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- PDB-2pfj: Crystal Structure of T7 Endo I resolvase in complex with a Hollid... -

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Basic information

Entry
Database: PDB / ID: 2pfj
TitleCrystal Structure of T7 Endo I resolvase in complex with a Holliday Junction
Components
  • (27-MER) x 2
  • Endodeoxyribonuclease 1
KeywordsHYDROLASE/DNA / hydrolase / Holliday junction resolvase / Homodimer / Domain Swapped / Composite active site / HYDROLASE-DNA COMPLEX
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
DNA / DNA (> 10) / Endonuclease I
Similarity search - Component
Biological speciesEnterobacteria phage T7 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsHadden, J.M. / Declais, A.C. / Carr, S.B. / Lilley, D.M. / Phillips, S.E.
CitationJournal: Nature / Year: 2007
Title: The structural basis of Holliday junction resolution by T7 endonuclease I.
Authors: Hadden, J.M. / Declais, A.C. / Carr, S.B. / Lilley, D.M. / Phillips, S.E.
History
DepositionApr 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_sheet
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_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_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_ref_seq_dif.details / _struct_sheet.number_strands
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Z: 27-MER
Y: 27-MER
A: Endodeoxyribonuclease 1
B: Endodeoxyribonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2578
Polymers52,0974
Non-polymers1604
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.977, 92.977, 124.265
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERLYSLYS1AC17 - 7717 - 77
21SERSERLYSLYS1BD17 - 7717 - 77
12HISHISHISHIS3AC7878
22HISHISHISHIS3BD7878
13LEULEULYSLYS1AC79 - 14579 - 145
23LEULEULYSLYS1BD79 - 14579 - 145
14CACACACA1A - YG - F150 - 30
24CACACACA1B - ZH - E150 - 30
DetailsThe biological assembly is a protein homodimer bound to a four stranded DNA junction. This is represented by the contents of the asymmteric unit.

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Components

#1: DNA chain 27-MER


Mass: 8829.697 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA Holliday Junction
#2: DNA chain 27-MER


Mass: 8971.766 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA Holliday Junction
#3: Protein Endodeoxyribonuclease 1 / E.C.3.1.21.2 / Endodeoxyribonuclease I / Endonuclease


Mass: 17147.787 Da / Num. of mol.: 2 / Mutation: K67A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T7 (virus) / Genus: T7-like viruses / Gene: 3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 (pLysS) / References: UniProt: P00641, deoxyribonuclease IV
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

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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: 2.93 Å3/Da / Density % sol: 58.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20 mM CaCl2, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1CaCl211
2H2O11
3CaCl212
4H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 28, 2006 / Details: Pt coated Si mirrors
RadiationMonochromator: Si (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. all: 11646 / Num. obs: 11577 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rsym value: 0.052 / Net I/σ(I): 14.8
Reflection shellResolution: 3.1→3.175 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 776 / Rsym value: 0.344 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MxCuBEdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Globular domain from pdb file 1FZR

1fzr


Resolution: 3.1→11.93 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.895 / SU B: 41.864 / SU ML: 0.542 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.52 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29776 538 4.7 %RANDOM
Rwork0.26704 ---
obs0.26848 10851 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 96.457 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refine analyzeLuzzati coordinate error obs: 0.811 Å / Luzzati d res low obs: 11.9 Å
Refinement stepCycle: LAST / Resolution: 3.1→11.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2139 1098 4 0 3241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223599
X-RAY DIFFRACTIONr_angle_refined_deg1.8932.4085141
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7435257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.71223.663101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.53215411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9651513
X-RAY DIFFRACTIONr_chiral_restr0.1160.2537
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023489
X-RAY DIFFRACTIONr_nbd_refined0.2290.21392
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22132
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.285
X-RAY DIFFRACTIONr_metal_ion_refined0.1930.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.219
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0940.22
X-RAY DIFFRACTIONr_mcbond_it0.641.51334
X-RAY DIFFRACTIONr_mcangle_it1.08522108
X-RAY DIFFRACTIONr_scbond_it1.17234698
X-RAY DIFFRACTIONr_scangle_it2.5984.53033
Refine LS restraints NCS

Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDNumberTypeRms dev position (Å)Weight position
11060tight positional0.050.05
16loose positional1.865
21060tight thermal0.090.5
26loose thermal1.6310
LS refinement shellResolution: 3.1→3.175 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.513 27 -
Rwork0.387 748 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.6229-0.5248-0.79934.7778-2.02484.6715-0.0619-0.49850.15660.6371-0.9775-1.0436-0.73362.28211.0394-0.224-0.4915-0.29930.58720.38-0.014432.0991.581-27.023
22.49861.1279-0.30422.5943-2.20755.2469-0.0914-0.8896-0.82230.1573-0.7089-0.67070.81131.70260.8003-0.16280.14010.10770.47810.50650.181926.587-17.326-19.231
35.35043.1942-1.12863.5595-3.74735.9545-0.3192-0.0973-0.3535-0.3026-0.1549-1.2923-0.57061.46230.474-0.30590.02810.08570.74620.62780.449944.478-10.866-22.245
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AC17 - 14517 - 145
2X-RAY DIFFRACTION2BD17 - 14517 - 145
3X-RAY DIFFRACTION3ZA1 - 81 - 8
4X-RAY DIFFRACTION3YB22 - 2922 - 29

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