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Yorodumi- PDB-1k47: Crystal Structure of the Streptococcus pneumoniae Phosphomevalona... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k47 | ||||||
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Title | Crystal Structure of the Streptococcus pneumoniae Phosphomevalonate Kinase (PMK) | ||||||
Components | phosphomevalonate kinase | ||||||
Keywords | TRANSFERASE / Alpha/beta single domain belonging to the GHMP kinase superfamily / MvaK2 / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information phosphomevalonate kinase / isopentenyl diphosphate biosynthetic process, mevalonate pathway / kinase activity / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Streptococcus pneumoniae R6 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Single anomalous scattering / Resolution: 2.42 Å | ||||||
Authors | Romanowski, M.J. / Bonanno, J.B. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: Proteins / Year: 2002 Title: Crystal structure of the Streptococcus pneumoniae phosphomevalonate kinase, a member of the GHMP kinase superfamily. Authors: Romanowski, M.J. / Bonanno, J.B. / Burley, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k47.cif.gz | 383.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k47.ent.gz | 327 KB | Display | PDB format |
PDBx/mmJSON format | 1k47.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k47_validation.pdf.gz | 484.5 KB | Display | wwPDB validaton report |
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Full document | 1k47_full_validation.pdf.gz | 543.6 KB | Display | |
Data in XML | 1k47_validation.xml.gz | 81.1 KB | Display | |
Data in CIF | 1k47_validation.cif.gz | 111.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k4/1k47 ftp://data.pdbj.org/pub/pdb/validation_reports/k4/1k47 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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5 |
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6 |
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Unit cell |
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Details | The protein is a monomer in solution and crystallizes as a hexameric asymetric unit of 3/222 noncrystallographic symmetry |
-Components
#1: Protein | Mass: 37706.867 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae R6 (bacteria) / Species: Streptococcus pneumoniae / Strain: ATCC BAA-255 / R6 / Gene: mvaK2 / Plasmid: pGEX6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8DR49, phosphomevalonate kinase #2: 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: 3.14 Å3/Da / Density % sol: 60.5 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: sodium dihydrogen phosphate, potassium dihydrogen phosphate, HEPES, ATP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: NSLS / Beamline: X25 / Wavelength: 0.9792 Å |
Detector | Type: BRANDEIS - B4 / Detector: CCD / Date: Feb 28, 2001 Details: 27-pole hybrid wiggler and vertical focusing mirror |
Radiation | Monochromator: double Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. all: 202265 / Num. obs: 198856 / % possible obs: 98.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.8 % / Biso Wilson estimate: 46 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 24.1 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 2.5 / Num. unique all: 18706 / Rsym value: 0.409 / % possible all: 92.3 |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 20 Å / Num. obs: 103387 / Num. measured all: 3616027 / Rmerge(I) obs: 0.082 |
Reflection shell | *PLUS % possible obs: 92.4 % / Rmerge(I) obs: 0.409 |
-Processing
Software |
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Refinement | Method to determine structure: Single anomalous scattering / Resolution: 2.42→20 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: anomalous scattering correction applied for 48 Se sites
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Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.42→20 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 9.2 % / Rfactor all: 0.217 / Rfactor obs: 0.215 / Rfactor Rfree: 0.257 / Rfactor Rwork: 0.215 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.312 / Rfactor Rwork: 0.305 / Rfactor obs: 0.305 |