+Open data
-Basic information
Entry | Database: PDB / ID: 4zev | ||||||||||||
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Title | Crystal structure of PfHAD1 in complex with mannose-6-phosphate | ||||||||||||
Components | PfHAD1 | ||||||||||||
Keywords | UNKNOWN FUNCTION / C2 HAD / sugar phosphatase / haloacid-dehalogenase / mannose-6-phosphate | ||||||||||||
Function / homology | Function and homology information Hydrolases; Acting on halide bonds; In carbon-halide compounds / negative regulation of isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / sugar-phosphatase activity / dephosphorylation / metal ion binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||||||||
Authors | Park, J. / Tolia, N.H. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2015 Title: Cap-domain closure enables diverse substrate recognition by the C2-type haloacid dehalogenase-like sugar phosphatase Plasmodium falciparum HAD1. Authors: Park, J. / Guggisberg, A.M. / Odom, A.R. / Tolia, N.H. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zev.cif.gz | 229.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zev.ent.gz | 185.8 KB | Display | PDB format |
PDBx/mmJSON format | 4zev.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/4zev ftp://data.pdbj.org/pub/pdb/validation_reports/ze/4zev | HTTPS FTP |
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-Related structure data
Related structure data | 4zewC 4zexC 4qjbS C: citing same article (ref.) 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33870.641 Da / Num. of mol.: 2 / Mutation: D27A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote) Gene: PF10_0325 / Plasmid: BG1861 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q8IJ74 #2: Chemical | #3: Sugar | ChemComp-M6P / | #4: Chemical | ChemComp-PO4 / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.69 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES, pH 7.5, 20% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å |
Detector | Type: NOIR-1 / Detector: CCD / Date: May 16, 2013 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 52537 / % possible obs: 99.3 % / Redundancy: 3.68 % / Rsym value: 0.056 / Net I/σ(I): 17.04 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.71 % / Mean I/σ(I) obs: 2.45 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4QJB Resolution: 1.8→19.6 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.87 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→19.6 Å
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Refine LS restraints |
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LS refinement shell |
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