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Yorodumi- PDB-2dut: Crystal structure of a M-loop deletion variant of MENT in the nat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dut | |||||||||
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Title | Crystal structure of a M-loop deletion variant of 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Whisstock, J.C. / Buckle, A.M. / McGowan, S. / Irving, J.A. | |||||||||
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 | 2dut.cif.gz | 290.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dut.ent.gz | 226.9 KB | Display | PDB format |
PDBx/mmJSON format | 2dut.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dut_validation.pdf.gz | 485.1 KB | Display | wwPDB validaton report |
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Full document | 2dut_full_validation.pdf.gz | 558.6 KB | Display | |
Data in XML | 2dut_validation.xml.gz | 61.6 KB | Display | |
Data in CIF | 2dut_validation.cif.gz | 82.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/du/2dut ftp://data.pdbj.org/pub/pdb/validation_reports/du/2dut | HTTPS FTP |
-Related structure data
Related structure data | 2h4pC 2h4qC 2h4rC 1ovaS 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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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 48855.910 Da / Num. of mol.: 4 / Mutation: deletion mutant Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: MENT-1 / Plasmid: pBAD-HisA / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: O73790 #2: 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: 4.76 Å3/Da / Density % sol: 74.16 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.4 Details: 1.7-1.9M AMMONIUM SULFATE, 0.1M SODIUM ACETATE, PH4.3-4.45, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 4, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. all: 71951 / Num. obs: 68817 / % possible obs: 95.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.5 % Rfree details: Random selection of twin-related reflection pairs Rmerge(I) obs: 0.114 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 3→3.1 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OVA Resolution: 3→20 Å / Redundancy reflection obs: 2.5 / Data cutoff high absF: 0 / Data cutoff low absF: 0 / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: THE DATA IS TWINNED. THE TWINNING OPERATOR IS (H,K,L)-> (H+K,-K,-L) AND THE ESTIMATED PARTIAL TWINNING FRACTION IS 0.44. THE TWINNED R-FACTORS ARE 29.7% (OBS), 29.7%(WORK) AND 32.4%(FREE). ...Details: THE DATA IS TWINNED. THE TWINNING OPERATOR IS (H,K,L)-> (H+K,-K,-L) AND THE ESTIMATED PARTIAL TWINNING FRACTION IS 0.44. THE TWINNED R-FACTORS ARE 29.7% (OBS), 29.7%(WORK) AND 32.4%(FREE). THE TWINNED BIN R-FACTORS ARE 36.0(WORK) AND 37.0(FREE). AT THIS TWINNING FRACTION, THE ESTIMATE IS LIKELY TO BE INACCURATE. HENCE, THE DATA WAS ARTIFICIALLY PERFECTLY TWINNED (=0.5) BY AVERAGING TWIN- RELATED REFLECTIONS. TO AVOID TEST-SET BIAS, TWIN-RELATED REFLECTIONS WERE RANDOMLY SELECTED IN PAIRS AND EXCLUDED FROM REFINEMENT FOR THE CALCULATION OF RFREE. CYCLES OF RIGID BODY REFINEMENT, SIMULATED ANNEALING, B-FACTOR REFINEMENT AND MAP BUILDING WERE UNDERTAKEN IN CNS USING THE XTAL_TWIN SUITE OF SCRIPTS.IN ORDER TO MAXIMISE THE OBSERVATION-TO-PARAMETER RATIO, STRICT CONSTRAINTS WERE APPLIED DURING REFINEMENT WITH CNS; AS SUCH, THE FOUR CHAINS ARE IDENTICAL AND RELATED PURELY BY COORDINATE TRANSFORMATION.
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Solvent computation | Solvent model: BULK / Bsol: 65.27 Å2 / ksol: 0.282 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso max: 103.164 Å2 / Biso mean: 41.015 Å2 / Biso min: 18.1339 Å2
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Refinement step | Cycle: LAST / Resolution: 3→20 Å
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LS refinement shell | Resolution: 3→3.1 Å / Total num. of bins used: 10
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