+Open data
-Basic information
Entry | Database: PDB / ID: 2h4p | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of wildtype MENT in the cleaved conformation | ||||||
Components | (Heterochromatin-associated protein MENT) x 2 | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Buckle, A.M. / McGowan, S. / Irving, J.A. / Whisstock, J.C. | ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2h4p.cif.gz | 97 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2h4p.ent.gz | 70.3 KB | Display | PDB format |
PDBx/mmJSON format | 2h4p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2h4p_validation.pdf.gz | 432.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2h4p_full_validation.pdf.gz | 434.9 KB | Display | |
Data in XML | 2h4p_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 2h4p_validation.cif.gz | 26.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h4/2h4p ftp://data.pdbj.org/pub/pdb/validation_reports/h4/2h4p | HTTPS FTP |
-Related structure data
Related structure data | 2dutC 2h4qC 2h4rC 1hleS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 45267.750 Da / Num. of mol.: 1 / Fragment: residues 1-369 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: ment-1 / Plasmid: PET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O73790 |
---|---|
#2: Protein/peptide | Mass: 4186.003 Da / Num. of mol.: 1 / Fragment: residues 377-409 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: ment-1 / Plasmid: PET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O73790 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.93 % |
---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 15% PEG 8000, 0.1M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 24, 2003 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Av σ(I) over netI: 21.2 / Number: 73300 / Rmerge(I) obs: 0.04 / Χ2: 1.26 / D res high: 1.7 Å / D res low: 30 Å / Num. obs: 40805 / % possible obs: 85.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→30 Å / Num. all: 40805 / Num. obs: 40805 / % possible obs: 85.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.04 / Χ2: 1.259 / Net I/σ(I): 21.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.159 / Num. unique all: 2435 / Χ2: 1.566 / % possible all: 51 |
-Phasing
Phasing MR |
|
---|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HLE Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.203 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.253 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→30 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.696→1.74 Å / Total num. of bins used: 20
|