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Yorodumi- PDB-1el4: STRUCTURE OF THE CALCIUM-REGULATED PHOTOPROTEIN OBELIN DETERMINED... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1el4 | ||||||
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Title | STRUCTURE OF THE CALCIUM-REGULATED PHOTOPROTEIN OBELIN DETERMINED BY SULFUR SAS | ||||||
Components | OBELIN | ||||||
Keywords | LUMINESCENT PROTEIN / BIOLUMINESCENCE / CALCIUM / PHOTOPROTEIN / OBELIN / SULFUR ANOMALOUS SCATTERING | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Obelia longissima (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SULFUR SAS / Resolution: 1.73 Å | ||||||
Authors | Liu, Z.J. / Vysotski, E.S. / Rose, J. / Lee, J. / Wang, B.C. | ||||||
Citation | Journal: Protein Sci. / Year: 2000 Title: Structure of the Ca2+-regulated photoprotein obelin at 1.7 A resolution determined directly from its sulfur substructure. Authors: Liu, Z.J. / Vysotski, E.S. / Chen, C.J. / Rose, J.P. / Lee, J. / Wang, B.C. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Preparation and preliminary study of crystals of the recombinant calcium-regulated photoprotein obelin from the bioluminescent hydroid obelia longissima Authors: Vysotski, E.S. / Liu, Z.J. / Rose, J. / Wang, B.C. / Lee, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1el4.cif.gz | 58.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1el4.ent.gz | 42.9 KB | Display | PDB format |
PDBx/mmJSON format | 1el4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1el4_validation.pdf.gz | 453.9 KB | Display | wwPDB validaton report |
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Full document | 1el4_full_validation.pdf.gz | 457.9 KB | Display | |
Data in XML | 1el4_validation.xml.gz | 6.1 KB | Display | |
Data in CIF | 1el4_validation.cif.gz | 10 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/el/1el4 ftp://data.pdbj.org/pub/pdb/validation_reports/el/1el4 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a monomer. |
-Components
#1: Protein | Mass: 22254.904 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Obelia longissima (invertebrata) / Plasmid: PT7-7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q27709 |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-CTZ / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 3.79 Å3/Da / Density % sol: 62 % Description: STRUCTURE DETERMINED USING THE SULFUR SAS SIGNAL RECORDED AT ID17, APS USING 1.74 ANGSTROM X-RAYS (SEE REMARK 3 REFINEMENT DETAILS) | |||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: HANGING DROP VAPOR DIFFUSION USING 5 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (10 MG/ML) AND RESERVOIR SOLUTION: CONTAINING 1.4 M SODIUM CITRATE, PH 6.0., VAPOR ...Details: HANGING DROP VAPOR DIFFUSION USING 5 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (10 MG/ML) AND RESERVOIR SOLUTION: CONTAINING 1.4 M SODIUM CITRATE, PH 6.0., VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.4 Details: Vysotski, E.S., (1999) Acta Crystallogr., Sect.D, 55, 1965. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.73→20 Å / Num. all: 33058 / Num. obs: 33694 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 37.6 | ||||||||||||||||||||
Reflection shell | Resolution: 1.73→1.79 Å / Redundancy: 5 % / Rmerge(I) obs: 0.216 / Num. unique all: 3274 / % possible all: 97.1 | ||||||||||||||||||||
Reflection | *PLUS Num. all: 33694 / Num. obs: 33058 |
-Processing
Software |
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Refinement | Method to determine structure: SULFUR SAS / Resolution: 1.73→19.84 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 260910.23 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: THE STRUCTURE WAS DETERMINED USING SINGLE WAVELENGTH ANOMALOUS SCATTERING DATA RECORDED FOR THE NATIVE PROTEIN. DATA WERE RECORDED ON TWO OBELIN CRYSTALS TO 2.5 ANGSTROMS RESOLUTION AT ...Details: THE STRUCTURE WAS DETERMINED USING SINGLE WAVELENGTH ANOMALOUS SCATTERING DATA RECORDED FOR THE NATIVE PROTEIN. DATA WERE RECORDED ON TWO OBELIN CRYSTALS TO 2.5 ANGSTROMS RESOLUTION AT BEAMLINE ID-17 (IMCA-CAT), ADVANCED PHOTON SOURCE (APS), ARGONNE NATIONAL LABORATORY USING A MARRESEARCH 165 MM CCD DETECTOR AND 1.74 ANGSTROM X-RAYS. A DATA COLLECTION STRATEGY (HKL2000) WAS DETERMINED FROM THE INITIAL IMAGE TO GIVE THE STARTING AND ENDING POINTS OF THE DATA COLLECTION TO INSURE A MINIMUM DATA COMPLETENESS OF 98 PERCENT. DATA WERE COLLECTED USING THE "FREIDEL FLIP" METHOD. DATA PROCESSING WAS CARRIED OUT USING HKL2000. THE PROCESSED DATA FORMING THE TWO DATA SETS WERE MERGED TO INCREASE REDUNDANCY (WU, ET AL., (2000) J. PROT. PEP. LETTS. 7, 25-32) AND SOLVE WAS USED TO DETERMINE THE SIX OF THE EIGHT SULFUR ATOM POSITIONS. PHASES WAS USED TO REFINE THE SULFUR POSITIONS AND TO LOCATE THE REMAINING SULFUR SITES BY BIJVOET DIFFERENCE FOURIER ANALYSIS. THREE ADDITIONAL SITES WERE IDENTIFIED SUGGESTING THAT ONE OF THE SULFUR SITES WAS MOST PROBABLY AN ANOMALOUS SOLVENT SUCH AS CHLORIDE. ALL ANOMALOUS SITES WERE TREATED AS SULFUR FOR THE PHASE CALCULATIONS. THE NINE SULFUR SITES WERE USED TO ESTIMATE THE INITIAL PROTEIN PHASES AT 3 ANGSTROM RESOLUTION USING SOLVENT FLATTENING (ISAS, WANG, (1985) METHODS ENZYMOL. 115, 90 112). A PRELIMINARY CHAIN TRACE WAS DONE USING THE 3.0 ANGSTROM MAP. SEQUENCE ASSIGNMENT WAS BASED ON 8 SULFUR ATOM POSITIONS. THE MODEL, 99 PERCENT COMPLETE WAS BUILT USING THE 3.0 ANGSTROM SAS MAP. RESIDUE 1 WAS NOT OBSERVED IN THE ELECTRON DENSITY AMPS AND IS PRESUMED TO BE DISORDERED. THE RESOLUTION OF THE STRUCTURE WAS THEN EXTENDED TO 1.73 ANGSTROMS RESOLUTION DURING THE FINAL STAGES OF REFINEMENT USING A MERGED DATA SET COLLECTED FROM A SINGLE CRYSTAL RECORDED AT APS (BEAMLINE ID19, WAVELENGTH 0.94 ANGSTROMS) AND AT ALS (BEAMLINE 5.0.2, WAVELENGTH 1.0 ANGSTROMS).
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.158 Å2 / ksol: 0.370428 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.73→19.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.73→1.84 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 8.1 % / Rfactor obs: 0.189 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 18.6 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.302 / % reflection Rfree: 7.5 % / Rfactor Rwork: 0.261 |