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- PDB-5hp4: Crystal structure bacteriohage T5 D15 flap endonuclease (D155K) p... -

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Basic information

Entry
Database: PDB / ID: 5hp4
TitleCrystal structure bacteriohage T5 D15 flap endonuclease (D155K) pseudo-enzyme-product complex with DNA and metal ions
Components
  • DNA (5'-D(*GP*AP*TP*CP*TP*AP*TP*AP*TP*GP*CP*CP*AP*TP*CP*GP*G)-3')
  • Exodeoxyribonuclease
KeywordsHYDROLASE / Enzyme-substrate-complex / flap endonuclease / metalloenzyme
Function / homology
Function and homology information


viral replication complex / exodeoxyribonuclease (lambda-induced) / late viral transcription / DNA replication, Okazaki fragment processing / double-stranded DNA 5'-3' DNA exonuclease activity / double-stranded DNA endonuclease activity / DNA exonuclease activity / 5'-flap endonuclease activity / viral DNA genome replication / 5'-3' exonuclease activity ...viral replication complex / exodeoxyribonuclease (lambda-induced) / late viral transcription / DNA replication, Okazaki fragment processing / double-stranded DNA 5'-3' DNA exonuclease activity / double-stranded DNA endonuclease activity / DNA exonuclease activity / 5'-flap endonuclease activity / viral DNA genome replication / 5'-3' exonuclease activity / 5'-3' DNA exonuclease activity / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA binding / metal ion binding
Similarity search - Function
Flap endonuclease D15-like / Flap endonuclease / 5'-nuclease / DNA polymerase I-like, H3TH domain / 5'-3' exonuclease, C-terminal SAM fold / 5'-3' exonuclease, alpha-helical arch, N-terminal / 5'-3' exonuclease, N-terminal resolvase-like domain / 5'-3' exonuclease / 5'-3' exonuclease / Helix-hairpin-helix motif, class 2 ...Flap endonuclease D15-like / Flap endonuclease / 5'-nuclease / DNA polymerase I-like, H3TH domain / 5'-3' exonuclease, C-terminal SAM fold / 5'-3' exonuclease, alpha-helical arch, N-terminal / 5'-3' exonuclease, N-terminal resolvase-like domain / 5'-3' exonuclease / 5'-3' exonuclease / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / PIN-like domain superfamily / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Flap endonuclease
Similarity search - Component
Biological speciesEscherichia phage T5 (virus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsAlmalki, F.A. / Zhang, J. / Sedelnikova, S.E. / Rafferty, J.B. / Sayers, J.R. / Artymiuk, P.A.
Funding support Saudi Arabia, United Kingdom, 2items
OrganizationGrant numberCountry
Taif UniversitySchoalrship Saudi Arabia
University of SheffieldScholarship United Kingdom
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Direct observation of DNA threading in flap endonuclease complexes.
Authors: AlMalki, F.A. / Flemming, C.S. / Zhang, J. / Feng, M. / Sedelnikova, S.E. / Ceska, T. / Rafferty, J.B. / Sayers, J.R. / Artymiuk, P.J.
History
DepositionJan 20, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Jun 22, 2016Group: Database references
Revision 1.3Jul 20, 2016Group: Database references
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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_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.ptnr2_symmetry / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: DNA (5'-D(*GP*AP*TP*CP*TP*AP*TP*AP*TP*GP*CP*CP*AP*TP*CP*GP*G)-3')
A: Exodeoxyribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7127
Polymers36,4782
Non-polymers2345
Water3,927218
1
X: DNA (5'-D(*GP*AP*TP*CP*TP*AP*TP*AP*TP*GP*CP*CP*AP*TP*CP*GP*G)-3')
A: Exodeoxyribonuclease
hetero molecules

X: DNA (5'-D(*GP*AP*TP*CP*TP*AP*TP*AP*TP*GP*CP*CP*AP*TP*CP*GP*G)-3')
hetero molecules

X: DNA (5'-D(*GP*AP*TP*CP*TP*AP*TP*AP*TP*GP*CP*CP*AP*TP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,32115
Polymers46,8834
Non-polymers43911
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_444-x-1/2,y-1/2,-z-1/41
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)67.510, 67.510, 187.810
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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DNA chain / Protein , 2 types, 2 molecules XA

#1: DNA chain DNA (5'-D(*GP*AP*TP*CP*TP*AP*TP*AP*TP*GP*CP*CP*AP*TP*CP*GP*G)-3')


Mass: 5202.384 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Oligonucleotide forms imperfect helical duplex with 3' overhang when annealed.
Source: (synth.) synthetic construct (others)
#2: Protein Exodeoxyribonuclease / 5'-exonuclease / T5FEN


Mass: 31275.475 Da / Num. of mol.: 1 / Fragment: UNP residues 20-291 / Mutation: Asp155Lys
Source method: isolated from a genetically manipulated source
Details: The expressed recombinant corresponded to residues 20-291 of the protein with a D155K substitution.
Source: (gene. exp.) Escherichia phage T5 (virus) / Gene: D15 / Plasmid: pJONEX4 derivative
Details (production host): Derived from pUC19 carrying a synthetic lambda promoter
Production host: Escherichia coli (E. coli) / Strain (production host): M72
References: UniProt: P06229, exodeoxyribonuclease (lambda-induced)

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Non-polymers , 5 types, 223 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.96 Å3/Da / Density % sol: 58.39 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Oligonucleotides was adjusted to 1.1 mM for the duplex molecule by dissolving each one in 10 mM MES pH 6.5 and 50 mM KCl. T5FenD155K with oligonucleotide 3ov6 prepared above, grew in 0.2 M ...Details: Oligonucleotides was adjusted to 1.1 mM for the duplex molecule by dissolving each one in 10 mM MES pH 6.5 and 50 mM KCl. T5FenD155K with oligonucleotide 3ov6 prepared above, grew in 0.2 M CaCl2, 0.1 M sodium acetate buffer pH 5, 20% w/v PEG 6000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.861→67.51 Å / Num. all: 37488 / Num. obs: 37488 / % possible obs: 99.8 % / Redundancy: 27.9 % / Rpim(I) all: 0.016 / Rrim(I) all: 0.083 / Rsym value: 0.08 / Net I/av σ(I): 6.281 / Net I/σ(I): 30.8 / Num. measured all: 1047650
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.86-1.9128.81.0430.67832327200.1981.0436.499.7
1.91-1.9628.70.8070.87595126430.1530.807899.8
1.96-2.0228.80.6021.17368125620.1140.60210.399.9
2.02-2.0828.70.4671.47206225110.0890.46712.699.9
2.08-2.1528.80.3511.96952124160.0670.3511699.9
2.15-2.2228.70.2742.46840823850.0520.27419.199.9
2.22-2.3128.60.1953.46463322590.0370.19524.199.9
2.31-2.428.60.17146347322220.0330.17126.699.9
2.4-2.5128.60.1424.86064721240.0270.1423099.9
2.51-2.6328.40.1116.25706120070.0210.11135.499.9
2.63-2.7728.40.0967.15472219300.0190.09638.6100
2.77-2.94280.0798.55162318420.0150.07944.299.9
2.94-3.1527.50.0699.54740917270.0140.06948.1100
3.15-3.426.60.05810.54345916310.0120.0585499.7
3.4-3.7226.70.05311.43988714920.0110.05359.499.8
3.72-4.1626.80.05211.63677713730.010.05262100
4.16-4.8260.04712.63219512400.0090.04763.1100
4.8-5.8826.60.04513.82782810480.0090.04564.8100
5.88-8.32250.04413.6214178580.0090.04462.3100
8.32-67.5117.20.04413.185734980.0110.04451.195.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
SCALA3.3.16data scaling
PDB_EXTRACT3.15data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HML

5hml


Resolution: 1.86→54.81 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.1958 / WRfactor Rwork: 0.1641 / FOM work R set: 0.8898 / SU B: 4.388 / SU ML: 0.068 / SU R Cruickshank DPI: 0.1008 / SU Rfree: 0.0996 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1883 1871 5 %RANDOM
Rwork0.158 ---
obs0.1595 35532 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 512.5 Å2 / Biso mean: 38.372 Å2 / Biso min: 19.47 Å2
Baniso -1Baniso -2Baniso -3
1-1.15 Å20 Å20 Å2
2--1.15 Å20 Å2
3----2.29 Å2
Refinement stepCycle: final / Resolution: 1.86→54.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2194 345 10 218 2767
Biso mean--54.39 39.99 -
Num. residues----289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0182635
X-RAY DIFFRACTIONr_bond_other_d0.0020.022336
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.833629
X-RAY DIFFRACTIONr_angle_other_deg1.0335386
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9375273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.00824.286112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56315402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6741514
X-RAY DIFFRACTIONr_chiral_restr0.0810.2387
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022738
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02606
X-RAY DIFFRACTIONr_mcbond_it5.3412.4261092
X-RAY DIFFRACTIONr_mcbond_other5.0192.4181091
X-RAY DIFFRACTIONr_mcangle_it5.7173.6061365
LS refinement shellResolution: 1.861→1.909 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 139 -
Rwork0.204 2575 -
all-2714 -
obs--99.74 %
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)
10.131-0.0231-0.04130.02620.10280.76830.0593-0.07520.0142-0.00560.01470.03320.0810.048-0.07410.1326-0.0044-0.03580.08560.01190.2018-19.4541-11.0449-9.2797
20.7120.02660.24350.9146-0.12750.66640.0221-0.00280.0276-0.04830.02130.0046-0.02550.1116-0.04340.04-0.0001-0.01520.029-0.02140.0305-5.4856-18.8612-17.4401
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1X1 - 17
2X-RAY DIFFRACTION2A20 - 291

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