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Yorodumi- PDB-1shk: THE THREE-DIMENSIONAL STRUCTURE OF SHIKIMATE KINASE FROM ERWINIA ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1shk | ||||||
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Title | THE THREE-DIMENSIONAL STRUCTURE OF SHIKIMATE KINASE FROM ERWINIA CHRYSANTHEMI | ||||||
Components | SHIKIMATE KINASE | ||||||
Keywords | TRANSFERASE / SHIKIMATE KINASE / PHOSPHORYL TRANSFER / ADP / SHIKIMATE PATHWAY / P-LOOP PROTEIN | ||||||
Function / homology | Function and homology information shikimate kinase / shikimate kinase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / phosphorylation / magnesium ion binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Erwinia chrysanthemi (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.9 Å | ||||||
Authors | Krell, T. / Coggins, J.R. / Lapthorn, A.J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1997 Title: Crystallization and preliminary X-ray crystallographic analysis of shikimate kinase from Erwinia chrysanthemi. Authors: Krell, T. / Coyle, J.E. / Horsburgh, M.J. / Coggins, J.R. / Lapthorn, A.J. #1: Journal: J.Mol.Biol. / Year: 1998 Title: The Three-Dimensional Structure of Shikimate Kinase Authors: Krell, T. / Coggins, J.R. / Lapthorn, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1shk.cif.gz | 82.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1shk.ent.gz | 66.5 KB | Display | PDB format |
PDBx/mmJSON format | 1shk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sh/1shk ftp://data.pdbj.org/pub/pdb/validation_reports/sh/1shk | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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5 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.497526, -0.860359, 0.110681), Vector: |
-Components
#1: Protein | Mass: 18975.754 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Erwinia chrysanthemi (bacteria) / Genus: Dickeya / Strain: NCPPB 1066 / Cellular location: CYTOPLASM / Gene: AROL / Plasmid: PTB361SK / Gene (production host): AROL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): (DE3) PLYSS / References: UniProt: P10880, shikimate kinase #2: Chemical | #3: Water | ChemComp-HOH / | Compound details | THE GAP IN THE MOLECULAR STRUCTURE CORRESPONDS TO RESIDUES OF THE LID-DOMAIN. BY ANALOGY TO ...THE GAP IN THE MOLECULAR STRUCTURE CORRESPOND | |
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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: 3.6 Å3/Da / Density % sol: 66 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.9 Details: 2.16M NACL, 100MM HEPES BUFFER PH 6.9, 5MM ADP, 5MM SHIKIMATE, 10MM MGCL2 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.6 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1996 / Details: MIRROR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→24 Å / Num. obs: 44761 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 1.2 / Rsym value: 0.94 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 1.9→20 Å / σ(F): 0 Details: X-PLOR WAS USED FOR INITIAL ROUNDS OF REFINEMENT AND PROVIDED THE BULK SOLVENT CORRECTION.
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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