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

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Basic information

Entry
Database: PDB / ID: 5hmm
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 endonuclease activity / DNA exonuclease activity / 5'-flap endonuclease activity / 5'-3' exonuclease activity / viral DNA genome replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters ...viral replication complex / exodeoxyribonuclease (lambda-induced) / late viral transcription / DNA replication, Okazaki fragment processing / double-stranded DNA endonuclease activity / DNA exonuclease activity / 5'-flap endonuclease activity / 5'-3' exonuclease activity / viral DNA genome replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / 5'-3' DNA exonuclease activity / 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
Biological speciesEscherichia phage T5 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsFlemming, C.S. / Sedelnikova, S.E. / 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

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Assembly

Deposited unit
A: Exodeoxyribonuclease
B: Exodeoxyribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,68715
Polymers62,2672
Non-polymers42113
Water10,773598
1
A: Exodeoxyribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3397
Polymers31,1331
Non-polymers2066
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Exodeoxyribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3488
Polymers31,1331
Non-polymers2157
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.831, 58.591, 59.729
Angle α, β, γ (deg.)66.880, 79.400, 73.780
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Exodeoxyribonuclease / / 5'-exonuclease / T5FEN / Exonuclease (flap endonuclease)


Mass: 31133.252 Da / Num. of mol.: 2 / Fragment: UNP residues 20-290
Source method: isolated from a genetically manipulated source
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)
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 598 / 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: 2.32 Å3/Da / Density % sol: 46.89 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PACT H2: 0.2M Na bromide, 0.1M Bis Tris propane pH 8.5, 20% PEG 3350
PH range: 8.0-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97836 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97836 Å / Relative weight: 1
ReflectionResolution: 1.5→54.735 Å / Num. all: 83343 / Num. obs: 83343 / % possible obs: 93.1 % / Redundancy: 3.8 % / Rpim(I) all: 0.042 / Rrim(I) all: 0.093 / Rsym value: 0.083 / Net I/av σ(I): 6.202 / Net I/σ(I): 10.5 / Num. measured all: 313085
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.5-1.582.20.3221.625799118120.2960.3222.590.4
1.58-1.682.20.2223.424543112490.2030.2223.290.4
1.68-1.792.20.1594.622972105170.1460.159490.6
1.79-1.942.20.1162.72135497940.1060.1165.390.4
1.94-2.124.50.173.84208893000.0820.178.293.7
2.12-2.375.80.1364.65048386540.0610.13611.996
2.37-2.745.60.0956.74337976880.0440.0951596.7
2.74-3.355.90.078.53828765280.0310.0721.497.3
3.35-4.745.60.05610.42831450380.0260.05634.297.7
4.74-38.735.70.03915.31586627630.0180.03938.197.3

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Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.15data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EXN

1exn


Resolution: 1.5→38.35 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.193 / WRfactor Rwork: 0.1505 / FOM work R set: 0.8622 / SU B: 3.501 / SU ML: 0.056 / SU R Cruickshank DPI: 0.0894 / SU Rfree: 0.0777 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1967 4123 5 %RANDOM
Rwork0.1477 ---
obs0.1501 79049 92.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 113.88 Å2 / Biso mean: 19.387 Å2 / Biso min: 5.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20.37 Å20.58 Å2
2--0.12 Å2-0.21 Å2
3----0.2 Å2
Refinement stepCycle: final / Resolution: 1.5→38.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4349 0 16 598 4963
Biso mean--25.94 29.53 -
Num. residues----537
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194533
X-RAY DIFFRACTIONr_bond_other_d0.0020.024322
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.966134
X-RAY DIFFRACTIONr_angle_other_deg1.81539943
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2945556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.0324.192229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.60915815
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9351530
X-RAY DIFFRACTIONr_chiral_restr0.0790.2676
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025160
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021072
X-RAY DIFFRACTIONr_mcbond_it2.7781.352194
X-RAY DIFFRACTIONr_mcbond_other2.7291.3492193
X-RAY DIFFRACTIONr_mcangle_it3.0662.0322754
X-RAY DIFFRACTIONr_rigid_bond_restr11.79438855
X-RAY DIFFRACTIONr_sphericity_free33.0095175
X-RAY DIFFRACTIONr_sphericity_bonded27.76759194
LS refinement shellResolution: 1.499→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 274 -
Rwork0.253 5448 -
all-5722 -
obs--86.5 %

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