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- PDB-1kkp: Crystal Structure of Serine Hydroxymethyltransferase complexed wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kkp | ||||||
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Title | Crystal Structure of Serine Hydroxymethyltransferase complexed with Serine | ||||||
![]() | Serine Hydroxymethyltransferase | ||||||
![]() | TRANSFERASE / SHMT PLP tetrahydrofolate | ||||||
Function / homology | ![]() glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / L-serine catabolic process / tetrahydrofolate interconversion / cobalt ion binding / folic acid metabolic process / pyridoxal phosphate binding / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Trivedi, V. / Gupta, A. / Jala, V.R. / Saravanan, P. / Rao, G.S.J. / Rao, N.A. / Savithri, H.S. / Subramanya, H.S. | ||||||
![]() | ![]() Title: Crystal structure of binary and ternary complexes of serine hydroxymethyltransferase from Bacillus stearothermophilus: insights into the catalytic mechanism. Authors: Trivedi, V. / Gupta, A. / Jala, V.R. / Saravanan, P. / Rao, G.S. / Rao, N.A. / Savithri, H.S. / Subramanya, H.S. | ||||||
History |
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Remark 999 | SEQUENCE AN APPROPRIATE SEQUENCE DATABASE REFERENCE WAS NOT AVAILABLE AT THE TIME OF PROCESSING. ...SEQUENCE AN APPROPRIATE SEQUENCE DATABASE REFERENCE WAS NOT AVAILABLE AT THE TIME OF PROCESSING. ALSO, RESIDUES 403-419 ARE CLONING ARTIFACTS. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 95 KB | Display | ![]() |
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PDB format | ![]() | 71.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.5 KB | Display | ![]() |
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Full document | ![]() | 464.9 KB | Display | |
Data in XML | ![]() | 19 KB | Display | |
Data in CIF | ![]() | 27.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1kkjSC ![]() 1kl1C ![]() 1kl2C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 45711.738 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: pRSETC / Species (production host): Escherichia coli / Production host: ![]() ![]() References: UniProt: Q7SIB6, glycine hydroxymethyltransferase |
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#2: Chemical | ChemComp-PLP / |
#3: Chemical | ChemComp-SER / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 38.98 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Hepes MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 9, 2001 / Details: mirrors |
Radiation | Monochromator: mar mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→15 Å / Num. all: 27597 / Num. obs: 27573 / % possible obs: 96.9 % / Observed criterion σ(F): -4 / Observed criterion σ(I): -3 / Redundancy: 2.52 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 30.7 |
Reflection shell | Resolution: 1.93→2 Å / Redundancy: 2.31 % / Rmerge(I) obs: 0.056 / Num. unique all: 2565 / % possible all: 91.9 |
Reflection | *PLUS Num. measured all: 69596 / Rmerge(I) obs: 0.037 |
Reflection shell | *PLUS Rmerge(I) obs: 0.056 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB Entry 1KKJ Resolution: 1.93→10 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.93→10 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 10 Å / Rfactor Rfree: 0.2059 / Rfactor Rwork: 0.179 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |