+Open data
-Basic information
Entry | Database: PDB / ID: 3ier | ||||||
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Title | Firefly luciferase apo structure (P41 form) with PEG 400 bound | ||||||
Components | Luciferin 4-monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / MONOOXYGENASE / PHOTOPROTEIN / LUMINESCENCE / ATP-binding / Magnesium / Metal-binding / Nucleotide-binding / Peroxisome | ||||||
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 / molecular replacement / Resolution: 2.05 Å | ||||||
Authors | Lovell, S. / Battaile, K.P. / Auld, D.S. / Thorne, N. / Lea, W.A. / Maloney, D.J. / Shen, M. / Raj, G. / Thomas, C.J. / Simeonov, A. ...Lovell, S. / Battaile, K.P. / Auld, D.S. / Thorne, N. / Lea, W.A. / Maloney, D.J. / Shen, M. / Raj, G. / Thomas, C.J. / Simeonov, A. / Hanzlik, R.P. / Inglese, J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Molecular basis for the high-affinity binding and stabilization of firefly luciferase by PTC124. Authors: Auld, D.S. / Lovell, S. / Thorne, N. / Lea, W.A. / Maloney, D.J. / Shen, M. / Rai, G. / Battaile, K.P. / Thomas, C.J. / Simeonov, A. / Hanzlik, R.P. / Inglese, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ier.cif.gz | 104.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ier.ent.gz | 77.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ier.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ie/3ier ftp://data.pdbj.org/pub/pdb/validation_reports/ie/3ier | HTTPS FTP |
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-Related structure data
Related structure data | 3iepSC 3iesC 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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Unit cell |
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-Components
#1: Protein | Mass: 60918.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Photinus pyralis (common eastern firefly) / References: UniProt: P08659, firefly luciferase |
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#2: Chemical | ChemComp-PG4 / |
#3: 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: 2.82 Å3/Da / Density % sol: 56.41 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 8.5 Details: 25% PEG 400, 20% PEG 3350, 0.1M MgCl2, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 13, 2009 |
Diffraction measurement | Details: 1.00 degrees, 12.0 sec, detector distance 150.00 mm |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Av R equivalents: 0.123 / Number: 207798 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 42128 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.123 / Rsym value: 0.123 / Net I/σ(I): 11.075 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2.19 / Rsym value: 0.479 / % possible all: 98.7 |
Cell measurement | Reflection used: 207798 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3IEP Resolution: 2.05→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.199 / WRfactor Rwork: 0.168 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.349 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: REFINED INDIVIDUALLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.32 Å2 / Biso mean: 23.931 Å2 / Biso min: 9.45 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→50 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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