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Yorodumi- PDB-2osd: Crystal structure of a vinyl-4-reductase family protein (mj_1460)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2osd | ||||||
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Title | Crystal structure of a vinyl-4-reductase family protein (mj_1460) from methanocaldococcus jannaschii dsm at 2.40 A resolution | ||||||
Components | Hypothetical protein MJ1460Hypothesis | ||||||
Keywords | METAL BINDING PROTEIN / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Function and homology information 4-vinyl reductase, 4VR / V4R domain / V4R / Trafficking protein particle complex subunit 3 / Muramoyl-pentapeptide Carboxypeptidase; domain 2 / NO signalling/Golgi transport ligand-binding domain superfamily / N-6 Adenine-specific DNA methylases signature. / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Methanocaldococcus jannaschii DSM 2661 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of hypothetical protein MJ_1460 (1592102) from Methanococcus jannaschii at 2.30 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Remark 999 | SEQUENCE 1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE 1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. 2. THE CONSTRUCT WAS ENGINEERED WITH THE FOLLOWING MUTATIONS: K132Y, K133Y AND K134Y |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2osd.cif.gz | 45.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2osd.ent.gz | 33.1 KB | Display | PDB format |
PDBx/mmJSON format | 2osd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/os/2osd ftp://data.pdbj.org/pub/pdb/validation_reports/os/2osd | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 19201.564 Da / Num. of mol.: 1 / Fragment: V4R domain / Mutation: K132Y, K133Y, K134Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea) Species: Methanocaldococcus jannaschii / Strain: DSM 2661, JAL-1, JCM 10045, NBRC 100440 / Gene: 1592102, MJ1460 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q58855 |
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-Non-polymers , 5 types, 37 molecules
#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-ZN / | #5: Chemical | #6: 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: 2.41 Å3/Da / Density % sol: 48.95 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.1 Details: NANODROP, 0.2M CaCl2, 20.0% PEG 3350, No Buffer, pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97879, 0.97908 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 7, 2007 / Details: Flat mirror (vertical focusing) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Single crystal Si(111) bent (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.3→29.748 Å / Num. obs: 8939 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 6.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.3→29.748 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.951 / SU B: 15.426 / SU ML: 0.198 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.305 / ESU R Free: 0.217 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. RESIDUES 45-46 ARE DISORDERED AND NOT VISIBLE IN THE ELECTRON DENSITY MAPS. THEY WERE NOT MODELED. 5. TWO CA, THREE ETHYLENE GLYCOL MOLECULES, ONE CL ION FROM THE CRYSTALLIZATION BUFFER WERE MODELED INTO THE STRUCTURE. 6. A ZN ATOM OF THE SUBUNIT IN THE ASYMMETRIC UNIT IS COORDINATED TO THE SIDE CHAINS OF HIS 116, GLU 139, CYS 142 AND CYS 150. X-RAY FLUORESCENCE EXPERIMENTS SUPPORT THE ASSIGNMENT OF THE ZINC ION.
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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: 54.04 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→29.748 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 12.696 Å / Origin y: 4.8495 Å / Origin z: 28.4007 Å
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Refinement TLS group | Selection: ALL |