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Yorodumi- PDB-4bg4: Crystal structure of Litopenaeus vannamei arginine kinase in a te... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bg4 | ||||||
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Title | Crystal structure of Litopenaeus vannamei arginine kinase in a ternary analog complex with arginine, ADP-Mg and NO3 | ||||||
Components | (ARGININE KINASE) x 2 | ||||||
Keywords | TRANSFERASE / BINARY COMPLEX | ||||||
Function / homology | Function and homology information dTDP metabolic process / arginine kinase / arginine kinase activity / phosphocreatine biosynthetic process / creatine kinase activity / arginine binding / phosphorylation / ATP binding Similarity search - Function | ||||||
Biological species | LITOPENAEUS VANNAMEI (Pacific white shrimp) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 Å | ||||||
Authors | Lopez-Zavala, A.A. / Garcia-Orozco, K.D. / Carrasco-Miranda, J.S. / Sugich-Miranda, R. / Velazquez-Contreras, E.F. / Criscitiello, M.F. / GBrieba, L. / Rudino-Pinera, E. / Sotelo-Mundo, R.R. | ||||||
Citation | Journal: J.Bioenerg.Biomembr. / Year: 2013 Title: Crystal Structure of Shrimp Arginine Kinase in Binary Complex with Arginine-A Molecular View of the Phosphagen Precursor Binding to the Enzyme. Authors: Lopez-Zavala, A.A. / Garcia-Orozco, K.D. / Carrasco-Miranda, J.S. / Sugich-Miranda, R. / Velazquez-Contreras, E.F. / Criscitiello, M.F. / Brieba, L.G. / Rudino-Pinera, E. / Sotelo-Mundo, R.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bg4.cif.gz | 172.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bg4.ent.gz | 134.1 KB | Display | PDB format |
PDBx/mmJSON format | 4bg4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bg4_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4bg4_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4bg4_validation.xml.gz | 33.8 KB | Display | |
Data in CIF | 4bg4_validation.cif.gz | 50.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/4bg4 ftp://data.pdbj.org/pub/pdb/validation_reports/bg/4bg4 | HTTPS FTP |
-Related structure data
Related structure data | 4bhlC 4am1S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 40238.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) LITOPENAEUS VANNAMEI (Pacific white shrimp) Tissue: TAIL MUSCLE / References: UniProt: Q004B5, arginine kinase |
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#2: Protein | Mass: 40236.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) LITOPENAEUS VANNAMEI (Pacific white shrimp) Tissue: TAIL MUSCLE / References: UniProt: Q004B5, arginine kinase |
-Non-polymers , 6 types, 594 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | BETA-MERCAPTOETSequence details | THE SEQUENCE IS DESCRIBED IN GARCIA-OROZCO ETL AL. (2007) INT. ARCH. ALLERGY IMMUNOL. 144, P.23-28 | |
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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 Å3/Da / Density % sol: 41.2 % / Description: NONE |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PROTEIN WAS CRYSTALLIZED FROM 0.2 M SODIUM ACETATE, 0.1 M SODIUM CACODYLATE AND 30 % (W/V) PEG 8000 PH 6.5 AT 289 K USING HANGING DROP METHOD. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9795 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 12, 2012 / Details: TOROIDAL FOCUSING MIRROR |
Radiation | Monochromator: SI(111) CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→14.8 Å / Num. obs: 86201 / % possible obs: 99 % / Observed criterion σ(I): 1.36 / Redundancy: 6.3 % / Biso Wilson estimate: 11.73 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 1.6→14.8 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.9 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4AM1 Resolution: 1.601→14.847 Å / SU ML: 0.25 / σ(F): 1.36 / Phase error: 21.8 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.765 Å2 / ksol: 0.398 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.601→14.847 Å
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Refine LS restraints |
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LS refinement shell |
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