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Yorodumi- PDB-2q1w: Crystal structure of the Bordetella bronchiseptica enzyme WbmH in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2q1w | ||||||
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Title | Crystal structure of the Bordetella bronchiseptica enzyme WbmH in complex with NAD+ | ||||||
Components | Putative nucleotide sugar epimerase/ dehydratase | ||||||
Keywords | SUGAR BINDING PROTEIN / ROSSMANN FOLD / PROTEIN-NAD COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bordetella bronchiseptica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å | ||||||
Authors | King, J.D. / Harmer, N.J. / Maskell, D.J. / Blundell, T.L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Predicting protein function from structure--the roles of short-chain dehydrogenase/reductase enzymes in Bordetella O-antigen biosynthesis. Authors: King, J.D. / Harmer, N.J. / Preston, A. / Palmer, C.M. / Rejzek, M. / Field, R.A. / Blundell, T.L. / Maskell, D.J. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2007 Title: Cloning, expression, purification and preliminary crystallographic analysis of the short-chain dehydrogenase enzymes WbmF, WbmG and WbmH from Bordetella bronchiseptica. Authors: Harmer, N.J. / King, J.D. / Palmer, C.M. / Preston, A. / Maskell, D.J. / Blundell, T.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2q1w.cif.gz | 192.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2q1w.ent.gz | 152 KB | Display | PDB format |
PDBx/mmJSON format | 2q1w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2q1w_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 2q1w_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 2q1w_validation.xml.gz | 37.5 KB | Display | |
Data in CIF | 2q1w_validation.cif.gz | 53.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q1/2q1w ftp://data.pdbj.org/pub/pdb/validation_reports/q1/2q1w | HTTPS FTP |
-Related structure data
Related structure data | 2pzjC 2pzkSC 2pzlC 2pzmC 2q1sC 2q1tC 2q1uC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Details | The biological unit is a dimer. The asymmetric unit contains one complete dimer, formed by chains B and C. A second dimer is formed by chain A, together with a second molecule that is related by rotation around the two-fold axis 0,0,z. |
-Components
#1: Protein | Mass: 36637.246 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Gene: BbLPS1.14, wbmH / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O87987 #2: Chemical | #3: 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: 2.31 Å3/Da / Density % sol: 46.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M Hepes, 10 % (v/v) isopropanol, 20 % (w/v) PEG 4000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.19→30 Å / Num. all: 53222 / Num. obs: 49975 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 5.22 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 15.2 | ||||||||||||||||||
Reflection shell | Resolution: 2.2→2.25 Å / Redundancy: 3.58 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.63 / % possible all: 91.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2PZK Resolution: 2.19→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.096 / SU ML: 0.132 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 3.5 / ESU R: 0.257 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.505 Å2
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Refinement step | Cycle: LAST / Resolution: 2.19→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.185→2.242 Å / Total num. of bins used: 20
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