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Yorodumi- PDB-5hml: Crystal Structure of T5 D15 Protein Co-crystallized with Metal Ions -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hml | ||||||
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Title | Crystal Structure of T5 D15 Protein Co-crystallized with Metal Ions | ||||||
Components | Exodeoxyribonuclease | ||||||
Keywords | HYDROLASE / 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 / DNA exonuclease activity / double-stranded DNA endonuclease activity / 5'-flap endonuclease activity / 5'-3' exonuclease activity / viral DNA genome replication ...viral replication complex / exodeoxyribonuclease (lambda-induced) / late viral transcription / DNA replication, Okazaki fragment processing / double-stranded DNA 5'-3' DNA exonuclease activity / DNA exonuclease activity / double-stranded DNA endonuclease 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 | ||||||
Biological species | Escherichia phage T5 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.482 Å | ||||||
Authors | Flemming, C.S. / Feng, M. / Sedelnikova, S.E. / Zhang, J. / Rafferty, J.B. / Sayers, J.R. / Artymiuk, P.J. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hml.cif.gz | 261.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hml.ent.gz | 209 KB | Display | PDB format |
PDBx/mmJSON format | 5hml.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hml_validation.pdf.gz | 697.6 KB | Display | wwPDB validaton report |
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Full document | 5hml_full_validation.pdf.gz | 699.2 KB | Display | |
Data in XML | 5hml_validation.xml.gz | 26.3 KB | Display | |
Data in CIF | 5hml_validation.cif.gz | 40.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hm/5hml ftp://data.pdbj.org/pub/pdb/validation_reports/hm/5hml | HTTPS FTP |
-Related structure data
Related structure data | 5hmmC 5hnkC 5hp4C 1ut5S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | 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 | #3: Chemical | ChemComp-CL / #4: Chemical | #5: Chemical | ChemComp-B3P / | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.15 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: Bis-Tris propane, PEG 3350, MgCl2, NaI / PH range: 7.5-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 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: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 136.3 Å2 / Biso mean: 19.889 Å2 / Biso min: 6.82 Å2
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Refinement step | Cycle: final / Resolution: 1.482→54.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.482→1.52 Å / Total num. of bins used: 20
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