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Yorodumi- PDB-1vm8: Crystal structure of UDP-N-acetylglucosamine pyrophosphorylase (A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vm8 | ||||||
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Title | Crystal structure of UDP-N-acetylglucosamine pyrophosphorylase (Agx2) from Mus musculus at 2.50 A resolution | ||||||
Components | UDP-N-acetylglucosamine pyrophosphorylase | ||||||
Keywords | TRANSFERASE / Agx2 / 16741099 / UDP-N-acetylglucosamine pyrophosphorylase / STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI / Joint Center for Structural Genomics | ||||||
Function / homology | Function and homology information Synthesis of UDP-N-acetyl-glucosamine / UDP-N-acetylgalactosamine diphosphorylase / UDP-N-acetylgalactosamine diphosphorylase activity / UDP-N-acetylglucosamine metabolic process / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process / carbohydrate binding / nucleoplasm / identical protein binding ...Synthesis of UDP-N-acetyl-glucosamine / UDP-N-acetylgalactosamine diphosphorylase / UDP-N-acetylgalactosamine diphosphorylase activity / UDP-N-acetylglucosamine metabolic process / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process / carbohydrate binding / nucleoplasm / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of UDP-N-acetylglucosamine pyrophosphorylase (Agx2) from Mus musculus at 2.50 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Remark 999 | SEQUENCE CLONING ARTIFACT: EXPERIMENTAL PHASING RESULTS REVEALED THAT RESIDUE 31 IS ... SEQUENCE CLONING ARTIFACT: EXPERIMENTAL PHASING RESULTS REVEALED THAT RESIDUE 31 IS SELENOMETHIONINE IN THE EXPRESSED CONSTRUCT AND NOT A VALINE AS PREDICTED BY THE SEQUENCE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vm8.cif.gz | 198.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vm8.ent.gz | 161.3 KB | Display | PDB format |
PDBx/mmJSON format | 1vm8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vm/1vm8 ftp://data.pdbj.org/pub/pdb/validation_reports/vm/1vm8 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: ASN / End label comp-ID: GLU / Refine code: 4 / Auth seq-ID: 2 - 516 / Label seq-ID: 14 - 528
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-Components
#1: Protein | Mass: 60878.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) References: UniProt: Q91YN5, UDP-N-acetylglucosamine diphosphorylase #2: Chemical | ChemComp-CL / #3: Chemical | #4: 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: 2.9 Å3/Da / Density % sol: 57.25 % Description: 1JV1 MODEL WAS USED TO GENERATE SE SITES FOR THREE WAVELENGTH MAD PHASING, WHICH WAS USED TO GENERATE RESTRAINTS FOR REFINEMENT. |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6.5 Details: 1.6M (NH4)2SO4, 0.1M Cacodylate pH 6.5, 0.2M NaCl , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K |
-Data collection
Diffraction |
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Diffraction source |
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Detector | Type: ADSC / Detector: CCD / Date: Jun 5, 2003 | ||||||||||||||||||
Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.5→29.11 Å / Num. obs: 42134 / % possible obs: 99.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 54.17 Å2 / Rsym value: 0.073 / Net I/σ(I): 9.5 | ||||||||||||||||||
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 5964 / Rsym value: 0.402 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.5→29.11 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.9 / SU B: 25.032 / SU ML: 0.256 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.476 / ESU R Free: 0.297 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOMS WITH INSUFFICIENT DENSITY HAVE NOT BEEN MODELED, INCLUDING REGIONS A453-476 AND B454-476.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.392 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→29.11 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 6982 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.5→2.569 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL
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