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- PDB-5hml: Crystal Structure of T5 D15 Protein Co-crystallized with Metal Ions -

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Basic information

Entry
Database: PDB / ID: 5hml
TitleCrystal Structure of T5 D15 Protein Co-crystallized with Metal Ions
ComponentsExodeoxyribonuclease
KeywordsHYDROLASE / Metal ion complex / flap endonuclease / alternative conformations
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
IODIDE ION / Flap endonuclease
Similarity search - Component
Biological speciesEscherichia phage T5 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.482 Å
AuthorsFlemming, C.S. / Feng, M. / Sedelnikova, S.E. / Zhang, J. / Rafferty, J.B. / Sayers, J.R. / Artymiuk, P.J.
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 16, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exodeoxyribonuclease
B: Exodeoxyribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,71022
Polymers62,5512
Non-polymers1,15920
Water10,070559
1
A: Exodeoxyribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5307
Polymers31,2751
Non-polymers2556
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Exodeoxyribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,17915
Polymers31,2751
Non-polymers90414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.380, 58.380, 59.720
Angle α, β, γ (deg.)66.530, 79.480, 73.710
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Exodeoxyribonuclease / 5'-exonuclease / T5FEN / T5 Flap Endonuclease


Mass: 31275.475 Da / Num. of mol.: 2 / Fragment: UNP residues 20-291 / Mutation: D134K
Source method: isolated from a genetically manipulated source
Details: Structure derived from recombinant protein corresponding to residues 20 - 291 (known as delta19 and had a D153K mutation compared to wt.
Source: (gene. exp.) Escherichia phage T5 (virus) / Gene: D15 / Plasmid: pJONEX4
Details (production host): pUC19 derivative with a lambda promoter/operator system
Production host: Escherichia coli (E. coli) / Strain (production host): M72
References: UniProt: P06229, exodeoxyribonuclease (lambda-induced)

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Non-polymers , 6 types, 579 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#6: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 559 / 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: 2.33 Å3/Da / Density % sol: 47.15 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: Bis-Tris propane, PEG 3350, MgCl2, NaI / PH range: 7.5-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.482→54.602 Å / Num. all: 87441 / Num. obs: 87441 / % possible obs: 93.7 % / Redundancy: 3 % / Rpim(I) all: 0.039 / Rrim(I) all: 0.069 / Rsym value: 0.057 / Net I/av σ(I): 10.07 / Net I/σ(I): 11.4 / Num. measured all: 264840
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
1.482-1.5630.4911.338322126240.3410.4912.292.6
1.56-1.6630.32.536626120180.210.33.393
1.66-1.7730.1993.834543113400.1390.1994.793.6
1.77-1.9130.126632147105770.0880.1267.293.9
1.91-2.130.0799.42963797700.0550.07911.294.3
2.1-2.3430.05612.72673988620.0380.0561594.5
2.34-2.7130.04614.42358178280.0320.04617.794.5
2.71-3.3130.03816.61962965640.0250.03822.694
3.31-4.6930.028221492050130.0190.02834.292.9
4.69-30.8613.10.02921.8869628450.0190.02936.596.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
SCALA3.3.15data scaling
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UT5

1ut5


Resolution: 1.482→54.6 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.1968 / WRfactor Rwork: 0.1415 / FOM work R set: 0.8709 / SU B: 3.215 / SU ML: 0.052 / SU R Cruickshank DPI: 0.0793 / SU Rfree: 0.0743 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1958 4367 5 %RANDOM
Rwork0.1406 ---
obs0.1433 83074 93.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 136.3 Å2 / Biso mean: 19.889 Å2 / Biso min: 6.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20.15 Å2-0.25 Å2
2--0.15 Å2-0.02 Å2
3----0.08 Å2
Refinement stepCycle: final / Resolution: 1.482→54.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4380 0 46 559 4985
Biso mean--27.38 31.5 -
Num. residues----542
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194560
X-RAY DIFFRACTIONr_bond_other_d0.0020.024350
X-RAY DIFFRACTIONr_angle_refined_deg1.3241.966160
X-RAY DIFFRACTIONr_angle_other_deg1.007310012
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0145556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.47724.211228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.79615816
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7021529
X-RAY DIFFRACTIONr_chiral_restr0.0780.2678
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025157
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021076
X-RAY DIFFRACTIONr_mcbond_it3.9281.5662200
X-RAY DIFFRACTIONr_mcbond_other3.9211.5652199
X-RAY DIFFRACTIONr_mcangle_it4.3332.3582758
X-RAY DIFFRACTIONr_rigid_bond_restr2.19438910
X-RAY DIFFRACTIONr_sphericity_free36.8725162
X-RAY DIFFRACTIONr_sphericity_bonded15.26359233
LS refinement shellResolution: 1.482→1.52 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 342 -
Rwork0.271 6037 -
all-6379 -
obs--92.33 %

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