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Yorodumi- PDB-2b30: Initial Crystallographic Structural Analysis of a putative HAD/CO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2b30 | ||||||
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Title | Initial Crystallographic Structural Analysis of a putative HAD/COF-like hydrolase from Plasmodium vivax | ||||||
Components | Pvivax hypothetical protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / SGPP / PSI / PROTEIN STRUCTURE INITIATIVE / Structural Genomics of Pathogenic Protozoa Consortium | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Plasmodium vivax (malaria parasite P. vivax) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Robien, M.A. / Bosch, J. / Hol, W.G.J. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP) | ||||||
Citation | Journal: To be Published Title: Initial Crystallographic Structural Analysis of a putative HAD/COF-like hydrolase from Plasmodium vivax Authors: Robien, M.A. / Bosch, J. / Hol, W.G.J. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP) | ||||||
History |
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Remark 300 | BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ...BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). THE BIOLOGICAL UNIT IS NOT KNOWN, THE DIMERS (AB) AND (CD) ARE SUSPECTED BIOLOGICAL UNITS. | ||||||
Remark 999 | SEQUENCE The sequence of this protein is not available at either SWS or GB sequence database at the ...SEQUENCE The sequence of this protein is not available at either SWS or GB sequence database at the time of processing. This protein is a homolog of Plasmodium falciparum PFL1270w, gi:23508948. The sequence is present in TargetDB as PVIV002324AAA, and in PlasmoDB v4.4 with gene identifier Pv_5271.phat_1. The N-terminus residues 1-8 are cloning artifacts. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2b30.cif.gz | 235.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b30.ent.gz | 188.3 KB | Display | PDB format |
PDBx/mmJSON format | 2b30.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2b30_validation.pdf.gz | 459.9 KB | Display | wwPDB validaton report |
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Full document | 2b30_full_validation.pdf.gz | 479.4 KB | Display | |
Data in XML | 2b30_validation.xml.gz | 41.8 KB | Display | |
Data in CIF | 2b30_validation.cif.gz | 57.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/2b30 ftp://data.pdbj.org/pub/pdb/validation_reports/b3/2b30 | HTTPS FTP |
-Related structure data
Related structure data | 1l6rS 1nf2S 1nrwS 1rkqS 1rlmS 1tj3S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 34232.215 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax) Plasmid: PET14B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21STAR(DE3) / References: UniProt: A5K063 #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-CL / #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: 2.3 Å3/Da / Density % sol: 46 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: PEG 8000, calcium chloride, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9739 Å |
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Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 13, 2005 |
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9739 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→40 Å / Num. all: 34235 / Num. obs: 34235 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 54.3 Å2 / Rsym value: 0.102 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 4944 / Rsym value: 0.3 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entries 1L6R, 1NF2, 1NRW, 1RKQ, 1TJ3, and 1RLM Resolution: 2.7→37.24 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.852 / SU B: 13.216 / SU ML: 0.274 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.151 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→37.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.845 Å / Total num. of bins used: 10
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