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Yorodumi- PDB-1xah: CRYSTAL STRUCTURE OF STAPHLYOCOCCUS AUREUS 3-DEHYDROQUINATE SYNTH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xah | ||||||
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Title | CRYSTAL STRUCTURE OF STAPHLYOCOCCUS AUREUS 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+ AND NAD+ | ||||||
Components | 3-dehydroquinate synthase | ||||||
Keywords | LYASE / SHIKIMATE PATHWAY / AROMATIC AMINO ACID BIOSYNTHESIS / DHQS / SADHQS / OPEN FORM / FORM B / DOMAIN MOVEMENT / CYCLASE | ||||||
Function / homology | Function and homology information 3-dehydroquinate synthase / 3-dehydroquinate synthase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / nucleotide binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Nichols, C.E. / Ren, J. / Leslie, K. / Dhaliwal, B. / Lockyer, M. / Charles, I. / Hawkins, A.R. / Stammers, D.K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Comparison of ligand induced conformational changes and domain closure mechanisms, between prokaryotic and eukaryotic dehydroquinate synthases. Authors: Nichols, C.E. / Ren, J. / Leslie, K. / Dhaliwal, B. / Lockyer, M. / Charles, I. / Hawkins, A.R. / Stammers, D.K. | ||||||
History |
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Remark 999 | SEQUENCE These conflicts reflect clonal variation from database sequence. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xah.cif.gz | 147.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xah.ent.gz | 116.9 KB | Display | PDB format |
PDBx/mmJSON format | 1xah.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xa/1xah ftp://data.pdbj.org/pub/pdb/validation_reports/xa/1xah | HTTPS FTP |
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-Related structure data
Related structure data | 1xagC 1xaiC 1xajC 1xalC 1nr5S 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 40358.895 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: aroB / Plasmid: pMUT27 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3 pLysS) / References: UniProt: Q6GGU4, 3-dehydroquinate synthase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.15 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PEG3350, KCL, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 1, 2001 / Details: OSMIC MULTILAYER |
Radiation | Monochromator: OSMIC MULTILAYER OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. all: 35210 / Num. obs: 34989 / Observed criterion σ(I): -1.5 / Redundancy: 12.5 % / Biso Wilson estimate: 41.6 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 26.22 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 2.38 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NR5 Resolution: 2.2→24.18 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2449728.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 80.6072 Å2 / ksol: 0.374029 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→24.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.24 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 20
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Xplor file |
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