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Yorodumi- PDB-1ne7: HUMAN GLUCOSAMINE-6-PHOSPHATE DEAMINASE ISOMERASE AT 1.75 A RESOL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ne7 | ||||||||||||
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Title | HUMAN GLUCOSAMINE-6-PHOSPHATE DEAMINASE ISOMERASE AT 1.75 A RESOLUTION COMPLEXED WITH N-ACETYL-GLUCOSAMINE-6-PHOSPHATE AND 2-DEOXY-2-AMINO-GLUCITOL-6-PHOSPHATE | ||||||||||||
Components | Glucosamine-6-phosphate isomerase | ||||||||||||
Keywords | HYDROLASE / V-TYPE LIKE ALLOSTERIC ENZYME / CONFORMATIONAL DISORDER / CONFORMATIONAL DIFFERENCES | ||||||||||||
Function / homology | Function and homology information glucosamine catabolic process / glucosamine-6-phosphate deaminase / glucosamine-6-phosphate deaminase activity / N-acetylglucosamine catabolic process / N-acetylneuraminate catabolic process / UDP-N-acetylglucosamine biosynthetic process / Glycolysis / single fertilization / generation of precursor metabolites and energy / carbohydrate metabolic process ...glucosamine catabolic process / glucosamine-6-phosphate deaminase / glucosamine-6-phosphate deaminase activity / N-acetylglucosamine catabolic process / N-acetylneuraminate catabolic process / UDP-N-acetylglucosamine biosynthetic process / Glycolysis / single fertilization / generation of precursor metabolites and energy / carbohydrate metabolic process / extracellular exosome / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||||||||
Authors | Arreola, R. / Valderrama, B. / Morante, M.L. / Horjales, E. | ||||||||||||
Citation | Journal: Febs Lett. / Year: 2003 Title: Two mammalian glucosamine-6-phosphate deaminases: a structural and genetic study. Authors: Arreola, R. / Valderrama, B. / Morante, M.L. / Horjales, E. #1: Journal: BIOCHIM.BIOPHYS.ACTA / Year: 1998 Title: Glucosamine-6-phosphate deaminase from beef kidney is an allosteric system of the V-type. Authors: Lara-Lemus, R. / Calcagno, M.L. #2: Journal: Structure / Year: 1995 Title: Structure and catalytic mechanism of glucosamine 6-phosphate deaminase from Escherichia coli at 2.1 A resolution. Authors: Oliva, G. / Fontes, M.R. / Garratt, R.C. / Altamirano, M.M. / Calcagno, M.L. / Horjales, E. | ||||||||||||
History |
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Remark 600 | HETEROGEN THE LIGANDS SO4 AND AGP ARE IN ALTERNATE POSITIONS. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ne7.cif.gz | 396.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ne7.ent.gz | 319.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ne7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ne/1ne7 ftp://data.pdbj.org/pub/pdb/validation_reports/ne/1ne7 | HTTPS FTP |
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-Related structure data
Related structure data | 1deaS S: Starting model for refinement |
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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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Details | The biological assembly is the hexamer in the asymmetric unit reported in this entry. Chains: A, B, C, D, E & F. |
-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 32712.506 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GNPI OR HLN OR KIAA0060 / Production host: Escherichia coli (E. coli) References: UniProt: P46926, glucosamine-6-phosphate deaminase |
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-Sugars , 2 types, 12 molecules
#2: Polysaccharide | alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose #3: Sugar | ChemComp-16G / |
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-Non-polymers , 3 types, 2207 molecules
#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-AGP / #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: 2.81 Å3/Da / Density % sol: 56.17 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.68 M ammonium sulphate, 10 mM N-acetyl-glucosamine-6-phosphate and 0.1 mM 2-deoxy-2-amino D-glucitol 6-phosphate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 7 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.78 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 18, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.78 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→19.97 Å / Num. all: 221759 / Num. obs: 209143 / % possible obs: 94.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 19.5 Å2 / Rsym value: 0.052 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.75→1.86 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 32182 / Rsym value: 0.224 / % possible all: 95.8 |
Reflection | *PLUS Rmerge(I) obs: 0.052 |
Reflection shell | *PLUS % possible obs: 96.8 % / Rmerge(I) obs: 0.224 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DEA Resolution: 1.75→19.97 Å / Rfactor Rfree error: 0.002 / 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: 67.2697 Å2 / ksol: 0.376291 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→19.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.76 Å / Rfactor Rfree error: 0.004 / Total num. of bins used: 6
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Refinement | *PLUS % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 1.86 Å / Rfactor Rfree: 0.245 / Rfactor Rwork: 0.223 |