS WERE GROWN AT 20 DEGREES, USING THE METHOD MICRO-BATCH UNDER OIL. 2.5 UL PROTEIN SOLUTION (3 MG/ML) WAS MIXED USING VORTEX WITH 1.75 OR 2 UL OF CRYSTALLIZATION SOLUTION CONTAINING ...Details: CRYSTALS WERE GROWN AT 20 DEGREES, USING THE METHOD MICRO-BATCH UNDER OIL. 2.5 UL PROTEIN SOLUTION (3 MG/ML) WAS MIXED USING VORTEX WITH 1.75 OR 2 UL OF CRYSTALLIZATION SOLUTION CONTAINING 30% PEG 3350, 100 MM BIS-TRIS BUFFER PH 7 AND 1% (W/V) N-OCTYL-B-D- GLUCOSIDE AND IMMEDIATELY PLACED UNDER PARAFFIN OIL. THE DROPS WERE IMMEDIATELY STREAK SEEDED AND CRYSTALS GREW IN A FEW HOURS.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 25, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.9→53.07 Å / Num. obs: 49469 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 25.89 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.6
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.6 / % possible all: 90.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→53.042 Å / SU ML: 0.29 / σ(F): 1.18 / Phase error: 25.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2471 4572 5.1 %
Rwork0.1997 --
obs0.202 49469 92.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.809 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso mean: 31.98 Å2
Baniso -1Baniso -2Baniso -3
1--2.5176 Å20 Å2-3.4359 Å2
2--0.6631 Å2-0 Å2
3---1.8545 Å2
Refinement stepCycle: LAST / Resolution: 1.9→53.042 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4295 0 19 373 4687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034492
X-RAY DIFFRACTIONf_angle_d0.7746071
X-RAY DIFFRACTIONf_dihedral_angle_d16.0471673
X-RAY DIFFRACTIONf_chiral_restr0.056681
X-RAY DIFFRACTIONf_plane_restr0.002765
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92160.34341240.34172226X-RAY DIFFRACTION72
1.9216-1.94420.34941320.34212356X-RAY DIFFRACTION77
1.9442-1.96790.37521450.31322533X-RAY DIFFRACTION82
1.9679-1.99280.29651250.29332696X-RAY DIFFRACTION85
1.9928-2.01910.27381410.2712712X-RAY DIFFRACTION90
2.0191-2.04670.26461110.28362929X-RAY DIFFRACTION92
2.0467-2.0760.29241530.27422802X-RAY DIFFRACTION92
2.076-2.10690.33631730.25742861X-RAY DIFFRACTION92
2.1069-2.13990.28291410.24582906X-RAY DIFFRACTION92
2.1399-2.17490.25841570.23472825X-RAY DIFFRACTION93
2.1749-2.21250.26321520.23992863X-RAY DIFFRACTION93
2.2125-2.25270.25451590.23672836X-RAY DIFFRACTION93
2.2527-2.2960.30041680.22692924X-RAY DIFFRACTION93
2.296-2.34290.30661450.21992853X-RAY DIFFRACTION94
2.3429-2.39380.27831350.2122948X-RAY DIFFRACTION94
2.3938-2.44950.23851550.21882897X-RAY DIFFRACTION94
2.4495-2.51080.25891640.21172894X-RAY DIFFRACTION94
2.5108-2.57860.2651450.21952873X-RAY DIFFRACTION94
2.5786-2.65450.27081580.21122964X-RAY DIFFRACTION95
2.6545-2.74020.26262010.20592929X-RAY DIFFRACTION95
2.7402-2.83810.24711790.20352923X-RAY DIFFRACTION95
2.8381-2.95180.25931740.19652894X-RAY DIFFRACTION96
2.9518-3.08610.30281590.19822986X-RAY DIFFRACTION96
3.0861-3.24880.25321450.18453024X-RAY DIFFRACTION97
3.2488-3.45230.24861590.17622977X-RAY DIFFRACTION97
3.4523-3.71880.21741450.16763045X-RAY DIFFRACTION97
3.7188-4.09290.20971570.15423021X-RAY DIFFRACTION98
4.0929-4.68480.17671420.14183036X-RAY DIFFRACTION98
4.6848-5.90110.18071790.15353037X-RAY DIFFRACTION99
5.9011-53.0630.19011490.18462959X-RAY DIFFRACTION95

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