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Yorodumi- PDB-4g37: Structure of cross-linked firefly luciferase in second catalytic ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4g37 | ||||||
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Title | Structure of cross-linked firefly luciferase in second catalytic conformation | ||||||
Components | Luciferin 4-monooxygenase | ||||||
Keywords | LIGASE / ANL Superfamily / adenylating enzymes / luciferase / domain alternation / trapped conformation / chemical cross-linker | ||||||
Function / homology | Function and homology information Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing) activity / firefly luciferase / bioluminescence / peroxisome / protein-folding chaperone binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Photinus pyralis (common eastern firefly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.396 Å | ||||||
Authors | Sundlov, J.A. / Branchini, B.R. / Gulick, A.M. | ||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Crystal structure of firefly luciferase in a second catalytic conformation supports a domain alternation mechanism. Authors: Sundlov, J.A. / Fontaine, D.M. / Southworth, T.L. / Branchini, B.R. / Gulick, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4g37.cif.gz | 221.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4g37.ent.gz | 174.4 KB | Display | PDB format |
PDBx/mmJSON format | 4g37.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/4g37 ftp://data.pdbj.org/pub/pdb/validation_reports/g3/4g37 | HTTPS FTP |
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-Related structure data
Related structure data | 4g36C 1lciS 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 , 1 types, 2 molecules AB
#1: Protein | Mass: 61016.133 Da / Num. of mol.: 2 Mutation: C82S, I108C, T214A, A215L, C216A, I232A, C258S, F295L, E354K, C391S, Y447C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Photinus pyralis (common eastern firefly) Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P08659, firefly luciferase |
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-Non-polymers , 5 types, 199 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-CL / | #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: 2.43 Å3/Da / Density % sol: 49.43 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30 % PEG 4000, 50 mM NaCl, 50 mM HEPPS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 13, 2012 / Details: SSRL BL 9-2 |
Radiation | Monochromator: SSRL BL 9-2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.396→30 Å / Num. all: 47067 / Num. obs: 44431 / % possible obs: 94.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.067 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2.4→2.5 Å / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 3.8 / % possible all: 82.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LCI Resolution: 2.396→29.219 Å / SU ML: 0.65 / σ(F): 1.35 / Phase error: 28 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 24.659 Å2 / ksol: 0.27 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.396→29.219 Å
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Refine LS restraints |
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LS refinement shell |
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