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Yorodumi- PDB-1vra: Crystal structure of Arginine biosynthesis bifunctional protein a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vra | ||||||
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Title | Crystal structure of Arginine biosynthesis bifunctional protein argJ (10175521) from Bacillus halodurans at 2.00 A resolution | ||||||
Components | (Arginine biosynthesis bifunctional protein ...) x 2 | ||||||
Keywords | TRANSFERASE / 10175521 / arginine biosynthesis bifunctional protein argJ / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI | ||||||
Function / homology | Function and homology information glutamate N-acetyltransferase / glutamate N-acetyltransferase activity / L-methionine N-acyltransferase activity / amino-acid N-acetyltransferase / L-glutamate N-acetyltransferase activity / L-arginine biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus halodurans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of Arginine biosynthesis bifunctional protein argJ (10175521) from Bacillus halodurans at 2.00 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Remark 999 | SEQUENCE CLONING ARTIFACT: THE DENSITY FOR RESIDUE 252 SUGGESTS THAT THIS RESIDUE WAS A THREONINE ...SEQUENCE CLONING ARTIFACT: THE DENSITY FOR RESIDUE 252 SUGGESTS THAT THIS RESIDUE WAS A THREONINE AND NOT AN ALANINE. SEQUENCING OF THE CONSTRUCT IS CONSISTENT WITH RESIDUE 252 BEING A THREONINE IN THE EXPRESSED PROTEIN. | ||||||
Remark 400 | COMPOUND THERE IS A BREAK IN THE CHAIN BETWEEN RESIDUES 196 AND 197. SIMILAR PROTEOLYSIS HAS BEEN ...COMPOUND THERE IS A BREAK IN THE CHAIN BETWEEN RESIDUES 196 AND 197. SIMILAR PROTEOLYSIS HAS BEEN SHOWN TO BE THE RESULT OF AUTO-PROTEOLYTIC SELF-ACTIVATION OF THE ENZYME IN HOMOLOGS. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vra.cif.gz | 98.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vra.ent.gz | 78 KB | Display | PDB format |
PDBx/mmJSON format | 1vra.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vra_validation.pdf.gz | 433.9 KB | Display | wwPDB validaton report |
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Full document | 1vra_full_validation.pdf.gz | 435.3 KB | Display | |
Data in XML | 1vra_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 1vra_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vr/1vra ftp://data.pdbj.org/pub/pdb/validation_reports/vr/1vra | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Arginine biosynthesis bifunctional protein ... , 2 types, 2 molecules AB
#1: Protein | Mass: 22350.490 Da / Num. of mol.: 1 / Fragment: alpha chain, residues 1-196 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus halodurans (bacteria) Description: both chain A and chain B were expressed from a single construct which encodes residues 1-411 of the ARGJ gene Gene: argJ / Production host: Escherichia coli (E. coli) References: UniProt: Q9K8V3, glutamate N-acetyltransferase, amino-acid N-acetyltransferase |
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#2: Protein | Mass: 23196.146 Da / Num. of mol.: 1 / Fragment: beta chain, residues 197-411 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus halodurans (bacteria) Description: both chain A and chain B were expressed from a single construct which encodes residues 1-411 of the ARGJ gene Gene: argJ / Production host: Escherichia coli (E. coli) References: UniProt: Q9K8V3, glutamate N-acetyltransferase, amino-acid N-acetyltransferase |
-Non-polymers , 4 types, 407 molecules
#3: Chemical | #4: Chemical | ChemComp-UNL / | Num. of mol.: 1 / Source method: obtained synthetically #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal |
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Crystal grow |
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-Data collection
Diffraction |
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Diffraction source |
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Detector | Type: ADSC / Detector: CCD / Date: Jan 21, 2005 | ||||||||||||||||||
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→29.81 Å / Num. obs: 38627 / % possible obs: 98.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 27.75 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 21 | ||||||||||||||||||
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 3 % / Rmerge(I) obs: 0.109 / Mean I/σ(I) obs: 10.2 / Num. unique all: 2387 / % possible all: 90.7 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→29.81 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.1 / SU ML: 0.06 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.1 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2) AN UNIDENTIFIABLE LIGAND, UNL, HAS BEEN MODELED INTO DENSITY NEAR RESIDUES A35-A37.
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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: 25.334 Å2
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Refinement step | Cycle: LAST / Resolution: 2→29.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.053 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
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