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Yorodumi- PDB-3mmz: CRYSTAL STRUCTURE OF putative HAD family hydrolase from Streptomy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mmz | ||||||
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Title | CRYSTAL STRUCTURE OF putative HAD family hydrolase from Streptomyces avermitilis MA-4680 | ||||||
Components | putative HAD family hydrolase | ||||||
Keywords | HYDROLASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / PSI-2 / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Function and homology information N-acylneuraminate cytidylyltransferase / N-acylneuraminate cytidylyltransferase activity / N-acetylneuraminate metabolic process / hydrolase activity, acting on ester bonds / metal ion binding Similarity search - Function | ||||||
Biological species | Streptomyces avermitilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 1.84 Å | ||||||
Authors | Malashkevich, V.N. / Ramagopal, U.A. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: Biochemistry / Year: 2013 Title: Structural basis for the divergence of substrate specificity and biological function within HAD phosphatases in lipopolysaccharide and sialic acid biosynthesis. Authors: Daughtry, K.D. / Huang, H. / Malashkevich, V. / Patskovsky, Y. / Liu, W. / Ramagopal, U. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / Dunaway-Mariano, D. / Allen, K.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mmz.cif.gz | 142.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mmz.ent.gz | 116.9 KB | Display | PDB format |
PDBx/mmJSON format | 3mmz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mmz_validation.pdf.gz | 451.8 KB | Display | wwPDB validaton report |
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Full document | 3mmz_full_validation.pdf.gz | 456.7 KB | Display | |
Data in XML | 3mmz_validation.xml.gz | 28.7 KB | Display | |
Data in CIF | 3mmz_validation.cif.gz | 41.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mm/3mmz ftp://data.pdbj.org/pub/pdb/validation_reports/mm/3mmz | HTTPS FTP |
-Related structure data
Related structure data | 3mn1C 3n07C 4hgnC 4hgoC 4hgpC 4hgqC 4hgrC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 18990.213 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avermitilis (bacteria) / Strain: MA-4680 / Gene: 29829917, SAV3374, SAV_3374 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q82HY3 #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-CL / #4: 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: 2.2 Å3/Da / Density % sol: 44.14 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.1 M Na-acetate, 30% PEG 400, 0.2 M Ca-acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.84→45 Å / Num. obs: 111339 / % possible obs: 100 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.096 / Χ2: 1.324 / Net I/σ(I): 9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: SAD / Resolution: 1.84→19.75 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.203 / WRfactor Rwork: 0.17 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.876 / SU B: 5.789 / SU ML: 0.08 / SU R Cruickshank DPI: 0.133 / SU Rfree: 0.123 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 58.23 Å2 / Biso mean: 18.368 Å2 / Biso min: 7.58 Å2
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Refinement step | Cycle: LAST / Resolution: 1.84→19.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.843→1.891 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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