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- PDB-1en7: ENDONUCLEASE VII (ENDOVII) FROM PHAGE T4 -

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Basic information

Entry
Database: PDB / ID: 1en7
TitleENDONUCLEASE VII (ENDOVII) FROM PHAGE T4
ComponentsRECOMBINATION ENDONUCLEASE VII
KeywordsHYDROLASE / ENDONUCLEASE / RESOLVASE / HOLLIDAY JUNCTION / DNASE
Function / homology
Function and homology information


endonuclease activity / Hydrolases; Acting on ester bonds / metal ion binding
Similarity search - Function
T4 recombination endonuclease VII, dimerisation / T4 recombination endonuclease VII, dimerisation domain superfamily / T4 recombination endonuclease VII, dimerisation / His-Me finger endonucleases / Recombination endonuclease VII / Recombination endonuclease VII superfamily / Recombination endonuclease VII / His-Me finger endonuclease fold / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 - #10 / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 ...T4 recombination endonuclease VII, dimerisation / T4 recombination endonuclease VII, dimerisation domain superfamily / T4 recombination endonuclease VII, dimerisation / His-Me finger endonucleases / Recombination endonuclease VII / Recombination endonuclease VII superfamily / Recombination endonuclease VII / His-Me finger endonuclease fold / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 - #10 / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / His-Me finger superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Recombination endonuclease VII
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.4 Å
AuthorsRaaijmakers, H. / Vix, O. / Toro, I. / Suck, D.
CitationJournal: EMBO J. / Year: 1999
Title: X-ray structure of T4 endonuclease VII: a DNA junction resolvase with a novel fold and unusual domain-swapped dimer architecture.
Authors: Raaijmakers, H. / Vix, O. / Toro, I. / Golz, S. / Kemper, B. / Suck, D.
History
DepositionFeb 7, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Feb 7, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RECOMBINATION ENDONUCLEASE VII
B: RECOMBINATION ENDONUCLEASE VII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5997
Polymers36,3482
Non-polymers2515
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6860 Å2
ΔGint-76 kcal/mol
Surface area17630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.990, 39.450, 75.750
Angle α, β, γ (deg.)90.00, 106.20, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-437-

HOH

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Components

#1: Protein RECOMBINATION ENDONUCLEASE VII / E.C.3.1.22.4 / PROTEIN GP49


Mass: 18173.777 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ONE ZN BOUND TO CYS 23,26,58,61 OF EACH CHAIN CA LIGANDED TO ASP40 AND ASN 62
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: GP49 / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P13340, crossover junction endodeoxyribonuclease
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.8 Å3/Da / Density % sol: 57.01 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.2
Details: HANGING DROP VAPOUR DIFFUSION 1 + 1 UL OF PROTEIN SOLUTION: 16 MG/ML ENDOVII, 175 MM NACL, 20 MM MGCL2, 2 MM ZNCL2, 10 MM 2-MERCAPTO-ETHANOL, 10 % GLYCEROL, 10 MM MOPS PH6.5; WELL: 16-18% ...Details: HANGING DROP VAPOUR DIFFUSION 1 + 1 UL OF PROTEIN SOLUTION: 16 MG/ML ENDOVII, 175 MM NACL, 20 MM MGCL2, 2 MM ZNCL2, 10 MM 2-MERCAPTO-ETHANOL, 10 % GLYCEROL, 10 MM MOPS PH6.5; WELL: 16-18% PEG 5000 MME, 200 MM CACL2, 20 MM AMMONIUM SULPHATE, 10 MM 2-MERCAPTO-ETHANOL, 100 MM TRIS PH 8.2, ~ 1 MM SODIUM AZIDE, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1NaClSodium chloride11
2MgCl211
3ZnCl211
42-MERCAPTO-ETHANOL11
5GLYCEROL11
6MOPS11
7PEG 500012
8CaCl212
9(NH4)2SO412
102-MERCAPTO-ETHANOL12
11TRIS12
12NaN312
Crystal grow
*PLUS
Temperature: 4 ℃
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
116 mg/mlprotein1drop
2200 mM1reservoirCaCl2
316.5-20 %mPEG20001reservoir
4100 mMTris-HCl1reservoir
55 mM1reservoirZnCl2
65 mMammonium sulfate1reservoir
710 mMbeta-mercaptoethanol1reservoir
81
91
101
111
121

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1998 / Details: NI COATED MIRRORS
RadiationMonochromator: NI COATED MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.33→44.281 Å / Num. obs: 17578 / % possible obs: 99.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 36.81 Å2 / Rsym value: 0.06 / Net I/σ(I): 11.8
Reflection shellResolution: 2.33→2.46 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3 / Rsym value: 0.253 / % possible all: 99.3
Reflection
*PLUS
Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 99.3 % / Rmerge(I) obs: 0.253

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Processing

Software
NameVersionClassification
XDSdata scaling
SCALAdata scaling
SHARPphasing
REFMACrefinement
XDSdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SIRAS
Starting model: ENDOVII N62D MUTANT

Resolution: 2.4→10 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.308 828 5 %RANDOM
Rwork0.2395 ---
all-15326 --
obs-15326 99.5 %-
Displacement parametersBiso mean: 46.84 Å2
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2544 0 5 73 2622
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0270.03
X-RAY DIFFRACTIONp_angle_d0.0320.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0240.03
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.9552
X-RAY DIFFRACTIONp_mcangle_it2.943
X-RAY DIFFRACTIONp_scbond_it2.0922
X-RAY DIFFRACTIONp_scangle_it3.3013
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1570.15
X-RAY DIFFRACTIONp_singtor_nbd0.1770.3
X-RAY DIFFRACTIONp_multtor_nbd0.2680.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1770.3
X-RAY DIFFRACTIONp_planar_tor5.57
X-RAY DIFFRACTIONp_staggered_tor15.27
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor32.520
X-RAY DIFFRACTIONp_special_tor

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