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Yorodumi- PDB-1xag: CRYSTAL STRUCTURE OF STAPHLYOCOCCUS AUREUS 3-DEHYDROQUINATE SYNTH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xag | ||||||
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Title | CRYSTAL STRUCTURE OF STAPHLYOCOCCUS AUREUS 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+, NAD+ AND CARBAPHOSPHONATE | ||||||
Components | 3-dehydroquinate synthase | ||||||
Keywords | LYASE / SHIKIMATE PATHWAY / AROMATIC AMINO ACID BIOSYNTHESIS / DHQS / SADHQS / CLOSED FORM / FORM A / 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: 2.45 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 | 1xag.cif.gz | 90.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xag.ent.gz | 67.5 KB | Display | PDB format |
PDBx/mmJSON format | 1xag.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xag_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1xag_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1xag_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 1xag_validation.cif.gz | 24.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xa/1xag ftp://data.pdbj.org/pub/pdb/validation_reports/xa/1xag | HTTPS FTP |
-Related structure data
Related structure data | 1xahC 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 40358.895 Da / Num. of mol.: 1 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 |
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-Non-polymers , 5 types, 119 molecules
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-NAD / | #5: Chemical | ChemComp-CRB / [ | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.75 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: MPD, HEPES, pH 7.0, 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: 2.45→30 Å / Num. all: 13585 / Num. obs: 12933 / Observed criterion σ(I): -1.5 / Redundancy: 6.7 % / Biso Wilson estimate: 53.6 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 18.89 |
Reflection shell | Resolution: 2.45→2.54 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 2.69 / % possible all: 86.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NR5 Resolution: 2.45→29.64 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2079419.32 / 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: 43.8457 Å2 / ksol: 0.315184 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.45→29.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.54 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 10
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Xplor file |
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