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Yorodumi- PDB-5hmm: Crystal Structure of T5 D15 Protein Co-crystallized with Metal Ions -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hmm | ||||||
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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: 1.5 Å | ||||||
Authors | Flemming, C.S. / Sedelnikova, S.E. / 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 | 5hmm.cif.gz | 258.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hmm.ent.gz | 206.3 KB | Display | PDB format |
PDBx/mmJSON format | 5hmm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hmm_validation.pdf.gz | 438.7 KB | Display | wwPDB validaton report |
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Full document | 5hmm_full_validation.pdf.gz | 440.5 KB | Display | |
Data in XML | 5hmm_validation.xml.gz | 26.3 KB | Display | |
Data in CIF | 5hmm_validation.cif.gz | 40.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hm/5hmm ftp://data.pdbj.org/pub/pdb/validation_reports/hm/5hmm | HTTPS FTP |
-Related structure data
Related structure data | 5hmlC 5hnkC 5hp4C 1exnS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | 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 / | #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-CL / #5: 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: 2.32 Å3/Da / Density % sol: 46.89 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97836 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97836 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 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: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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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: 113.88 Å2 / Biso mean: 19.387 Å2 / Biso min: 5.49 Å2
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Refinement step | Cycle: final / Resolution: 1.5→38.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.499→1.538 Å / Total num. of bins used: 20
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