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Yorodumi- PDB-4v7n: Glycocyamine kinase, beta-beta homodimer from marine worm Namalyc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v7n | |||||||||
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Title | Glycocyamine kinase, beta-beta homodimer from marine worm Namalycastis sp., with transition state analog Mg(II)-ADP-NO3-glycocyamine. | |||||||||
Components | Glycocyamine kinase beta chain | |||||||||
Keywords | TRANSFERASE / phosphagen kinase / glycocyamine kinase / transition state analog / Kinase | |||||||||
Function / homology | Function and homology information phosphocreatine biosynthetic process / creatine kinase activity / phosphorylation / ATP binding Similarity search - Function | |||||||||
Biological species | Namalycastis sp. ST01 (invertebrata) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Lim, K. / Pullalarevu, S. / Herzberg, O. | |||||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Structural basis for the mechanism and substrate specificity of glycocyamine kinase, a phosphagen kinase family member. Authors: Lim, K. / Pullalarevu, S. / Surabian, K.T. / Howard, A. / Suzuki, T. / Moult, J. / Herzberg, O. #1: Journal: COMP.BIOCHEM.PHYSIOL. B: BIOCHEM.MOL.BIOL. / Year: 2005 Title: Isolation, characterization, and cDNA-derived amino acid sequence of glycocyamine kinase from the tropical marine worm Namalycastis sp. Authors: Mizuta, C. / Tanaka, K. / Suzuki, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4v7n.cif.gz | 2.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4v7n.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v7n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/4v7n ftp://data.pdbj.org/pub/pdb/validation_reports/v7/4v7n | HTTPS FTP |
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-Related structure data
Related structure data | 3l2dC 3l2eC 1u6rS 1vrpS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
-Components
-Protein , 1 types, 36 molecules AAABACADAEAFAGAHAIAJAKALAMANAOAPAQARBABBBCBDBEBFBGBHBIBJBKBL...
#1: Protein | Mass: 44108.363 Da / Num. of mol.: 36 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Namalycastis sp. ST01 (invertebrata) / Gene: GK-beta, GK_beta / Plasmid: pGK_beta221 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21star(DE3) / References: UniProt: Q6AW42, EC: 2.7.3.1 |
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-Non-polymers , 5 types, 4918 molecules
#2: Chemical | ChemComp-NMG / #3: Chemical | ChemComp-ADP / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-NO3 / #6: 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: 2.27 Å3/Da / Density % sol: 45.9 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 22.5% polyethylene glycol monomethyl ether (PMME) 2000, 0.1M calcium acetate, 0.1M Tris HCl, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 1, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 610182 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 3.1 / % possible all: 81.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 1u6r and 1vrp Resolution: 2.3→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Used twinning refinement with twin operator (-h,-k,l) in Phenix program. Estimated twin fraction was 0.31.
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Displacement parameters | Biso mean: 28 Å2 | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å / Rfactor Rfree: 0.344 / Rfactor Rwork: 0.273 |