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Yorodumi- PDB-1vp8: CRYSTAL STRUCTURE OF an alpha/beta domain of a putative pyruvate ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vp8 | ||||||
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Title | CRYSTAL STRUCTURE OF an alpha/beta domain of a putative pyruvate kinase (AF0103) FROM ARCHAEOGLOBUS FULGIDUS DSM 4304 AT 1.30 A RESOLUTION | ||||||
Components | hypothetical protein AF0103 | ||||||
Keywords | FLAVOPROTEIN / PUTATIVE PYRUVATE KINASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.3 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of hypothetical protein (NP_068944.1) from Archaeoglobus fulgidus at 1.30 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vp8.cif.gz | 53.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vp8.ent.gz | 40.8 KB | Display | PDB format |
PDBx/mmJSON format | 1vp8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vp8_validation.pdf.gz | 788.7 KB | Display | wwPDB validaton report |
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Full document | 1vp8_full_validation.pdf.gz | 789.5 KB | Display | |
Data in XML | 1vp8_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 1vp8_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vp/1vp8 ftp://data.pdbj.org/pub/pdb/validation_reports/vp/1vp8 | HTTPS FTP |
-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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-Components
#1: Protein | Mass: 22697.963 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: NP_068944.1 / Production host: Escherichia coli (E. coli) / References: UniProt: O30133 |
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#2: Chemical | ChemComp-FMN / |
#3: Chemical | ChemComp-UNL / Num. of mol.: 1 / Source method: obtained synthetically |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.45 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7.5 Details: 50.0% PEG-200, 0.1M HEPES pH 7.5, 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: Aug 28, 2004 | ||||||||||||||||||
Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.3→24.9 Å / Num. obs: 66691 / % possible obs: 100 % / Redundancy: 14.4 % / Biso Wilson estimate: 18.46 Å2 / Rsym value: 0.085 / Net I/σ(I): 21.9 | ||||||||||||||||||
Reflection shell | Resolution: 1.3→1.33 Å / Redundancy: 10.1 % / Mean I/σ(I) obs: 2 / Num. unique all: 4852 / Rsym value: 0.974 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.3→24.61 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.004 / SU ML: 0.022 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.036 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. AN UNKNOWN LIGAND HAS BEEN MODELED NEAR THE FMN GROUP.
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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: 14.017 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→24.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.334 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 41.035 Å / Origin y: 8.271 Å / Origin z: 23.207 Å
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Refinement TLS group | Selection: ALL |