+Open data
-Basic information
Entry | Database: PDB / ID: 2h4r | ||||||
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Title | Crystal structure of wildtype MENT in the native conformation | ||||||
Components | Heterochromatin-associated protein MENT | ||||||
Keywords | HYDROLASE INHIBITOR / Serine protease inhibitor / Serpin | ||||||
Function / homology | Function and homology information nucleate erythrocyte maturation / chromosome condensation / serine-type endopeptidase inhibitor activity / chromatin DNA binding / chromatin organization / chromatin / extracellular space / nucleoplasm Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Irving, J.A. / Whisstock, J.C. / Buckle, A.M. / McGowan, S. | ||||||
Citation | Journal: Embo J. / Year: 2006 Title: X-ray crystal structure of MENT: evidence for functional loop-sheet polymers in chromatin condensation. Authors: McGowan, S. / Buckle, A.M. / Irving, J.A. / Ong, P.C. / Bashtannyk-Puhalovich, T.A. / Kan, W.T. / Henderson, K.N. / Bulynko, Y.A. / Popova, E.Y. / Smith, A.I. / Bottomley, S.P. / Rossjohn, J. ...Authors: McGowan, S. / Buckle, A.M. / Irving, J.A. / Ong, P.C. / Bashtannyk-Puhalovich, T.A. / Kan, W.T. / Henderson, K.N. / Bulynko, Y.A. / Popova, E.Y. / Smith, A.I. / Bottomley, S.P. / Rossjohn, J. / Grigoryev, S.A. / Pike, R.N. / Whisstock, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2h4r.cif.gz | 92.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h4r.ent.gz | 68.2 KB | Display | PDB format |
PDBx/mmJSON format | 2h4r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h4/2h4r ftp://data.pdbj.org/pub/pdb/validation_reports/h4/2h4r | HTTPS FTP |
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-Related structure data
Related structure data | 2dutC 2h4pC 2h4qC 2h4s 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 48029.277 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: ment-1 / Plasmid: PET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O73790 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.63 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20% PEG-4000, 0.1M sodium acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 19, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→40 Å / Num. obs: 10420 / % possible obs: 97.1 % / Redundancy: 3 % / Rmerge(I) obs: 0.185 / Χ2: 1.176 / Net I/σ(I): 4.4 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 2.4 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2H4S 2h4s Resolution: 2.7→18.96 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.828 / WRfactor Rfree: 0.254 / WRfactor Rwork: 0.18 / SU B: 27.441 / SU ML: 0.371 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.44 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 1.3 Å / Shrinkage radii: 1.3 Å / VDW probe radii: 1.3 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.724 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→18.96 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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