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Yorodumi- PDB-3stc: Crystal structure of loop 7 truncated mutant of 3-deoxy-D-manno-o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3stc | ||||||
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Title | Crystal structure of loop 7 truncated mutant of 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8PS) from Neisseria meningitidis | ||||||
Components | 2-dehydro-3-deoxyphosphooctonate aldolase | ||||||
Keywords | TRANSFERASE / MANNO-OCTULOSONATE / SYNTHASE / LIPOPOLYSACCHARIDE / KDOP / KDO8 KDOPS / KDO8PS / TIM BARREL / BIOSYNTHESIS / LYASE / LIPOPOLYSACCHARIDE BIOSYNTHESIS | ||||||
Function / homology | Function and homology information 3-deoxy-8-phosphooctulonate synthase / 3-deoxy-8-phosphooctulonate synthase activity / keto-3-deoxy-D-manno-octulosonic acid biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | Neisseria meningitidis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å | ||||||
Authors | Allison, T.M. / Jameson, G.B. / Parker, E.J. | ||||||
Citation | Journal: Biochemistry / Year: 2011 Title: An Extended (beta)7(alpha)7 Substrate-Binding Loop Is Essential for Efficient Catalysis by 3-Deoxy-D-manno-Octulosonate 8-Phosphate Synthase Authors: Allison, T.M. / Hutton, R.D. / Jiao, W. / Gloyne, B.J. / Nimmo, E.B. / Jameson, G.B. / Parker, E.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3stc.cif.gz | 407.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3stc.ent.gz | 335.6 KB | Display | PDB format |
PDBx/mmJSON format | 3stc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3stc_validation.pdf.gz | 461 KB | Display | wwPDB validaton report |
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Full document | 3stc_full_validation.pdf.gz | 471.6 KB | Display | |
Data in XML | 3stc_validation.xml.gz | 44.3 KB | Display | |
Data in CIF | 3stc_validation.cif.gz | 64.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/st/3stc ftp://data.pdbj.org/pub/pdb/validation_reports/st/3stc | HTTPS FTP |
-Related structure data
Related structure data | 3steC 3stfC 3stgC 2qkfS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29516.324 Da / Num. of mol.: 4 / Mutation: DELETED RESIDUES Q202-G212 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: MC58 / Gene: kdsA, NMB1283 / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9JZ55, 3-deoxy-8-phosphooctulonate synthase #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-NA / | #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: 2.42 Å3/Da / Density % sol: 49.26 % / Mosaicity: 0.52 ° |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 20 mg/mL protein (in 10 mM BTP pH 7.5) mixed 1:1 with reservoir liquor containing 100 mM NaOAc (pH 4.6) and 0.6-3.0 M NaCl. Immediately prior to data collection, crystals were harvested and ...Details: 20 mg/mL protein (in 10 mM BTP pH 7.5) mixed 1:1 with reservoir liquor containing 100 mM NaOAc (pH 4.6) and 0.6-3.0 M NaCl. Immediately prior to data collection, crystals were harvested and soaked briefly in cryoprotectant solution, comprising 20% glycerol and the reservoir solution, Vapor diffusion, hanging drop, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95368 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Sep 1, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.95368 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.91→36.56 Å / Num. all: 88598 / Num. obs: 88598 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rsym value: 0.062 / Net I/σ(I): 14.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2QKF Resolution: 1.91→36.56 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.2358 / WRfactor Rwork: 0.1996 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8099 / SU B: 6.827 / SU ML: 0.106 / SU R Cruickshank DPI: 0.1693 / SU Rfree: 0.1537 / Cross valid method: THROUGHOUT / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: WITH TLS ADDED
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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: 100.09 Å2 / Biso mean: 31.2399 Å2 / Biso min: 10.59 Å2
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Refinement step | Cycle: LAST / Resolution: 1.91→36.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.914→1.964 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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