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Yorodumi- PDB-1vjr: Crystal structure of 4-nitrophenylphosphatase (TM1742) from Therm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vjr | ||||||
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Title | Crystal structure of 4-nitrophenylphosphatase (TM1742) from Thermotoga maritima at 2.40 A resolution | ||||||
Components | 4-nitrophenylphosphatase | ||||||
Keywords | HYDROLASE / TM1742 / 4-nitrophenylphosphatase / STRUCTURAL GENOMICS / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics | ||||||
Function / homology | Function and homology information phosphoglycolate phosphatase activity / alkaline phosphatase activity / phosphatase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of 4-nitrophenylphosphatase (TM1742) from Thermotoga maritima at 2.40 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Remark 999 | SEQUENCE FOR THE VAL/MET CONFLICT AT RESIDUE 1: THIS GENE USES AN ALTERNATE INITIATION CODON THAT ...SEQUENCE FOR THE VAL/MET CONFLICT AT RESIDUE 1: THIS GENE USES AN ALTERNATE INITIATION CODON THAT RESULTS IN A VALINE AT POSITION 1 WHEN EXPRESSED AS A FUSION. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vjr.cif.gz | 70.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vjr.ent.gz | 54.6 KB | Display | PDB format |
PDBx/mmJSON format | 1vjr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vjr_validation.pdf.gz | 430.5 KB | Display | wwPDB validaton report |
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Full document | 1vjr_full_validation.pdf.gz | 430.9 KB | Display | |
Data in XML | 1vjr_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 1vjr_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vj/1vjr ftp://data.pdbj.org/pub/pdb/validation_reports/vj/1vjr | 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: 30554.322 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1742 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X264, EC: 3.1.3.41 | ||
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#2: Chemical | ChemComp-NI / | ||
#3: Chemical | #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: 5.35 Å3/Da / Density % sol: 76.82 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6.5 Details: 2M sodium chloride, 0.1M MES pH 6.5, 0.1M sodium dihydrogen phosphate, 0.1M potassium dihydrogen phosphate, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 273K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9797, 0.9999, 0.9799 | ||||||||||||
Detector | Type: ADSC / Detector: CCD / Date: May 22, 2003 | ||||||||||||
Radiation | Monochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.4→94 Å / Num. obs: 28916 / % possible obs: 100 % / Redundancy: 4.6 % / Biso Wilson estimate: 57.98 Å2 / Rsym value: 0.072 / Net I/σ(I): 14.5 | ||||||||||||
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 2087 / Rsym value: 0.537 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.4→51.17 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.956 / SU B: 7.955 / SU ML: 0.101 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.14
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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: 44.646 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→51.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 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 / Auth asym-ID: A / Label asym-ID: A
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