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- PDB-1e7d: Endonuclease VII (ENDOVII) Ffrom Phage T4 -

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Basic information

Entry
Database: PDB / ID: 1e7d
TitleEndonuclease VII (ENDOVII) Ffrom 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 speciesBACTERIOPHAGE T4 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRaaijmakers, H.C.A. / Vix, O. / Toro, I. / Suck, D.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Conformational Flexibility in T4 Endonuclease Vii Revealed by Crystallography: Implications for Substrate Binding and Cleavage
Authors: Raaijmakers, H.C.A. / Toro, I. / Birkenbihl, R. / Kemper, B. / Suck, D.
#1: Journal: 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
DepositionAug 28, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 30, 2018Group: Advisory / Data collection / Structure summary / Category: pdbx_unobs_or_zero_occ_atoms / struct / Item: _struct.title
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.5Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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

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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)36,6659
Polymers36,3482
Non-polymers3177
Water54030
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8010 Å2
ΔGint-67.8 kcal/mol
Surface area20910 Å2
MethodPQS
Unit cell
Length a, b, c (Å)60.900, 37.400, 74.000
Angle α, β, γ (deg.)90.00, 108.20, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.4964, 0.8391, -0.2226), (0.8464, 0.4109, -0.3388), (-0.1928, -0.3566, -0.9142)
Vector: 35.1893, -14.9125, 42.758)
DetailsBIOLOGICAL_UNIT: DIMERIC

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Components

#1: Protein RECOMBINATION ENDONUCLEASE VII / 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.) BACTERIOPHAGE T4 (virus) / Cellular location: CYTOPLASM / Gene: GP49 / Plasmid: PET11A / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
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.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.18 Å3/Da / Density % sol: 44.16 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.2
Details: HANGING DROP VAPOUR DIFFUSION DROP SIZE: 1 + 1 UL 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: ...Details: HANGING DROP VAPOUR DIFFUSION DROP SIZE: 1 + 1 UL 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, C.A. 1 MM SODIUM AZIDE
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
116 mg/mlprotein1drop
218 %(w/v)PEG2000 MME1reservoir
3100 mMTris1reservoir
4200 mM1reservoirCaCl2
55 mMammonium sulfate1reservoir
65 mM1reservoirZnCl2
710 mMbeta-mercaptoethanol1reservoir

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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: Jan 15, 1999 / 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: 2.8→44.281 Å / Num. obs: 8966 / % possible obs: 99.8 % / Redundancy: 3.2 % / Rsym value: 0.096 / Net I/σ(I): 7.2
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 3.2 / Rsym value: 0.283 / % possible all: 99.7
Reflection
*PLUS
Num. measured all: 28458 / Rmerge(I) obs: 0.096
Reflection shell
*PLUS
% possible obs: 99.7 % / Rmerge(I) obs: 0.283

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Processing

Software
NameClassification
REFMACrefinement
XDSdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E7L

1e7l


Resolution: 2.8→10 Å / SU B: 7.34 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.52
Details: TIGHT NCS RESTRAINTS SIMILAR TO ENTRY 1EN7, BUT IN A DIFFERENT SPACE GROUP THE ATOMS WITH ZERO OCCUPANCY ARE DISORDERED, AND THOSE WITH HALF OCCUPANCY ARE PARTLY DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.315 413 5 %RANDOM
Rwork0.245 ---
obs-8966 99.8 %-
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2544 0 7 30 2581
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.025
X-RAY DIFFRACTIONp_angle_d0.0220.028
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0310.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.12
X-RAY DIFFRACTIONp_mcangle_it3.33
X-RAY DIFFRACTIONp_scbond_it2.32
X-RAY DIFFRACTIONp_scangle_it3.63
X-RAY DIFFRACTIONp_plane_restr0.009
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd0.1850.3
X-RAY DIFFRACTIONp_multtor_nbd0.2630.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor5.915
X-RAY DIFFRACTIONp_staggered_tor18.210
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor30.420
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 27 Å / Num. reflection obs: 12364 / Rfactor obs: 0.245
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.30.028

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