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Yorodumi- PDB-3mzo: Crystal structure of a HD-domain phosphohydrolase (lin2634) from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mzo | ||||||
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Title | Crystal structure of a HD-domain phosphohydrolase (lin2634) from LISTERIA INNOCUA at 1.98 A resolution | ||||||
Components | Lin2634 protein | ||||||
Keywords | HYDROLASE / HD-domain phosphohydrolase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Hypothetical protein af1432 / Hypothetical protein af1432 / HD/PDEase domain / Orthogonal Bundle / Mainly Alpha / metal ion binding / DI(HYDROXYETHYL)ETHER / Lin2634 protein Function and homology information | ||||||
Biological species | Listeria innocua (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.98 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a HD-domain phosphohydrolase (lin2634) from LISTERIA INNOCUA at 1.98 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mzo.cif.gz | 268.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mzo.ent.gz | 221.7 KB | Display | PDB format |
PDBx/mmJSON format | 3mzo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mzo_validation.pdf.gz | 459.4 KB | Display | wwPDB validaton report |
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Full document | 3mzo_full_validation.pdf.gz | 464.4 KB | Display | |
Data in XML | 3mzo_validation.xml.gz | 27.5 KB | Display | |
Data in CIF | 3mzo_validation.cif.gz | 39.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mz/3mzo ftp://data.pdbj.org/pub/pdb/validation_reports/mz/3mzo | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 25168.629 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria innocua (bacteria) / Gene: lin2634 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q928A2 #2: Chemical | ChemComp-CA / #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATI | |
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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: 47.07 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2000M calcium chloride, 28.0000% polyethylene glycol 400, 0.1M HEPES pH 7.5, 0.005M 2'-deoxyadenosine 5'-monophosphate (dAMP), NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97939,0.97925 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 11, 2010 / Details: Flat collimating mirror, toroid focusing mirror | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.98→48.741 Å / Num. obs: 47810 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 29.174 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 15.73 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.98→48.741 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 6.819 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.14 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. POLYETHYLENE GLYCOL (PEG), CALCIUM (CA) MODELED ARE PRESENT IN CRYSTALLIZATION/CRYO CANDITIONS.
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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: 90.44 Å2 / Biso mean: 36.888 Å2 / Biso min: 5.38 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→48.741 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 2445 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.98→2.031 Å / 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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