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- PDB-3oc9: Crystal structure of putative UDP-N-acetylglucosamine pyrophospho... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3oc9 | ||||||
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Title | Crystal structure of putative UDP-N-acetylglucosamine pyrophosphorylase from Entamoeba histolytica | ||||||
![]() | UDP-N-acetylglucosamine pyrophosphorylase | ||||||
![]() | TRANSFERASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / anaerobic parasitic protozoan / amoebic dysentery / amoebic liver abscess / cysts / UDP-N-acetylglucosamine diphosphorylase / nucleotidyl transferase | ||||||
Function / homology | ![]() UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
![]() | ![]() Title: Structure of uridine diphosphate N-acetylglucosamine pyrophosphorylase from Entamoeba histolytica. Authors: Edwards, T.E. / Gardberg, A.S. / Phan, I.Q. / Zhang, Y. / Staker, B.L. / Myler, P.J. / Lorimer, D.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 183.6 KB | Display | ![]() |
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PDB format | ![]() | 145 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1jv1S S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 46600.402 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: C4M036, UDP-N-acetylglucosamine diphosphorylase |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-EDO / |
#4: Water | ChemComp-HOH / |
Sequence details | THE PLASMID USED TO EXPRESS THE SEQUENCE WAS GENERATED FROM GENOMIC DNA. THE SEQUENCE WAS VERIFIED ...THE PLASMID USED TO EXPRESS THE SEQUENCE WAS GENERATED FROM GENOMIC DNA. THE SEQUENCE WAS VERIFIED IN BOTH THE FORWARD AND REVERSE DIRECTION, YET DIFFERS AT THESE TWO AMINO ACIDS FROM THE PREVIOUSLY |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.52 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 96.3 mg/mL of EnhiA.01126.b.A1 PS00631 3C cleaved against JCSG+ condition H9, 0.2 M lithium sulfate, 0.1 M BisTris pH 5.5, 25% PEG 3350 with 15% ethylene glycol as cryo-protectant, crystal ...Details: 96.3 mg/mL of EnhiA.01126.b.A1 PS00631 3C cleaved against JCSG+ condition H9, 0.2 M lithium sulfate, 0.1 M BisTris pH 5.5, 25% PEG 3350 with 15% ethylene glycol as cryo-protectant, crystal tracking ID 216241h9, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 31, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→50 Å / Num. all: 48592 / Num. obs: 48589 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Biso Wilson estimate: 32.461 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 30.45 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing MR | Rfactor: 59.43 / Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1jv1 molecule A residues 68-407 Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.224 / WRfactor Rwork: 0.1865 / Occupancy max: 1 / Occupancy min: 0.15 / FOM work R set: 0.8605 / SU B: 5.172 / SU ML: 0.074 / SU R Cruickshank DPI: 0.119 / SU Rfree: 0.1176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.86 Å2 / Biso mean: 31.9097 Å2 / Biso min: 10.56 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 67.9234 Å / Origin y: 70.8686 Å / Origin z: 18.2509 Å
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