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Yorodumi- PDB-3fm2: CRYSTAL STRUCTURE OF A PUTATIVE HEME-BINDING PROTEIN (AVA_4353) F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fm2 | ||||||
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Title | CRYSTAL STRUCTURE OF A PUTATIVE HEME-BINDING PROTEIN (AVA_4353) FROM ANABAENA VARIABILIS ATCC 29413 AT 1.80 A RESOLUTION | ||||||
Components | Uncharacterized protein, distantly related to a heme binding/degrading HemS (PF05171) family | ||||||
Keywords | HEME-BINDING PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2 | ||||||
Function / homology | Intracellular heme transport protein HutX-like / Haem utilisation ChuX/HutX / HemS/ChuS/ChuX like domains / Heme iron utilization protein-like fold / 3-Layer(aba) Sandwich / metal ion binding / Alpha Beta / ACETATE ION / Uncharacterized protein Function and homology information | ||||||
Biological species | Anabaena variabilis ATCC 29413 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of uncharacterized protein, distantly related to a heme binding/degrading HemS (PF05171) family (YP_324846.1) from Anabaena variabilis ATCC 29413 at 1.80 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fm2.cif.gz | 67.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fm2.ent.gz | 52.1 KB | Display | PDB format |
PDBx/mmJSON format | 3fm2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/3fm2 ftp://data.pdbj.org/pub/pdb/validation_reports/fm/3fm2 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | CRYSTAL PACKING ANALYSIS SUGGESTS THAT THE DIMER IS THE STABLE OLIGOMERIC FORM IN SOLUTION. ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIC FORM IN SOLUTION. |
-Components
#1: Protein | Mass: 15564.246 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anabaena variabilis ATCC 29413 (bacteria) Gene: Ava_4353, YP_324846.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q3M4Y5 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATI | |
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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: 2.15 Å3/Da / Density % sol: 42.71 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: NANODROP, 0.2M Ca(OAc)2, 40.0% PEG 400, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91162, 0.97870, 0.97828 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 14, 2008 / Details: Flat mirror (vertical focusing) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Single crystal Si(111) bent (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→29.001 Å / Num. obs: 25482 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 25.168 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 11.16 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.8→29.001 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 5.696 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.123 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ACETATE (ACT) FROM THE CRYSTALLIZATION CONDITION HAS BEEN MODELED IN THE SOLVENT STRUCTURE. 4. ZINC (ZN) HAS BEEN MODELED IN BOTH PROTEIN MOLECULES BASED ON A FLUORESCENCE SCAN AND ANOMALOUS DIFFERENCE FOURIER MAPS.
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.15 Å2 / Biso mean: 29.96 Å2 / Biso min: 14.9 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→29.001 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.845 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 |
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