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- PDB-1e7l: Endonuclease VII (EndoVII) N62D mutant from phage T4 -

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Basic information

Entry
Database: PDB / ID: 1e7l
TitleEndonuclease VII (EndoVII) N62D mutant from phage T4
ComponentsRECOMBINATION ENDONUCLEASE VII
KeywordsENDONUCLEASE / 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 / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 - #10 / His-Me finger endonuclease fold / 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 / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 - #10 / His-Me finger endonuclease fold / 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 / SYNCHROTRON / MIRAS / Resolution: 1.32 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 (in: No.6)
Authors: Raaijmakers, H. / Vix, O. / Toro, I. / Golz, S. / Kemper, B. / Suck, D.
History
DepositionAug 29, 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 8, 2019Group: Data collection / 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
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5May 8, 2024Group: 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
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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)37,82518
Polymers36,3502
Non-polymers1,47616
Water7,710428
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7910 Å2
ΔGint-61.9 kcal/mol
Surface area21360 Å2
MethodPQS
Unit cell
Length a, b, c (Å)58.240, 35.830, 91.930
Angle α, β, γ (deg.)90.00, 103.93, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBIOLOGICAL_UNIT: DIMERIC

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Components

#1: Protein RECOMBINATION ENDONUCLEASE VII / GP49


Mass: 18174.762 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: ONE ZN BOUND TO CYS 23,26,58,61 OF EACH CHAIN / Source: (gene. exp.) BACTERIOPHAGE T4 (virus) / Gene: GP49 / Plasmid: PET24D / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P13340, crossover junction endodeoxyribonuclease
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A, B ENGINEERED MUTATION ASN62ASP ASN62ASP IS AN INACTIVE MUTANT THE ENZYME CLEAVES DNA ...CHAIN A, B ENGINEERED MUTATION ASN62ASP ASN62ASP IS AN INACTIVE MUTANT THE ENZYME CLEAVES DNA CRUCIFORM AND Y-STRUCTURES AND HETERODUPLEX LOOPS

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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: 2.56 Å3/Da / Density % sol: 51.97 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.5
Details: HANGING DROP VAPOUR DIFFUSION DROP SIZE: 1 + 1 UL PROTEIN SOLUTION: 12 MG/ML ENDOVII, 175 MM NACL, 20 MM MGCL2, 2 MM ZNCL2, 10 MM 2-MERCAPTO-ETHANOL, 10 % GLYCEROL, 10 MM MOPS PH6 WELL: 16- ...Details: HANGING DROP VAPOUR DIFFUSION DROP SIZE: 1 + 1 UL PROTEIN SOLUTION: 12 MG/ML ENDOVII, 175 MM NACL, 20 MM MGCL2, 2 MM ZNCL2, 10 MM 2-MERCAPTO-ETHANOL, 10 % GLYCEROL, 10 MM MOPS PH6 WELL: 16-18% PEG5KMME, 200 MM AMMONIUM SULPHATE, 10 MM 2-MERCAPTO-ETHANOL, 100 MM TRIS PH 4.5, ~1 MM SODIUM AZIDE, 20 MM MAGNESIUM ACETATE
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlprotein1drop
215.5-16 %(w/v)PEG5000 MME1reservoir
3100 mMsodium acetate1reservoir
4160 mMammonium sulfate1reservoir
520 mMmagnesium acetate1reservoir
610 mMbeta-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8345
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8345 Å / Relative weight: 1
ReflectionResolution: 1.32→27 Å / Num. obs: 81068 / % possible obs: 96.5 % / Redundancy: 2.99 % / Biso Wilson estimate: 17.3 Å2 / Rsym value: 0.06 / Net I/σ(I): 9.9
Reflection shellResolution: 1.32→1.37 Å / Mean I/σ(I) obs: 2.3 / Rsym value: 0.301 / % possible all: 88.9
Reflection
*PLUS
Lowest resolution: 27 Å / Num. measured all: 243182 / Rmerge(I) obs: 0.075
Reflection shell
*PLUS
% possible obs: 88.9 % / Rmerge(I) obs: 0.301

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.32→35 Å / SU B: 0.228 / SU ML: 0.01 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.051
RfactorNum. reflection% reflectionSelection details
Rfree0.186 4207 5 %RANDOM
Rwork0.146 ---
obs0.145 83878 96.5 %-
Displacement parametersBiso mean: 30 Å2
Refinement stepCycle: LAST / Resolution: 1.32→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2544 0 72 428 3044
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d0.019
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.025
X-RAY DIFFRACTIONp_hb_or_metal_coord0.119
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.008
X-RAY DIFFRACTIONp_chiral_restr0.091
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 35 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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